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<a href="Martel-module.html">Package Martel</a> ::
Module msre_parse
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<h1 class="epydoc">Source Code for <a href="Martel.msre_parse-module.html">Module Martel.msre_parse</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment">#</tt> </tt>
<a name="L2"></a><tt class="py-lineno"> 2</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Secret Labs' Regular Expression Engine</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># convert re-style regular expression to sre pattern</tt> </tt>
<a name="L5"></a><tt class="py-lineno"> 5</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Copyright (c) 1998-2001 by Secret Labs AB. All rights reserved.</tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L8"></a><tt class="py-lineno"> 8</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># See the sre.py file in Python 2.1 for information on usage and</tt> </tt>
<a name="L9"></a><tt class="py-lineno"> 9</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># redistribution.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">#</tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Changes for Martel Copyright 2000-2001 by Dalke Scientific Software, LLC</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Distributed under the Biopython License Agreement (see the LICENSE file).</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt class="py-comment"># XXX: show string offset and offending character for all errors</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L16"></a><tt class="py-lineno"> 16</tt> <tt class="py-line"><tt class="py-comment"># this module works under 1.5.2 and later. don't use string methods</tt> </tt>
<a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">import</tt> <tt class="py-name">string</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt> </tt>
<a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="L19"></a><tt class="py-lineno"> 19</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt id="link-0" class="py-name" targets="Module Martel.msre_constants=Martel.msre_constants-module.html"><a title="Martel.msre_constants" class="py-name" href="#" onclick="return doclink('link-0', 'msre_constants', 'link-0');">msre_constants</a></tt> <tt class="py-keyword">import</tt> <tt class="py-op">*</tt> <tt class="py-comment"># Modified version of Secret Labs' sre_constants</tt> </tt>
<a name="L20"></a><tt class="py-lineno"> 20</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">re</tt> <tt class="py-comment"># needed to verify the attr format</tt> </tt>
<a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> </tt>
<a name="L22"></a><tt class="py-lineno"> 22</tt> <tt class="py-line"><tt id="link-1" class="py-name" targets="Variable Martel.msre_parse.SPECIAL_CHARS=Martel.msre_parse-module.html#SPECIAL_CHARS"><a title="Martel.msre_parse.SPECIAL_CHARS" class="py-name" href="#" onclick="return doclink('link-1', 'SPECIAL_CHARS', 'link-1');">SPECIAL_CHARS</a></tt> <tt class="py-op">=</tt> <tt class="py-string">".\\[{()*+?^$|"</tt> </tt>
<a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"><tt id="link-2" class="py-name" targets="Variable Martel.msre_parse.REPEAT_CHARS=Martel.msre_parse-module.html#REPEAT_CHARS"><a title="Martel.msre_parse.REPEAT_CHARS" class="py-name" href="#" onclick="return doclink('link-2', 'REPEAT_CHARS', 'link-2');">REPEAT_CHARS</a></tt> <tt class="py-op">=</tt> <tt class="py-string">"*+?{"</tt> </tt>
<a name="L24"></a><tt class="py-lineno"> 24</tt> <tt class="py-line"> </tt>
<a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"><tt id="link-3" class="py-name" targets="Variable Martel.msre_parse.DIGITS=Martel.msre_parse-module.html#DIGITS"><a title="Martel.msre_parse.DIGITS" class="py-name" href="#" onclick="return doclink('link-3', 'DIGITS', 'link-3');">DIGITS</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-string">"0123456789"</tt><tt class="py-op">)</tt> </tt>
<a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="L27"></a><tt class="py-lineno"> 27</tt> <tt class="py-line"><tt id="link-4" class="py-name" targets="Variable Martel.msre_parse.OCTDIGITS=Martel.msre_parse-module.html#OCTDIGITS"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-4', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-string">"01234567"</tt><tt class="py-op">)</tt> </tt>
<a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"><tt id="link-5" class="py-name" targets="Variable Martel.msre_parse.HEXDIGITS=Martel.msre_parse-module.html#HEXDIGITS"><a title="Martel.msre_parse.HEXDIGITS" class="py-name" href="#" onclick="return doclink('link-5', 'HEXDIGITS', 'link-5');">HEXDIGITS</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-string">"0123456789abcdefABCDEF"</tt><tt class="py-op">)</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"><tt id="link-6" class="py-name" targets="Variable Bio.Nexus.Nexus.WHITESPACE=Bio.Nexus.Nexus-module.html#WHITESPACE,Variable Martel.msre_parse.WHITESPACE=Martel.msre_parse-module.html#WHITESPACE"><a title="Bio.Nexus.Nexus.WHITESPACE
Martel.msre_parse.WHITESPACE" class="py-name" href="#" onclick="return doclink('link-6', 'WHITESPACE', 'link-6');">WHITESPACE</a></tt> <tt class="py-op">=</tt> <tt class="py-name">tuple</tt><tt class="py-op">(</tt><tt class="py-string">" \t\n\r\v\f"</tt><tt class="py-op">)</tt> </tt>
<a name="L31"></a><tt class="py-lineno"> 31</tt> <tt class="py-line"> </tt>
<a name="L32"></a><tt class="py-lineno"> 32</tt> <tt class="py-line"><tt id="link-7" class="py-name" targets="Variable Martel.msre_parse.ESCAPES=Martel.msre_parse-module.html#ESCAPES"><a title="Martel.msre_parse.ESCAPES" class="py-name" href="#" onclick="return doclink('link-7', 'ESCAPES', 'link-7');">ESCAPES</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-string">r"\a"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-8" class="py-name" targets="Variable Martel.msre_constants.LITERAL=Martel.msre_constants-module.html#LITERAL,Variable Martel.msre_parse.LITERAL=Martel.msre_parse-module.html#LITERAL"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-8', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\a"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> <tt class="py-string">r"\b"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-9" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-9', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\b"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-string">r"\f"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-10', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\f"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-string">r"\n"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-11" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-11', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\n"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-string">r"\r"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-12', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\r"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-string">r"\R"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-13" class="py-name" targets="Variable Martel.msre_constants.IN=Martel.msre_constants-module.html#IN,Variable Martel.msre_parse.IN=Martel.msre_parse-module.html#IN"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-13', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-14" class="py-name" targets="Variable Martel.msre_constants.CATEGORY=Martel.msre_constants-module.html#CATEGORY,Variable Martel.msre_parse.CATEGORY=Martel.msre_parse-module.html#CATEGORY"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-14', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">,</tt> <tt id="link-15" class="py-name" targets="Variable Martel.msre_constants.CATEGORY_NEWLINE=Martel.msre_constants-module.html#CATEGORY_NEWLINE,Variable Martel.msre_parse.CATEGORY_NEWLINE=Martel.msre_parse-module.html#CATEGORY_NEWLINE"><a title="Martel.msre_constants.CATEGORY_NEWLINE
Martel.msre_parse.CATEGORY_NEWLINE" class="py-name" href="#" onclick="return doclink('link-15', 'CATEGORY_NEWLINE', 'link-15');">CATEGORY_NEWLINE</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># Martel extension</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> <tt class="py-string">r"\t"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-16" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-16', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\t"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-string">r"\v"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-17" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-17', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\v"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-string">r"\\"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-18" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-18', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"\\"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L42"></a><tt class="py-lineno"> 42</tt> <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"><tt id="link-19" class="py-name" targets="Variable Martel.msre_parse.CATEGORIES=Martel.msre_parse-module.html#CATEGORIES"><a title="Martel.msre_parse.CATEGORIES" class="py-name" href="#" onclick="return doclink('link-19', 'CATEGORIES', 'link-19');">CATEGORIES</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L45"></a><tt class="py-lineno"> 45</tt> <tt class="py-line"> <tt class="py-string">r"\A"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-20" class="py-name" targets="Variable Martel.msre_constants.AT=Martel.msre_constants-module.html#AT,Variable Martel.msre_parse.AT=Martel.msre_parse-module.html#AT"><a title="Martel.msre_constants.AT
Martel.msre_parse.AT" class="py-name" href="#" onclick="return doclink('link-20', 'AT', 'link-20');">AT</a></tt><tt class="py-op">,</tt> <tt id="link-21" class="py-name" targets="Variable Martel.msre_constants.AT_BEGINNING_STRING=Martel.msre_constants-module.html#AT_BEGINNING_STRING,Variable Martel.msre_parse.AT_BEGINNING_STRING=Martel.msre_parse-module.html#AT_BEGINNING_STRING"><a title="Martel.msre_constants.AT_BEGINNING_STRING
Martel.msre_parse.AT_BEGINNING_STRING" class="py-name" href="#" onclick="return doclink('link-21', 'AT_BEGINNING_STRING', 'link-21');">AT_BEGINNING_STRING</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># start of string</tt> </tt>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-string">r"\b"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-22" class="py-name"><a title="Martel.msre_constants.AT
Martel.msre_parse.AT" class="py-name" href="#" onclick="return doclink('link-22', 'AT', 'link-20');">AT</a></tt><tt class="py-op">,</tt> <tt id="link-23" class="py-name" targets="Variable Martel.msre_constants.AT_BOUNDARY=Martel.msre_constants-module.html#AT_BOUNDARY,Variable Martel.msre_parse.AT_BOUNDARY=Martel.msre_parse-module.html#AT_BOUNDARY"><a title="Martel.msre_constants.AT_BOUNDARY
Martel.msre_parse.AT_BOUNDARY" class="py-name" href="#" onclick="return doclink('link-23', 'AT_BOUNDARY', 'link-23');">AT_BOUNDARY</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-string">r"\B"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Martel.msre_constants.AT
Martel.msre_parse.AT" class="py-name" href="#" onclick="return doclink('link-24', 'AT', 'link-20');">AT</a></tt><tt class="py-op">,</tt> <tt id="link-25" class="py-name" targets="Variable Martel.msre_constants.AT_NON_BOUNDARY=Martel.msre_constants-module.html#AT_NON_BOUNDARY,Variable Martel.msre_parse.AT_NON_BOUNDARY=Martel.msre_parse-module.html#AT_NON_BOUNDARY"><a title="Martel.msre_constants.AT_NON_BOUNDARY
Martel.msre_parse.AT_NON_BOUNDARY" class="py-name" href="#" onclick="return doclink('link-25', 'AT_NON_BOUNDARY', 'link-25');">AT_NON_BOUNDARY</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> <tt class="py-string">r"\d"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-26" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-26', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-27" class="py-name"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-27', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">,</tt> <tt id="link-28" class="py-name" targets="Variable Martel.msre_constants.CATEGORY_DIGIT=Martel.msre_constants-module.html#CATEGORY_DIGIT,Variable Martel.msre_parse.CATEGORY_DIGIT=Martel.msre_parse-module.html#CATEGORY_DIGIT"><a title="Martel.msre_constants.CATEGORY_DIGIT
Martel.msre_parse.CATEGORY_DIGIT" class="py-name" href="#" onclick="return doclink('link-28', 'CATEGORY_DIGIT', 'link-28');">CATEGORY_DIGIT</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-string">r"\D"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-29', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-30" class="py-name"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-30', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">,</tt> <tt id="link-31" class="py-name" targets="Variable Martel.msre_constants.CATEGORY_NOT_DIGIT=Martel.msre_constants-module.html#CATEGORY_NOT_DIGIT,Variable Martel.msre_parse.CATEGORY_NOT_DIGIT=Martel.msre_parse-module.html#CATEGORY_NOT_DIGIT"><a title="Martel.msre_constants.CATEGORY_NOT_DIGIT
Martel.msre_parse.CATEGORY_NOT_DIGIT" class="py-name" href="#" onclick="return doclink('link-31', 'CATEGORY_NOT_DIGIT', 'link-31');">CATEGORY_NOT_DIGIT</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-string">r"\R"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-32" class="py-name" targets="Variable Martel.msre_constants.NEWLINE=Martel.msre_constants-module.html#NEWLINE,Variable Martel.msre_parse.NEWLINE=Martel.msre_parse-module.html#NEWLINE"><a title="Martel.msre_constants.NEWLINE
Martel.msre_parse.NEWLINE" class="py-name" href="#" onclick="return doclink('link-32', 'NEWLINE', 'link-32');">NEWLINE</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># Martel extension</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-string">r"\s"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-33', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-34', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">,</tt> <tt id="link-35" class="py-name" targets="Variable Martel.msre_constants.CATEGORY_SPACE=Martel.msre_constants-module.html#CATEGORY_SPACE,Variable Martel.msre_parse.CATEGORY_SPACE=Martel.msre_parse-module.html#CATEGORY_SPACE"><a title="Martel.msre_constants.CATEGORY_SPACE
Martel.msre_parse.CATEGORY_SPACE" class="py-name" href="#" onclick="return doclink('link-35', 'CATEGORY_SPACE', 'link-35');">CATEGORY_SPACE</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-string">r"\S"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-36" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-36', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-37" class="py-name"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-37', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">,</tt> <tt id="link-38" class="py-name" targets="Variable Martel.msre_constants.CATEGORY_NOT_SPACE=Martel.msre_constants-module.html#CATEGORY_NOT_SPACE,Variable Martel.msre_parse.CATEGORY_NOT_SPACE=Martel.msre_parse-module.html#CATEGORY_NOT_SPACE"><a title="Martel.msre_constants.CATEGORY_NOT_SPACE
Martel.msre_parse.CATEGORY_NOT_SPACE" class="py-name" href="#" onclick="return doclink('link-38', 'CATEGORY_NOT_SPACE', 'link-38');">CATEGORY_NOT_SPACE</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-string">r"\w"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-39" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-39', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-40" class="py-name"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-40', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">,</tt> <tt id="link-41" class="py-name" targets="Variable Martel.msre_constants.CATEGORY_WORD=Martel.msre_constants-module.html#CATEGORY_WORD,Variable Martel.msre_parse.CATEGORY_WORD=Martel.msre_parse-module.html#CATEGORY_WORD"><a title="Martel.msre_constants.CATEGORY_WORD
Martel.msre_parse.CATEGORY_WORD" class="py-name" href="#" onclick="return doclink('link-41', 'CATEGORY_WORD', 'link-41');">CATEGORY_WORD</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-string">r"\W"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-42" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-42', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt class="py-op">[</tt><tt class="py-op">(</tt><tt id="link-43" class="py-name"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-43', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">,</tt> <tt id="link-44" class="py-name" targets="Variable Martel.msre_constants.CATEGORY_NOT_WORD=Martel.msre_constants-module.html#CATEGORY_NOT_WORD,Variable Martel.msre_parse.CATEGORY_NOT_WORD=Martel.msre_parse-module.html#CATEGORY_NOT_WORD"><a title="Martel.msre_constants.CATEGORY_NOT_WORD
Martel.msre_parse.CATEGORY_NOT_WORD" class="py-name" href="#" onclick="return doclink('link-44', 'CATEGORY_NOT_WORD', 'link-44');">CATEGORY_NOT_WORD</a></tt><tt class="py-op">)</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L55"></a><tt class="py-lineno"> 55</tt> <tt class="py-line"> <tt class="py-string">r"\Z"</tt><tt class="py-op">:</tt> <tt class="py-op">(</tt><tt id="link-45" class="py-name"><a title="Martel.msre_constants.AT
Martel.msre_parse.AT" class="py-name" href="#" onclick="return doclink('link-45', 'AT', 'link-20');">AT</a></tt><tt class="py-op">,</tt> <tt id="link-46" class="py-name" targets="Variable Martel.msre_constants.AT_END_STRING=Martel.msre_constants-module.html#AT_END_STRING,Variable Martel.msre_parse.AT_END_STRING=Martel.msre_parse-module.html#AT_END_STRING"><a title="Martel.msre_constants.AT_END_STRING
Martel.msre_parse.AT_END_STRING" class="py-name" href="#" onclick="return doclink('link-46', 'AT_END_STRING', 'link-46');">AT_END_STRING</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># end of string</tt> </tt>
<a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="L57"></a><tt class="py-lineno"> 57</tt> <tt class="py-line"> </tt>
<a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"><tt id="link-47" class="py-name" targets="Variable Martel.msre_parse.FLAGS=Martel.msre_parse-module.html#FLAGS"><a title="Martel.msre_parse.FLAGS" class="py-name" href="#" onclick="return doclink('link-47', 'FLAGS', 'link-47');">FLAGS</a></tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt> </tt>
<a name="L59"></a><tt class="py-lineno"> 59</tt> <tt class="py-line"> <tt class="py-comment"># standard flags</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-string">"i"</tt><tt class="py-op">:</tt> <tt id="link-48" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_IGNORECASE=Martel.msre_constants-module.html#SRE_FLAG_IGNORECASE,Variable Martel.msre_parse.SRE_FLAG_IGNORECASE=Martel.msre_parse-module.html#SRE_FLAG_IGNORECASE"><a title="Martel.msre_constants.SRE_FLAG_IGNORECASE
Martel.msre_parse.SRE_FLAG_IGNORECASE" class="py-name" href="#" onclick="return doclink('link-48', 'SRE_FLAG_IGNORECASE', 'link-48');">SRE_FLAG_IGNORECASE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> <tt class="py-string">"L"</tt><tt class="py-op">:</tt> <tt id="link-49" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_LOCALE=Martel.msre_constants-module.html#SRE_FLAG_LOCALE,Variable Martel.msre_parse.SRE_FLAG_LOCALE=Martel.msre_parse-module.html#SRE_FLAG_LOCALE"><a title="Martel.msre_constants.SRE_FLAG_LOCALE
Martel.msre_parse.SRE_FLAG_LOCALE" class="py-name" href="#" onclick="return doclink('link-49', 'SRE_FLAG_LOCALE', 'link-49');">SRE_FLAG_LOCALE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-string">"m"</tt><tt class="py-op">:</tt> <tt id="link-50" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_MULTILINE=Martel.msre_constants-module.html#SRE_FLAG_MULTILINE,Variable Martel.msre_parse.SRE_FLAG_MULTILINE=Martel.msre_parse-module.html#SRE_FLAG_MULTILINE"><a title="Martel.msre_constants.SRE_FLAG_MULTILINE
Martel.msre_parse.SRE_FLAG_MULTILINE" class="py-name" href="#" onclick="return doclink('link-50', 'SRE_FLAG_MULTILINE', 'link-50');">SRE_FLAG_MULTILINE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-string">"s"</tt><tt class="py-op">:</tt> <tt id="link-51" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_DOTALL=Martel.msre_constants-module.html#SRE_FLAG_DOTALL,Variable Martel.msre_parse.SRE_FLAG_DOTALL=Martel.msre_parse-module.html#SRE_FLAG_DOTALL"><a title="Martel.msre_constants.SRE_FLAG_DOTALL
Martel.msre_parse.SRE_FLAG_DOTALL" class="py-name" href="#" onclick="return doclink('link-51', 'SRE_FLAG_DOTALL', 'link-51');">SRE_FLAG_DOTALL</a></tt><tt class="py-op">,</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-string">"x"</tt><tt class="py-op">:</tt> <tt id="link-52" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_VERBOSE=Martel.msre_constants-module.html#SRE_FLAG_VERBOSE,Variable Martel.msre_parse.SRE_FLAG_VERBOSE=Martel.msre_parse-module.html#SRE_FLAG_VERBOSE"><a title="Martel.msre_constants.SRE_FLAG_VERBOSE
Martel.msre_parse.SRE_FLAG_VERBOSE" class="py-name" href="#" onclick="return doclink('link-52', 'SRE_FLAG_VERBOSE', 'link-52');">SRE_FLAG_VERBOSE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-comment"># extensions</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> <tt class="py-string">"t"</tt><tt class="py-op">:</tt> <tt id="link-53" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_TEMPLATE=Martel.msre_constants-module.html#SRE_FLAG_TEMPLATE,Variable Martel.msre_parse.SRE_FLAG_TEMPLATE=Martel.msre_parse-module.html#SRE_FLAG_TEMPLATE"><a title="Martel.msre_constants.SRE_FLAG_TEMPLATE
Martel.msre_parse.SRE_FLAG_TEMPLATE" class="py-name" href="#" onclick="return doclink('link-53', 'SRE_FLAG_TEMPLATE', 'link-53');">SRE_FLAG_TEMPLATE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-string">"u"</tt><tt class="py-op">:</tt> <tt id="link-54" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_UNICODE=Martel.msre_constants-module.html#SRE_FLAG_UNICODE,Variable Martel.msre_parse.SRE_FLAG_UNICODE=Martel.msre_parse-module.html#SRE_FLAG_UNICODE"><a title="Martel.msre_constants.SRE_FLAG_UNICODE
Martel.msre_parse.SRE_FLAG_UNICODE" class="py-name" href="#" onclick="return doclink('link-54', 'SRE_FLAG_UNICODE', 'link-54');">SRE_FLAG_UNICODE</a></tt><tt class="py-op">,</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"><tt class="py-op">}</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"><tt class="py-comment"># figure out best way to convert hex/octal numbers to integers</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-string">"10"</tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-name">atoi</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt> <tt class="py-comment"># 2.0 and later</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"><tt class="py-keyword">except</tt> <tt class="py-name">TypeError</tt><tt class="py-op">:</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> <tt class="py-name">atoi</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">atoi</tt> <tt class="py-comment"># 1.5.2</tt> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> </tt>
<a name="Pattern"></a><div id="Pattern-def"><a name="L77"></a><tt class="py-lineno"> 77</tt> <a class="py-toggle" href="#" id="Pattern-toggle" onclick="return toggle('Pattern');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.msre_parse.Pattern-class.html">Pattern</a><tt class="py-op">:</tt> </tt>
</div><div id="Pattern-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Pattern-expanded"><a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> <tt class="py-comment"># master pattern object. keeps track of global attributes</tt> </tt>
<a name="Pattern.__init__"></a><div id="Pattern.__init__-def"><a name="L79"></a><tt class="py-lineno"> 79</tt> <a class="py-toggle" href="#" id="Pattern.__init__-toggle" onclick="return toggle('Pattern.__init__');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Pattern-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pattern.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Pattern.__init__-expanded"><a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name" targets="Function Bio.Mindy.FlatDB.open()=Bio.Mindy.FlatDB-module.html#open,Function Bio.Mindy.open()=Bio.Mindy-module.html#open"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-55', 'open', 'link-55');">open</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-56" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.groups()=Bio.Prosite.Pattern.PrositeMatch-class.html#groups"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-56', 'groups', 'link-56');">groups</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">groupdict</tt> <tt class="py-op">=</tt> <tt class="py-op">{</tt><tt class="py-op">}</tt> </tt>
</div><a name="Pattern.opengroup"></a><div id="Pattern.opengroup-def"><a name="L84"></a><tt class="py-lineno"> 84</tt> <a class="py-toggle" href="#" id="Pattern.opengroup-toggle" onclick="return toggle('Pattern.opengroup');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Pattern-class.html#opengroup">opengroup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">name</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pattern.opengroup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Pattern.opengroup-expanded"><a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-name">gid</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-57" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-57', 'groups', 'link-56');">groups</a></tt> </tt>
<a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-58', 'groups', 'link-56');">groups</a></tt> <tt class="py-op">=</tt> <tt class="py-name">gid</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-59" class="py-name" targets="Variable Bio.Encodings.IUPACEncoding.name=Bio.Encodings.IUPACEncoding-module.html#name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-59', 'name', 'link-59');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L88"></a><tt class="py-lineno"> 88</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">groupdict</tt><tt class="py-op">[</tt><tt id="link-60" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-60', 'name', 'link-59');">name</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">gid</tt> </tt>
<a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-61', 'open', 'link-55');">open</a></tt><tt class="py-op">.</tt><tt id="link-62" class="py-name" targets="Method Bio.Crystal.Chain.append()=Bio.Crystal.Chain-class.html#append,Method Bio.EUtils.POM.ElementNode.append()=Bio.EUtils.POM.ElementNode-class.html#append,Method Bio.EUtils.sourcegen.SourceFile.append()=Bio.EUtils.sourcegen.SourceFile-class.html#append,Method Bio.SCOP.Raf.SeqMap.append()=Bio.SCOP.Raf.SeqMap-class.html#append,Method Bio.Seq.MutableSeq.append()=Bio.Seq.MutableSeq-class.html#append,Method Bio.Wise.psw.Alignment.append()=Bio.Wise.psw.Alignment-class.html#append,Method Bio.Wise.psw.AlignmentColumn.append()=Bio.Wise.psw.AlignmentColumn-class.html#append,Method Martel.msre_parse.SubPattern.append()=Martel.msre_parse.SubPattern-class.html#append"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-62', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">gid</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">gid</tt> </tt>
</div><a name="Pattern.closegroup"></a><div id="Pattern.closegroup-def"><a name="L91"></a><tt class="py-lineno"> 91</tt> <a class="py-toggle" href="#" id="Pattern.closegroup-toggle" onclick="return toggle('Pattern.closegroup');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Pattern-class.html#closegroup">closegroup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">gid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pattern.closegroup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Pattern.closegroup-expanded"><a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-63" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-63', 'open', 'link-55');">open</a></tt><tt class="py-op">.</tt><tt id="link-64" class="py-name" targets="Method Bio.Crystal.Chain.remove()=Bio.Crystal.Chain-class.html#remove,Method Bio.GFF.GenericTools.TempFile.remove()=Bio.GFF.GenericTools.TempFile-class.html#remove,Method Bio.Graphics.BasicChromosome._ChromosomeComponent.remove()=Bio.Graphics.BasicChromosome._ChromosomeComponent-class.html#remove,Method Bio.Pathway.Rep.HashSet.HashSet.remove()=Bio.Pathway.Rep.HashSet.HashSet-class.html#remove,Method Bio.Restriction.Restriction.RestrictionBatch.remove()=Bio.Restriction.Restriction.RestrictionBatch-class.html#remove,Method Bio.Seq.MutableSeq.remove()=Bio.Seq.MutableSeq-class.html#remove,Method BioSQL.Loader.DatabaseRemover.remove()=BioSQL.Loader.DatabaseRemover-class.html#remove"><a title="Bio.Crystal.Chain.remove
Bio.GFF.GenericTools.TempFile.remove
Bio.Graphics.BasicChromosome._ChromosomeComponent.remove
Bio.Pathway.Rep.HashSet.HashSet.remove
Bio.Restriction.Restriction.RestrictionBatch.remove
Bio.Seq.MutableSeq.remove
BioSQL.Loader.DatabaseRemover.remove" class="py-name" href="#" onclick="return doclink('link-64', 'remove', 'link-64');">remove</a></tt><tt class="py-op">(</tt><tt class="py-name">gid</tt><tt class="py-op">)</tt> </tt>
</div><a name="Pattern.checkgroup"></a><div id="Pattern.checkgroup-def"><a name="L93"></a><tt class="py-lineno"> 93</tt> <a class="py-toggle" href="#" id="Pattern.checkgroup-toggle" onclick="return toggle('Pattern.checkgroup');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Pattern-class.html#checkgroup">checkgroup</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">gid</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Pattern.checkgroup-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Pattern.checkgroup-expanded"><a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">gid</tt> <tt class="py-op"><</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-65" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-65', 'groups', 'link-56');">groups</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">gid</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-66" class="py-name"><a title="Bio.Mindy.FlatDB.open
Bio.Mindy.open" class="py-name" href="#" onclick="return doclink('link-66', 'open', 'link-55');">open</a></tt> </tt>
</div></div><a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> </tt>
<a name="SubPattern"></a><div id="SubPattern-def"><a name="L96"></a><tt class="py-lineno"> 96</tt> <a class="py-toggle" href="#" id="SubPattern-toggle" onclick="return toggle('SubPattern');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html">SubPattern</a><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="SubPattern-expanded"><a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-comment"># a subpattern, in intermediate form</tt> </tt>
<a name="SubPattern.__init__"></a><div id="SubPattern.__init__-def"><a name="L98"></a><tt class="py-lineno"> 98</tt> <a class="py-toggle" href="#" id="SubPattern.__init__-toggle" onclick="return toggle('SubPattern.__init__');">-</a><tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">pattern</tt><tt class="py-op">,</tt> <tt class="py-param">data</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.__init__-expanded"><a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-67" class="py-name" targets="Method Bio.Prosite._RecordConsumer.pattern()=Bio.Prosite._RecordConsumer-class.html#pattern"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-67', 'pattern', 'link-67');">pattern</a></tt> <tt class="py-op">=</tt> <tt id="link-68" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-68', 'pattern', 'link-67');">pattern</a></tt> </tt>
<a name="L100"></a><tt class="py-lineno">100</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-69" class="py-name" targets="Variable BioSQL.BioSeq.DBSeq.data=BioSQL.BioSeq.DBSeq-class.html#data"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-69', 'data', 'link-69');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L101"></a><tt class="py-lineno">101</tt> <tt class="py-line"> <tt id="link-70" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-70', 'data', 'link-69');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-71" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-71', 'data', 'link-69');">data</a></tt> <tt class="py-op">=</tt> <tt id="link-72" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-72', 'data', 'link-69');">data</a></tt> </tt>
<a name="L103"></a><tt class="py-lineno">103</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">width</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
</div><a name="SubPattern.dump"></a><div id="SubPattern.dump-def"><a name="L104"></a><tt class="py-lineno">104</tt> <a class="py-toggle" href="#" id="SubPattern.dump-toggle" onclick="return toggle('SubPattern.dump');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#dump">dump</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">level</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.dump-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.dump-expanded"><a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">op</tt><tt class="py-op">,</tt> <tt class="py-name">av</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-73', 'data', 'link-69');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L107"></a><tt class="py-lineno">107</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">level</tt><tt class="py-op">*</tt><tt class="py-string">" "</tt> <tt class="py-op">+</tt> <tt class="py-name">op</tt><tt class="py-op">,</tt><tt class="py-op">;</tt> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">op</tt> <tt class="py-op">==</tt> <tt class="py-string">"in"</tt><tt class="py-op">:</tt> </tt>
<a name="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-comment"># member sublanguage</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">print</tt><tt class="py-op">;</tt> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">op</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">av</tt><tt class="py-op">:</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">*</tt><tt class="py-string">" "</tt> <tt class="py-op">+</tt> <tt class="py-name">op</tt><tt class="py-op">,</tt> <tt class="py-name">a</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">op</tt> <tt class="py-op">==</tt> <tt class="py-string">"branch"</tt><tt class="py-op">:</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">print</tt><tt class="py-op">;</tt> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt id="link-74" class="py-name" targets="Variable Bio.PDB.Polypeptide.i=Bio.PDB.Polypeptide-module.html#i"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-74', 'i', 'link-74');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">av</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-75" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-75', 'i', 'link-74');">i</a></tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">:</tt> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">level</tt><tt class="py-op">*</tt><tt class="py-string">" "</tt> <tt class="py-op">+</tt> <tt class="py-string">"or"</tt> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-76" class="py-name" targets="Method Bio.DocSQL.Query.dump()=Bio.DocSQL.Query-class.html#dump,Method Martel.msre_parse.SubPattern.dump()=Martel.msre_parse.SubPattern-class.html#dump,Method Martel.test.support.Storage.dump()=Martel.test.support.Storage-class.html#dump,Function Martel.test.test_swissprot38.dump()=Martel.test.test_swissprot38-module.html#dump"><a title="Bio.DocSQL.Query.dump
Martel.msre_parse.SubPattern.dump
Martel.test.support.Storage.dump
Martel.test.test_swissprot38.dump" class="py-name" href="#" onclick="return doclink('link-76', 'dump', 'link-76');">dump</a></tt><tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt id="link-77" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-77', 'i', 'link-74');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-78" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-78', 'i', 'link-74');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-79" class="py-name" targets="Variable Bio.GenBank.LocationParser.Integer.type=Bio.GenBank.LocationParser.Integer-class.html#type,Variable Bio.GenBank.LocationParser.Symbol.type=Bio.GenBank.LocationParser.Symbol-class.html#type,Variable Bio.GenBank.LocationParser.UnsignedInteger.type=Bio.GenBank.LocationParser.UnsignedInteger-class.html#type"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-79', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">av</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-80', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt id="link-81" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-81', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-op">[</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L122"></a><tt class="py-lineno">122</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">a</tt> <tt class="py-keyword">in</tt> <tt class="py-name">av</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">isinstance</tt><tt class="py-op">(</tt><tt class="py-name">a</tt><tt class="py-op">,</tt> <tt id="link-82" class="py-name" targets="Class Martel.msre_parse.SubPattern=Martel.msre_parse.SubPattern-class.html"><a title="Martel.msre_parse.SubPattern" class="py-name" href="#" onclick="return doclink('link-82', 'SubPattern', 'link-82');">SubPattern</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">nl</tt><tt class="py-op">:</tt> <tt class="py-keyword">print</tt> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">.</tt><tt id="link-83" class="py-name"><a title="Bio.DocSQL.Query.dump
Martel.msre_parse.SubPattern.dump
Martel.test.support.Storage.dump
Martel.test.test_swissprot38.dump" class="py-name" href="#" onclick="return doclink('link-83', 'dump', 'link-76');">dump</a></tt><tt class="py-op">(</tt><tt class="py-name">level</tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">;</tt> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">a</tt><tt class="py-op">,</tt> <tt class="py-op">;</tt> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</tt> <tt class="py-line"> <tt class="py-keyword">print</tt> <tt class="py-name">av</tt><tt class="py-op">,</tt> <tt class="py-op">;</tt> <tt class="py-name">nl</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">nl</tt><tt class="py-op">:</tt> <tt class="py-keyword">print</tt> </tt>
</div><a name="SubPattern.__repr__"></a><div id="SubPattern.__repr__-def"><a name="L131"></a><tt class="py-lineno">131</tt> <a class="py-toggle" href="#" id="SubPattern.__repr__-toggle" onclick="return toggle('SubPattern.__repr__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#__repr__">__repr__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.__repr__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.__repr__-expanded"><a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-84" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-84', 'data', 'link-69');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="SubPattern.__len__"></a><div id="SubPattern.__len__-def"><a name="L133"></a><tt class="py-lineno">133</tt> <a class="py-toggle" href="#" id="SubPattern.__len__-toggle" onclick="return toggle('SubPattern.__len__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#__len__">__len__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.__len__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.__len__-expanded"><a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-85', 'data', 'link-69');">data</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="SubPattern.__delitem__"></a><div id="SubPattern.__delitem__-def"><a name="L135"></a><tt class="py-lineno">135</tt> <a class="py-toggle" href="#" id="SubPattern.__delitem__-toggle" onclick="return toggle('SubPattern.__delitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#__delitem__">__delitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.__delitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.__delitem__-expanded"><a name="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-86" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-86', 'data', 'link-69');">data</a></tt><tt class="py-op">[</tt><tt id="link-87" class="py-name" targets="Method Bio.Crystal.Chain.index()=Bio.Crystal.Chain-class.html#index,Method Bio.EUtils.POM.ElementNode.index()=Bio.EUtils.POM.ElementNode-class.html#index,Method Bio.SCOP.Raf.SeqMap.index()=Bio.SCOP.Raf.SeqMap-class.html#index,Method Bio.Seq.MutableSeq.index()=Bio.Seq.MutableSeq-class.html#index"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-87', 'index', 'link-87');">index</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="SubPattern.__getitem__"></a><div id="SubPattern.__getitem__-def"><a name="L137"></a><tt class="py-lineno">137</tt> <a class="py-toggle" href="#" id="SubPattern.__getitem__-toggle" onclick="return toggle('SubPattern.__getitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#__getitem__">__getitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.__getitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.__getitem__-expanded"><a name="L138"></a><tt class="py-lineno">138</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-88" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-88', 'data', 'link-69');">data</a></tt><tt class="py-op">[</tt><tt id="link-89" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-89', 'index', 'link-87');">index</a></tt><tt class="py-op">]</tt> </tt>
</div><a name="SubPattern.__setitem__"></a><div id="SubPattern.__setitem__-def"><a name="L139"></a><tt class="py-lineno">139</tt> <a class="py-toggle" href="#" id="SubPattern.__setitem__-toggle" onclick="return toggle('SubPattern.__setitem__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#__setitem__">__setitem__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">,</tt> <tt class="py-param">code</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.__setitem__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.__setitem__-expanded"><a name="L140"></a><tt class="py-lineno">140</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-90', 'data', 'link-69');">data</a></tt><tt class="py-op">[</tt><tt id="link-91" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-91', 'index', 'link-87');">index</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-name">code</tt> </tt>
</div><a name="SubPattern.__getslice__"></a><div id="SubPattern.__getslice__-def"><a name="L141"></a><tt class="py-lineno">141</tt> <a class="py-toggle" href="#" id="SubPattern.__getslice__-toggle" onclick="return toggle('SubPattern.__getslice__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#__getslice__">__getslice__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">start</tt><tt class="py-op">,</tt> <tt class="py-param">stop</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.__getslice__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.__getslice__-expanded"><a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-92" class="py-name"><a title="Martel.msre_parse.SubPattern" class="py-name" href="#" onclick="return doclink('link-92', 'SubPattern', 'link-82');">SubPattern</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-93" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-93', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-94', 'data', 'link-69');">data</a></tt><tt class="py-op">[</tt><tt id="link-95" class="py-name" targets="Method Bio.GFF.easy.Location.start()=Bio.GFF.easy.Location-class.html#start,Method Bio.Prosite.Pattern.PrositeMatch.start()=Bio.Prosite.Pattern.PrositeMatch-class.html#start,Variable Bio.Restriction._Update.RestrictionCompiler.start=Bio.Restriction._Update.RestrictionCompiler-module.html#start,Method Martel.LAX.LAX.start()=Martel.LAX.LAX-class.html#start"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-95', 'start', 'link-95');">start</a></tt><tt class="py-op">:</tt><tt class="py-name">stop</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
</div><a name="SubPattern.insert"></a><div id="SubPattern.insert-def"><a name="L143"></a><tt class="py-lineno">143</tt> <a class="py-toggle" href="#" id="SubPattern.insert-toggle" onclick="return toggle('SubPattern.insert');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#insert">insert</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">,</tt> <tt class="py-param">code</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.insert-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.insert-expanded"><a name="L144"></a><tt class="py-lineno">144</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-96" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-96', 'data', 'link-69');">data</a></tt><tt class="py-op">.</tt><tt id="link-97" class="py-name" targets="Method Bio.Crystal.Chain.insert()=Bio.Crystal.Chain-class.html#insert,Method Bio.EUtils.POM.Comment.insert()=Bio.EUtils.POM.Comment-class.html#insert,Method Bio.EUtils.POM.ElementNode.insert()=Bio.EUtils.POM.ElementNode-class.html#insert,Method Bio.EUtils.POM.IndentedText.insert()=Bio.EUtils.POM.IndentedText-class.html#insert,Method Bio.Seq.MutableSeq.insert()=Bio.Seq.MutableSeq-class.html#insert,Method Martel.msre_parse.SubPattern.insert()=Martel.msre_parse.SubPattern-class.html#insert"><a title="Bio.Crystal.Chain.insert
Bio.EUtils.POM.Comment.insert
Bio.EUtils.POM.ElementNode.insert
Bio.EUtils.POM.IndentedText.insert
Bio.Seq.MutableSeq.insert
Martel.msre_parse.SubPattern.insert" class="py-name" href="#" onclick="return doclink('link-97', 'insert', 'link-97');">insert</a></tt><tt class="py-op">(</tt><tt id="link-98" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-98', 'index', 'link-87');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">code</tt><tt class="py-op">)</tt> </tt>
</div><a name="SubPattern.append"></a><div id="SubPattern.append-def"><a name="L145"></a><tt class="py-lineno">145</tt> <a class="py-toggle" href="#" id="SubPattern.append-toggle" onclick="return toggle('SubPattern.append');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#append">append</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">code</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.append-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.append-expanded"><a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-99" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-99', 'data', 'link-69');">data</a></tt><tt class="py-op">.</tt><tt id="link-100" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-100', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">code</tt><tt class="py-op">)</tt> </tt>
</div><a name="SubPattern.getwidth"></a><div id="SubPattern.getwidth-def"><a name="L147"></a><tt class="py-lineno">147</tt> <a class="py-toggle" href="#" id="SubPattern.getwidth-toggle" onclick="return toggle('SubPattern.getwidth');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.SubPattern-class.html#getwidth">getwidth</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="SubPattern.getwidth-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="SubPattern.getwidth-expanded"><a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"> <tt class="py-comment"># determine the width (min, max) for this subpattern</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">width</tt><tt class="py-op">:</tt> </tt>
<a name="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">width</tt> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-number">0L</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">op</tt><tt class="py-op">,</tt> <tt class="py-name">av</tt> <tt class="py-keyword">in</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-101" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-101', 'data', 'link-69');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">op</tt> <tt class="py-keyword">is</tt> <tt id="link-102" class="py-name" targets="Variable Martel.msre_constants.BRANCH=Martel.msre_constants-module.html#BRANCH,Variable Martel.msre_parse.BRANCH=Martel.msre_parse-module.html#BRANCH"><a title="Martel.msre_constants.BRANCH
Martel.msre_parse.BRANCH" class="py-name" href="#" onclick="return doclink('link-102', 'BRANCH', 'link-102');">BRANCH</a></tt><tt class="py-op">:</tt> </tt>
<a name="L154"></a><tt class="py-lineno">154</tt> <tt class="py-line"> <tt id="link-103" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-103', 'i', 'link-74');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">maxint</tt> </tt>
<a name="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">av</tt> <tt class="py-keyword">in</tt> <tt class="py-name">av</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-name">l</tt><tt class="py-op">,</tt> <tt class="py-name">h</tt> <tt class="py-op">=</tt> <tt class="py-name">av</tt><tt class="py-op">.</tt><tt id="link-104" class="py-name" targets="Method Martel.msre_parse.SubPattern.getwidth()=Martel.msre_parse.SubPattern-class.html#getwidth"><a title="Martel.msre_parse.SubPattern.getwidth" class="py-name" href="#" onclick="return doclink('link-104', 'getwidth', 'link-104');">getwidth</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt id="link-105" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-105', 'i', 'link-74');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-name">min</tt><tt class="py-op">(</tt><tt id="link-106" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-106', 'i', 'link-74');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">l</tt><tt class="py-op">)</tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">max</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">,</tt> <tt class="py-name">h</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> <tt class="py-op">+</tt> <tt id="link-107" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-107', 'i', 'link-74');">i</a></tt> </tt>
<a name="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">+</tt> <tt class="py-name">j</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">op</tt> <tt class="py-keyword">is</tt> <tt id="link-108" class="py-name" targets="Variable Martel.msre_constants.CALL=Martel.msre_constants-module.html#CALL,Variable Martel.msre_parse.CALL=Martel.msre_parse-module.html#CALL"><a title="Martel.msre_constants.CALL
Martel.msre_parse.CALL" class="py-name" href="#" onclick="return doclink('link-108', 'CALL', 'link-108');">CALL</a></tt><tt class="py-op">:</tt> </tt>
<a name="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt id="link-109" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-109', 'i', 'link-74');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">av</tt><tt class="py-op">.</tt><tt id="link-110" class="py-name"><a title="Martel.msre_parse.SubPattern.getwidth" class="py-name" href="#" onclick="return doclink('link-110', 'getwidth', 'link-104');">getwidth</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> <tt class="py-op">+</tt> <tt id="link-111" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-111', 'i', 'link-74');">i</a></tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">+</tt> <tt class="py-name">j</tt> </tt>
<a name="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">op</tt> <tt class="py-keyword">is</tt> <tt id="link-112" class="py-name" targets="Variable Martel.msre_constants.SUBPATTERN=Martel.msre_constants-module.html#SUBPATTERN,Variable Martel.msre_parse.SUBPATTERN=Martel.msre_parse-module.html#SUBPATTERN"><a title="Martel.msre_constants.SUBPATTERN
Martel.msre_parse.SUBPATTERN" class="py-name" href="#" onclick="return doclink('link-112', 'SUBPATTERN', 'link-112');">SUBPATTERN</a></tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt id="link-113" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-113', 'i', 'link-74');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">av</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Martel.msre_parse.SubPattern.getwidth" class="py-name" href="#" onclick="return doclink('link-114', 'getwidth', 'link-104');">getwidth</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> <tt class="py-op">+</tt> <tt id="link-115" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-115', 'i', 'link-74');">i</a></tt> </tt>
<a name="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">+</tt> <tt class="py-name">j</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">op</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt id="link-116" class="py-name" targets="Variable Martel.msre_constants.MIN_REPEAT=Martel.msre_constants-module.html#MIN_REPEAT,Variable Martel.msre_parse.MIN_REPEAT=Martel.msre_parse-module.html#MIN_REPEAT"><a title="Martel.msre_constants.MIN_REPEAT
Martel.msre_parse.MIN_REPEAT" class="py-name" href="#" onclick="return doclink('link-116', 'MIN_REPEAT', 'link-116');">MIN_REPEAT</a></tt><tt class="py-op">,</tt> <tt id="link-117" class="py-name" targets="Variable Martel.msre_constants.MAX_REPEAT=Martel.msre_constants-module.html#MAX_REPEAT,Variable Martel.msre_parse.MAX_REPEAT=Martel.msre_parse-module.html#MAX_REPEAT"><a title="Martel.msre_constants.MAX_REPEAT
Martel.msre_parse.MAX_REPEAT" class="py-name" href="#" onclick="return doclink('link-117', 'MAX_REPEAT', 'link-117');">MAX_REPEAT</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt id="link-118" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-118', 'i', 'link-74');">i</a></tt><tt class="py-op">,</tt> <tt class="py-name">j</tt> <tt class="py-op">=</tt> <tt class="py-name">av</tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">.</tt><tt id="link-119" class="py-name"><a title="Martel.msre_parse.SubPattern.getwidth" class="py-name" href="#" onclick="return doclink('link-119', 'getwidth', 'link-104');">getwidth</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> <tt class="py-op">+</tt> <tt class="py-name">long</tt><tt class="py-op">(</tt><tt id="link-120" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-120', 'i', 'link-74');">i</a></tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">av</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">+</tt> <tt class="py-name">long</tt><tt class="py-op">(</tt><tt class="py-name">j</tt><tt class="py-op">)</tt> <tt class="py-op">*</tt> <tt class="py-name">av</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">op</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt id="link-121" class="py-name" targets="Variable Bio.EUtils.POM.ANY=Bio.EUtils.POM-module.html#ANY,Variable Martel.msre_constants.ANY=Martel.msre_constants-module.html#ANY,Variable Martel.msre_parse.ANY=Martel.msre_parse-module.html#ANY"><a title="Bio.EUtils.POM.ANY
Martel.msre_constants.ANY
Martel.msre_parse.ANY" class="py-name" href="#" onclick="return doclink('link-121', 'ANY', 'link-121');">ANY</a></tt><tt class="py-op">,</tt> <tt id="link-122" class="py-name" targets="Variable Martel.msre_constants.RANGE=Martel.msre_constants-module.html#RANGE,Variable Martel.msre_parse.RANGE=Martel.msre_parse-module.html#RANGE"><a title="Martel.msre_constants.RANGE
Martel.msre_parse.RANGE" class="py-name" href="#" onclick="return doclink('link-122', 'RANGE', 'link-122');">RANGE</a></tt><tt class="py-op">,</tt> <tt id="link-123" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-123', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt id="link-124" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-124', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt id="link-125" class="py-name" targets="Variable Martel.msre_constants.NOT_LITERAL=Martel.msre_constants-module.html#NOT_LITERAL,Variable Martel.msre_parse.NOT_LITERAL=Martel.msre_parse-module.html#NOT_LITERAL"><a title="Martel.msre_constants.NOT_LITERAL
Martel.msre_parse.NOT_LITERAL" class="py-name" href="#" onclick="return doclink('link-125', 'NOT_LITERAL', 'link-125');">NOT_LITERAL</a></tt><tt class="py-op">,</tt> <tt id="link-126" class="py-name"><a title="Martel.msre_constants.CATEGORY
Martel.msre_parse.CATEGORY" class="py-name" href="#" onclick="return doclink('link-126', 'CATEGORY', 'link-14');">CATEGORY</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">op</tt> <tt class="py-op">==</tt> <tt id="link-127" class="py-name" targets="Variable Martel.msre_constants.SUCCESS=Martel.msre_constants-module.html#SUCCESS,Variable Martel.msre_parse.SUCCESS=Martel.msre_parse-module.html#SUCCESS"><a title="Martel.msre_constants.SUCCESS
Martel.msre_parse.SUCCESS" class="py-name" href="#" onclick="return doclink('link-127', 'SUCCESS', 'link-127');">SUCCESS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">width</tt> <tt class="py-op">=</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">lo</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">maxint</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">int</tt><tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">(</tt><tt class="py-name">hi</tt><tt class="py-op">,</tt> <tt class="py-name">sys</tt><tt class="py-op">.</tt><tt class="py-name">maxint</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L180"></a><tt class="py-lineno">180</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">width</tt> </tt>
</div></div><a name="L181"></a><tt class="py-lineno">181</tt> <tt class="py-line"> </tt>
<a name="Tokenizer"></a><div id="Tokenizer-def"><a name="L182"></a><tt class="py-lineno">182</tt> <a class="py-toggle" href="#" id="Tokenizer-toggle" onclick="return toggle('Tokenizer');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.msre_parse.Tokenizer-class.html">Tokenizer</a><tt class="py-op">:</tt> </tt>
</div><div id="Tokenizer-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Tokenizer-expanded"><a name="Tokenizer.__init__"></a><div id="Tokenizer.__init__-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="Tokenizer.__init__-toggle" onclick="return toggle('Tokenizer.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Tokenizer-class.html#__init__">__init__</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tokenizer.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tokenizer.__init__-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">string</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-128" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-128', 'index', 'link-87');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name" targets="Method Martel.msre_parse.Tokenizer.__next()=Martel.msre_parse.Tokenizer-class.html#__next"><a title="Martel.msre_parse.Tokenizer.__next" class="py-name" href="#" onclick="return doclink('link-129', '__next', 'link-129');">__next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
</div><a name="Tokenizer.__next"></a><div id="Tokenizer.__next-def"><a name="L187"></a><tt class="py-lineno">187</tt> <a class="py-toggle" href="#" id="Tokenizer.__next-toggle" onclick="return toggle('Tokenizer.__next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Tokenizer-class.html#__next">__next</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tokenizer.__next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tokenizer.__next-expanded"><a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-130" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-130', 'index', 'link-87');">index</a></tt> <tt class="py-op">>=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">string</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-131" class="py-name" targets="Method Bio.AlignIO.ClustalIO.ClustalIterator.next()=Bio.AlignIO.ClustalIO.ClustalIterator-class.html#next,Method Bio.AlignIO.EmbossIO.EmbossIterator.next()=Bio.AlignIO.EmbossIO.EmbossIterator-class.html#next,Method Bio.AlignIO.FastaIO.FastaM10Iterator.next()=Bio.AlignIO.FastaIO.FastaM10Iterator-class.html#next,Method Bio.AlignIO.Interfaces.AlignmentIterator.next()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#next,Method Bio.AlignIO.PhylipIO.PhylipIterator.next()=Bio.AlignIO.PhylipIO.PhylipIterator-class.html#next,Method Bio.AlignIO.StockholmIO.StockholmIterator.next()=Bio.AlignIO.StockholmIO.StockholmIterator-class.html#next,Method Bio.Blast.NCBIStandalone.Iterator.next()=Bio.Blast.NCBIStandalone.Iterator-class.html#next,Method Bio.Blast.ParseBlastTable.BlastTableReader.next()=Bio.Blast.ParseBlastTable.BlastTableReader-class.html#next,Method Bio.CDD.Iterator.next()=Bio.CDD.Iterator-class.html#next,Method Bio.Compass.Iterator.next()=Bio.Compass.Iterator-class.html#next,Method Bio.DocSQL.IterationCursor.next()=Bio.DocSQL.IterationCursor-class.html#next,Method Bio.ECell.Iterator.next()=Bio.ECell.Iterator-class.html#next,Method Bio.Enzyme.Iterator.next()=Bio.Enzyme.Iterator-class.html#next,Method Bio.Fasta.Iterator.next()=Bio.Fasta.Iterator-class.html#next,Method Bio.GenBank.Iterator.next()=Bio.GenBank.Iterator-class.html#next,Method Bio.Gobase.Iterator.next()=Bio.Gobase.Iterator-class.html#next,Method Bio.IntelliGenetics.IntelliGeneticsReader.next()=Bio.IntelliGenetics.IntelliGeneticsReader-class.html#next,Method Bio.IntelliGenetics.Iterator.next()=Bio.IntelliGenetics.Iterator-class.html#next,Method Bio.LocusLink.Iterator.next()=Bio.LocusLink.Iterator-class.html#next,Method Bio.Medline.Iterator.next()=Bio.Medline.Iterator-class.html#next,Method Bio.MetaTool.Iterator.next()=Bio.MetaTool.Iterator-class.html#next,Method Bio.NBRF.Iterator.next()=Bio.NBRF.Iterator-class.html#next,Method Bio.Nexus.Nexus.CharBuffer.next()=Bio.Nexus.Nexus.CharBuffer-class.html#next,Method Bio.Prosite.Iterator.next()=Bio.Prosite.Iterator-class.html#next,Method Bio.Prosite.Prodoc.Iterator.next()=Bio.Prosite.Prodoc.Iterator-class.html#next,Method Bio.Rebase.Iterator.next()=Bio.Rebase.Iterator-class.html#next,Method Bio.SCOP.Cla.Iterator.next()=Bio.SCOP.Cla.Iterator-class.html#next,Method Bio.SCOP.Des.Iterator.next()=Bio.SCOP.Des.Iterator-class.html#next,Method Bio.SCOP.Dom.Iterator.next()=Bio.SCOP.Dom.Iterator-class.html#next,Method Bio.SCOP.Hie.Iterator.next()=Bio.SCOP.Hie.Iterator-class.html#next,Method Bio.SCOP.Raf.Iterator.next()=Bio.SCOP.Raf.Iterator-class.html#next,Method Bio.Saf.Iterator.next()=Bio.Saf.Iterator-class.html#next,Method Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next()=Bio.SeqIO.Interfaces.InterlacedSequenceIterator-class.html#next,Method Bio.SeqIO.Interfaces.SequenceIterator.next()=Bio.SeqIO.Interfaces.SequenceIterator-class.html#next,Method Bio.Sequencing.Ace.Iterator.next()=Bio.Sequencing.Ace.Iterator-class.html#next,Method Bio.Sequencing.Phd.Iterator.next()=Bio.Sequencing.Phd.Iterator-class.html#next,Method Bio.SwissProt.SProt.Iterator.next()=Bio.SwissProt.SProt.Iterator-class.html#next,Method Bio.UniGene.Iterator.next()=Bio.UniGene.Iterator-class.html#next,Method Martel.Iterator.EventStream.next()=Martel.Iterator.EventStream-class.html#next,Method Martel.Iterator.HeaderFooterEventStream.next()=Martel.Iterator.HeaderFooterEventStream-class.html#next,Method Martel.Iterator.Iterate.next()=Martel.Iterator.Iterate-class.html#next,Method Martel.Iterator.RecordEventStream.next()=Martel.Iterator.RecordEventStream-class.html#next,Method Martel.RecordReader.CountLines.next()=Martel.RecordReader.CountLines-class.html#next,Method Martel.RecordReader.EndsWith.next()=Martel.RecordReader.EndsWith-class.html#next,Method Martel.RecordReader.Everything.next()=Martel.RecordReader.Everything-class.html#next,Method Martel.RecordReader.Nothing.next()=Martel.RecordReader.Nothing-class.html#next,Method Martel.RecordReader.RecordReader.next()=Martel.RecordReader.RecordReader-class.html#next,Method Martel.RecordReader.StartsWith.next()=Martel.RecordReader.StartsWith-class.html#next,Method Martel.RecordReader.Until.next()=Martel.RecordReader.Until-class.html#next"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-131', 'next', 'link-131');">next</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> </tt>
<a name="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">string</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-132" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-132', 'index', 'link-87');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"\\"</tt><tt class="py-op">:</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> <tt class="py-name">c</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">string</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-133" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-133', 'index', 'link-87');">index</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IndexError</tt><tt class="py-op">:</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-134" class="py-name" targets="Method Bio.Parsers.spark.GenericParser.error()=Bio.Parsers.spark.GenericParser-class.html#error,Method Bio.Parsers.spark.GenericScanner.error()=Bio.Parsers.spark.GenericScanner-class.html#error,Method Martel.Iterator.StoreEvents.error()=Martel.Iterator.StoreEvents-class.html#error,Class Martel.msre_constants.error=Martel.msre_constants.error-class.html,Method Martel.test.support.Dump.error()=Martel.test.support.Dump-class.html#error,Method Martel.test.test_Parser.CountErrors.error()=Martel.test.test_Parser.CountErrors-class.html#error,Method Martel.test.test_optimize.GetErrorPos.error()=Martel.test.test_optimize.GetErrorPos-class.html#error"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-134', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bogus escape"</tt> </tt>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt class="py-name">char</tt> <tt class="py-op">+</tt> <tt class="py-name">c</tt> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-135', 'index', 'link-87');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-136" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-136', 'index', 'link-87');">index</a></tt> <tt class="py-op">+</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">char</tt><tt class="py-op">)</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-137', 'next', 'link-131');">next</a></tt> <tt class="py-op">=</tt> <tt class="py-name">char</tt> </tt>
</div><a name="Tokenizer.match"></a><div id="Tokenizer.match-def"><a name="L200"></a><tt class="py-lineno">200</tt> <a class="py-toggle" href="#" id="Tokenizer.match-toggle" onclick="return toggle('Tokenizer.match');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Tokenizer-class.html#match">match</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">char</tt><tt class="py-op">,</tt> <tt class="py-param">skip</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tokenizer.match-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tokenizer.match-expanded"><a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-op">==</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-138" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-138', 'next', 'link-131');">next</a></tt><tt class="py-op">:</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">skip</tt><tt class="py-op">:</tt> </tt>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-139" class="py-name"><a title="Martel.msre_parse.Tokenizer.__next" class="py-name" href="#" onclick="return doclink('link-139', '__next', 'link-129');">__next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
<a name="L205"></a><tt class="py-lineno">205</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
</div><a name="Tokenizer.get"></a><div id="Tokenizer.get-def"><a name="L206"></a><tt class="py-lineno">206</tt> <a class="py-toggle" href="#" id="Tokenizer.get-toggle" onclick="return toggle('Tokenizer.get');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Tokenizer-class.html#get">get</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tokenizer.get-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tokenizer.get-expanded"><a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-140" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-140', 'next', 'link-131');">next</a></tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-141" class="py-name"><a title="Martel.msre_parse.Tokenizer.__next" class="py-name" href="#" onclick="return doclink('link-141', '__next', 'link-129');">__next</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L209"></a><tt class="py-lineno">209</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">this</tt> </tt>
</div><a name="Tokenizer.tell"></a><div id="Tokenizer.tell-def"><a name="L210"></a><tt class="py-lineno">210</tt> <a class="py-toggle" href="#" id="Tokenizer.tell-toggle" onclick="return toggle('Tokenizer.tell');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Tokenizer-class.html#tell">tell</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tokenizer.tell-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tokenizer.tell-expanded"><a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-142', 'index', 'link-87');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-143" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-143', 'next', 'link-131');">next</a></tt> </tt>
</div><a name="Tokenizer.seek"></a><div id="Tokenizer.seek-def"><a name="L212"></a><tt class="py-lineno">212</tt> <a class="py-toggle" href="#" id="Tokenizer.seek-toggle" onclick="return toggle('Tokenizer.seek');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse.Tokenizer-class.html#seek">seek</a><tt class="py-op">(</tt><tt class="py-param">self</tt><tt class="py-op">,</tt> <tt class="py-param">index</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Tokenizer.seek-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Tokenizer.seek-expanded"><a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-144" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-144', 'index', 'link-87');">index</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-145" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-145', 'next', 'link-131');">next</a></tt> <tt class="py-op">=</tt> <tt id="link-146" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-146', 'index', 'link-87');">index</a></tt> </tt>
</div></div><a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"><tt class="py-comment">### Martel changes to allow all XML identifiers</tt> </tt>
<a name="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># '[a-zA-Z_:][-a-zA-Z0-9._:]*'</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"><tt class="py-comment"># Any (optional) attrs are stored after a '?'</tt> </tt>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># key/values are done in URL-style</tt> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># key1=value1&key2=value2;</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># only [-a-zA-Z0-9._] are allowed to be unescaped</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># escaping is done with URL-style hex escapes, so '=' becomes '%3D'</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># For example:</tt> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># seqdb format="swissprot" version="38"</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># can be represented as</tt> </tt>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># seqdb?format=swissprot&version=38</tt> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"><tt class="py-comment"># Martel specific changes</tt> </tt>
<a name="is_firstchar"></a><div id="is_firstchar-def"><a name="L230"></a><tt class="py-lineno">230</tt> <a class="py-toggle" href="#" id="is_firstchar-toggle" onclick="return toggle('is_firstchar');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#is_firstchar">is_firstchar</a><tt class="py-op">(</tt><tt class="py-param">char</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="is_firstchar-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="is_firstchar-expanded"><a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"a"</tt> <tt class="py-op"><=</tt> <tt class="py-name">char</tt> <tt class="py-op"><=</tt> <tt class="py-string">"z"</tt> <tt class="py-keyword">or</tt> <tt class="py-string">"A"</tt> <tt class="py-op"><=</tt> <tt class="py-name">char</tt> <tt class="py-op"><=</tt> <tt class="py-string">"Z"</tt> <tt class="py-keyword">or</tt> <tt class="py-name">char</tt> <tt class="py-keyword">in</tt> <tt class="py-string">"_:"</tt> </tt>
</div><a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> </tt>
<a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"><tt class="py-comment"># Martel specific changes</tt> </tt>
<a name="is_char"></a><div id="is_char-def"><a name="L234"></a><tt class="py-lineno">234</tt> <a class="py-toggle" href="#" id="is_char-toggle" onclick="return toggle('is_char');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#is_char">is_char</a><tt class="py-op">(</tt><tt class="py-param">char</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="is_char-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="is_char-expanded"><a name="L235"></a><tt class="py-lineno">235</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-string">"a"</tt> <tt class="py-op"><=</tt> <tt class="py-name">char</tt> <tt class="py-op"><=</tt> <tt class="py-string">"z"</tt> <tt class="py-keyword">or</tt> <tt class="py-string">"A"</tt> <tt class="py-op"><=</tt> <tt class="py-name">char</tt> <tt class="py-op"><=</tt> <tt class="py-string">"Z"</tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-string">"0"</tt> <tt class="py-op"><=</tt> <tt class="py-name">char</tt> <tt class="py-op"><=</tt> <tt class="py-string">"9"</tt> <tt class="py-keyword">or</tt> <tt class="py-name">char</tt> <tt class="py-keyword">in</tt> <tt class="py-string">"._:-"</tt> </tt>
</div><a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-comment"># Martel specific changes</tt> </tt>
<a name="isname"></a><div id="isname-def"><a name="L239"></a><tt class="py-lineno">239</tt> <a class="py-toggle" href="#" id="isname-toggle" onclick="return toggle('isname');">-</a><tt class="py-line"><tt class="py-comment"></tt><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#isname">isname</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="isname-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="isname-expanded"><a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-comment"># check that group name is a valid string</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-147" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-147', 'name', 'link-59');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L242"></a><tt class="py-lineno">242</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-148" class="py-name" targets="Function Martel.msre_parse.is_firstchar()=Martel.msre_parse-module.html#is_firstchar"><a title="Martel.msre_parse.is_firstchar" class="py-name" href="#" onclick="return doclink('link-148', 'is_firstchar', 'link-148');">is_firstchar</a></tt><tt class="py-op">(</tt><tt id="link-149" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-149', 'name', 'link-59');">name</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L244"></a><tt class="py-lineno">244</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">char</tt> <tt class="py-keyword">in</tt> <tt id="link-150" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-150', 'name', 'link-59');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L246"></a><tt class="py-lineno">246</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-151" class="py-name" targets="Function Martel.msre_parse.is_char()=Martel.msre_parse-module.html#is_char"><a title="Martel.msre_parse.is_char" class="py-name" href="#" onclick="return doclink('link-151', 'is_char', 'link-151');">is_char</a></tt><tt class="py-op">(</tt><tt class="py-name">char</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L247"></a><tt class="py-lineno">247</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">1</tt> </tt>
</div><a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"><tt class="py-comment"># More Martel specific changes</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># Checks if the serialized form of attrs is correct</tt> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-152" class="py-name" targets="Variable Martel.msre_parse._name_with_attr_pattern=Martel.msre_parse-module.html#_name_with_attr_pattern"><a title="Martel.msre_parse._name_with_attr_pattern" class="py-name" href="#" onclick="return doclink('link-152', '_name_with_attr_pattern', 'link-152');">_name_with_attr_pattern</a></tt> <tt class="py-op">=</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt id="link-153" class="py-name" targets="Function Bio.Prosite.Pattern.compile()=Bio.Prosite.Pattern-module.html#compile"><a title="Bio.Prosite.Pattern.compile" class="py-name" href="#" onclick="return doclink('link-153', 'compile', 'link-153');">compile</a></tt><tt class="py-op">(</tt><tt class="py-string">r"""</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"><tt class="py-string">[a-zA-Z_:] # first character of the tag</tt> </tt>
<a name="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"><tt class="py-string">[-a-zA-Z0-9._:]* # rest of the tag</tt> </tt>
<a name="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"><tt class="py-string">(\? # optional attrs flagged with '?'</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"><tt class="py-string"> (</tt> </tt>
<a name="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"><tt class="py-string"> ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))+ # name can contain % escapes</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"><tt class="py-string"> = # '=' flags value</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"><tt class="py-string"> ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))* # value can contain % escapes</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"><tt class="py-string"> (& # flag for additional args</tt> </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"><tt class="py-string"> ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))+ # name</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"><tt class="py-string"> = # '='</tt> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"><tt class="py-string"> ([-a-zA-Z0-9._]|(%[0-9A-Fa-f]{2}))* # value</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"><tt class="py-string"> )* # 0 or more add'l args</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"><tt class="py-string"> )? # can have nothing after the '?'</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"><tt class="py-string">)? # attrs are optional</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"><tt class="py-string">$ # must get full string</tt> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"><tt class="py-string">"""</tt><tt class="py-op">,</tt> <tt class="py-name">re</tt><tt class="py-op">.</tt><tt class="py-name">X</tt><tt class="py-op">)</tt> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> </tt>
<a name="isname_with_attrs"></a><div id="isname_with_attrs-def"><a name="L270"></a><tt class="py-lineno">270</tt> <a class="py-toggle" href="#" id="isname_with_attrs-toggle" onclick="return toggle('isname_with_attrs');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#isname_with_attrs">isname_with_attrs</a><tt class="py-op">(</tt><tt class="py-param">name</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="isname_with_attrs-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="isname_with_attrs-expanded"><a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-comment"># check that group name is a valid string</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-154" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-154', 'name', 'link-59');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-number">0</tt> </tt>
<a name="L274"></a><tt class="py-lineno">274</tt> <tt class="py-line"> <tt class="py-name">m</tt> <tt class="py-op">=</tt> <tt id="link-155" class="py-name"><a title="Martel.msre_parse._name_with_attr_pattern" class="py-name" href="#" onclick="return doclink('link-155', '_name_with_attr_pattern', 'link-152');">_name_with_attr_pattern</a></tt><tt class="py-op">.</tt><tt id="link-156" class="py-name" targets="Method Bio.Parsers.spark.GenericASTMatcher.match()=Bio.Parsers.spark.GenericASTMatcher-class.html#match,Method Bio.Prosite.Pattern.Prosite.match()=Bio.Prosite.Pattern.Prosite-class.html#match,Function Bio.triefind.match()=Bio.triefind-module.html#match,Method Martel.msre_parse.Tokenizer.match()=Martel.msre_parse.Tokenizer-class.html#match"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-156', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt id="link-157" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-157', 'name', 'link-59');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">m</tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L276"></a><tt class="py-lineno">276</tt> <tt class="py-line"> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-comment">### End of Martel changes</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="_group"></a><div id="_group-def"><a name="L280"></a><tt class="py-lineno">280</tt> <a class="py-toggle" href="#" id="_group-toggle" onclick="return toggle('_group');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#_group">_group</a><tt class="py-op">(</tt><tt class="py-param">escape</tt><tt class="py-op">,</tt> <tt class="py-param">groups</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_group-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_group-expanded"><a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-comment"># check if the escape string represents a valid group</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> <tt class="py-name">gid</tt> <tt class="py-op">=</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt id="link-158" class="py-name" targets="Function Martel.Dispatch.escape()=Martel.Dispatch-module.html#escape,Function Martel.Expression.escape()=Martel.Expression-module.html#escape"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-158', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">gid</tt> <tt class="py-keyword">and</tt> <tt class="py-name">gid</tt> <tt class="py-op"><</tt> <tt id="link-159" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-159', 'groups', 'link-56');">groups</a></tt><tt class="py-op">:</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">gid</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> <tt class="py-comment"># not a valid group</tt> </tt>
</div><a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> </tt>
<a name="_class_escape"></a><div id="_class_escape-def"><a name="L290"></a><tt class="py-lineno">290</tt> <a class="py-toggle" href="#" id="_class_escape-toggle" onclick="return toggle('_class_escape');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#_class_escape">_class_escape</a><tt class="py-op">(</tt><tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">escape</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_class_escape-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_class_escape-expanded"><a name="L291"></a><tt class="py-lineno">291</tt> <tt class="py-line"> <tt class="py-comment"># handle escape code inside character class</tt> </tt>
<a name="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt id="link-160" class="py-name"><a title="Martel.msre_parse.ESCAPES" class="py-name" href="#" onclick="return doclink('link-160', 'ESCAPES', 'link-7');">ESCAPES</a></tt><tt class="py-op">.</tt><tt id="link-161" class="py-name" targets="Method Bio.Crystal.Crystal.get()=Bio.Crystal.Crystal-class.html#get,Method Bio.Data.CodonTable.AmbiguousForwardTable.get()=Bio.Data.CodonTable.AmbiguousForwardTable-class.html#get,Method Bio.EUtils.MultiDict._BaseMultiDict.get()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#get,Method Bio.EUtils.POM.ElementNode.get()=Bio.EUtils.POM.ElementNode-class.html#get,Method Bio.GenBank.NCBIDictionary.get()=Bio.GenBank.NCBIDictionary-class.html#get,Method Bio.Mindy.BaseDB.DictLookup.get()=Bio.Mindy.BaseDB.DictLookup-class.html#get,Method Bio.Prosite.ExPASyDictionary.get()=Bio.Prosite.ExPASyDictionary-class.html#get,Method Bio.Prosite.Prodoc.ExPASyDictionary.get()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#get,Method Bio.PubMed.Dictionary.get()=Bio.PubMed.Dictionary-class.html#get,Method Bio.Restriction.Restriction.RestrictionBatch.get()=Bio.Restriction.Restriction.RestrictionBatch-class.html#get,Method Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get()=Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder-class.html#get,Method Bio.SeqUtils.MissingTable.get()=Bio.SeqUtils.MissingTable-class.html#get,Method Bio.SwissProt.SProt.ExPASyDictionary.get()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#get,Method Bio.config.DBRegistry.DBGroup.get()=Bio.config.DBRegistry.DBGroup-class.html#get,Method Bio.config.DBRegistry.DBObject.get()=Bio.config.DBRegistry.DBObject-class.html#get,Method Bio.config.Registry.Registry.get()=Bio.config.Registry.Registry-class.html#get,Method Martel.Parser.MartelAttributeList.get()=Martel.Parser.MartelAttributeList-class.html#get,Method Martel.msre_parse.Tokenizer.get()=Martel.msre_parse.Tokenizer-class.html#get"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-161', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt id="link-162" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-162', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> </tt>
<a name="L293"></a><tt class="py-lineno">293</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code</tt><tt class="py-op">:</tt> </tt>
<a name="L294"></a><tt class="py-lineno">294</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">code</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt id="link-163" class="py-name"><a title="Martel.msre_parse.CATEGORIES" class="py-name" href="#" onclick="return doclink('link-163', 'CATEGORIES', 'link-19');">CATEGORIES</a></tt><tt class="py-op">.</tt><tt id="link-164" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-164', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt id="link-165" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-165', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> </tt>
<a name="L296"></a><tt class="py-lineno">296</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code</tt><tt class="py-op">:</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">code</tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L299"></a><tt class="py-lineno">299</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-166" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-166', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"x"</tt><tt class="py-op">:</tt> </tt>
<a name="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-comment"># hexadecimal escape (exactly two digits)</tt> </tt>
<a name="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt id="link-167" class="py-name" targets="Method Bio.GenBank._FeatureConsumer.source()=Bio.GenBank._FeatureConsumer-class.html#source,Method Bio.GenBank._RecordConsumer.source()=Bio.GenBank._RecordConsumer-class.html#source,Method Bio.Medline._RecordConsumer.source()=Bio.Medline._RecordConsumer-class.html#source,Method Bio.Pathway.Network.source()=Bio.Pathway.Network-class.html#source,Method Bio.Rebase._RecordConsumer.source()=Bio.Rebase._RecordConsumer-class.html#source"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-167', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-168" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-168', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-169" class="py-name"><a title="Martel.msre_parse.HEXDIGITS" class="py-name" href="#" onclick="return doclink('link-169', 'HEXDIGITS', 'link-5');">HEXDIGITS</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-170" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-170', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> <tt id="link-171" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-171', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-172" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-172', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">+</tt> <tt id="link-173" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-173', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-174" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-174', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt id="link-175" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-175', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-176" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-176', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-177" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-177', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-178" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-178', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bogus escape: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-string">"\\"</tt> <tt class="py-op">+</tt> <tt id="link-179" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-179', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-180" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-180', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt id="link-181" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-181', 'escape', 'link-158');">escape</a></tt><tt class="py-op">,</tt> <tt class="py-number">16</tt><tt class="py-op">)</tt> <tt class="py-op">&</tt> <tt class="py-number">0xff</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">str</tt><tt class="py-op">(</tt><tt id="link-182" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-182', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-keyword">in</tt> <tt id="link-183" class="py-name"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-183', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-comment"># octal escape (up to three digits)</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt id="link-184" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-184', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-185" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-185', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-186" class="py-name"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-186', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-187" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-187', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">5</tt><tt class="py-op">:</tt> </tt>
<a name="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt id="link-188" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-188', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-189" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-189', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">+</tt> <tt id="link-190" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-190', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-191" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-191', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt id="link-192" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-192', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-193" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-193', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-194" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-194', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt id="link-195" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-195', 'escape', 'link-158');">escape</a></tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">&</tt> <tt class="py-number">0xff</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-196" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-196', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-197" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-197', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt id="link-198" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-198', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-199" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-199', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bogus escape: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-200" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-200', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"> </tt>
<a name="_escape"></a><div id="_escape-def"><a name="L319"></a><tt class="py-lineno">319</tt> <a class="py-toggle" href="#" id="_escape-toggle" onclick="return toggle('_escape');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#_escape">_escape</a><tt class="py-op">(</tt><tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">escape</tt><tt class="py-op">,</tt> <tt class="py-param">state</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_escape-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_escape-expanded"><a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-comment"># handle escape code in expression</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt id="link-201" class="py-name"><a title="Martel.msre_parse.CATEGORIES" class="py-name" href="#" onclick="return doclink('link-201', 'CATEGORIES', 'link-19');">CATEGORIES</a></tt><tt class="py-op">.</tt><tt id="link-202" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-202', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt id="link-203" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-203', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> </tt>
<a name="L322"></a><tt class="py-lineno">322</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code</tt><tt class="py-op">:</tt> </tt>
<a name="L323"></a><tt class="py-lineno">323</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">code</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt id="link-204" class="py-name"><a title="Martel.msre_parse.ESCAPES" class="py-name" href="#" onclick="return doclink('link-204', 'ESCAPES', 'link-7');">ESCAPES</a></tt><tt class="py-op">.</tt><tt id="link-205" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-205', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt id="link-206" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-206', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> </tt>
<a name="L325"></a><tt class="py-lineno">325</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code</tt><tt class="py-op">:</tt> </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">code</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-207" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-207', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"x"</tt><tt class="py-op">:</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-comment"># hexadecimal escape</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt id="link-208" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-208', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-209" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-209', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-210" class="py-name"><a title="Martel.msre_parse.HEXDIGITS" class="py-name" href="#" onclick="return doclink('link-210', 'HEXDIGITS', 'link-5');">HEXDIGITS</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-211" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-211', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt id="link-212" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-212', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-213" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-213', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">+</tt> <tt id="link-214" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-214', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-215" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-215', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-216" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-216', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-217" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-217', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt id="link-218" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-218', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">16</tt><tt class="py-op">)</tt> <tt class="py-op">&</tt> <tt class="py-number">0xff</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-219" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-219', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"0"</tt><tt class="py-op">:</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-comment"># octal escape</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt id="link-220" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-220', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-221" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-221', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-222" class="py-name"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-222', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt> <tt class="py-keyword">and</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-223" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-223', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-number">4</tt><tt class="py-op">:</tt> </tt>
<a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> <tt id="link-224" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-224', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-225" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-225', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">+</tt> <tt id="link-226" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-226', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-227" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-227', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L339"></a><tt class="py-lineno">339</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-228" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-228', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt id="link-229" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-229', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">&</tt> <tt class="py-number">0xff</tt> </tt>
<a name="L340"></a><tt class="py-lineno">340</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-230" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-230', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt id="link-231" class="py-name"><a title="Martel.msre_parse.DIGITS" class="py-name" href="#" onclick="return doclink('link-231', 'DIGITS', 'link-3');">DIGITS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L341"></a><tt class="py-lineno">341</tt> <tt class="py-line"> <tt class="py-comment"># octal escape *or* decimal group reference (sigh)</tt> </tt>
<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">here</tt> <tt class="py-op">=</tt> <tt id="link-232" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-232', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-233" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.tell()=Bio.EUtils.ReseekFile.ReseekFile-class.html#tell,Method Bio.File.UndoHandle.tell()=Bio.File.UndoHandle-class.html#tell,Method Martel.msre_parse.Tokenizer.tell()=Martel.msre_parse.Tokenizer-class.html#tell"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-233', 'tell', 'link-233');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-234" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-234', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-235" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-235', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-236" class="py-name"><a title="Martel.msre_parse.DIGITS" class="py-name" href="#" onclick="return doclink('link-236', 'DIGITS', 'link-3');">DIGITS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L344"></a><tt class="py-lineno">344</tt> <tt class="py-line"> <tt id="link-237" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-237', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-238" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-238', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">+</tt> <tt id="link-239" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-239', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-240" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-240', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L345"></a><tt class="py-lineno">345</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt id="link-241" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-241', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt id="link-242" class="py-name"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-242', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt> <tt class="py-keyword">and</tt> <tt id="link-243" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-243', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt id="link-244" class="py-name"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-244', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt> <tt class="py-keyword">and</tt> </tt>
<a name="L346"></a><tt class="py-lineno">346</tt> <tt class="py-line"> <tt id="link-245" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-245', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-246" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-246', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-247" class="py-name"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-247', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-comment"># got three octal digits; this is an octal escape</tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-248" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-248', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">=</tt> <tt id="link-249" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-249', 'escape', 'link-158');">escape</a></tt> <tt class="py-op">+</tt> <tt id="link-250" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-250', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-251" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-251', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-252" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-252', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt id="link-253" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-253', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">&</tt> <tt class="py-number">0xff</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-comment"># got at least one decimal digit; this is a group reference</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-254" class="py-name" targets="Method Bio.Prosite.Pattern.PrositeMatch.group()=Bio.Prosite.Pattern.PrositeMatch-class.html#group"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-254', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt id="link-255" class="py-name" targets="Function Martel._group()=Martel-module.html#_group,Function Martel.msre_parse._group()=Martel.msre_parse-module.html#_group"><a title="Martel._group
Martel.msre_parse._group" class="py-name" href="#" onclick="return doclink('link-255', '_group', 'link-255');">_group</a></tt><tt class="py-op">(</tt><tt id="link-256" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-256', 'escape', 'link-158');">escape</a></tt><tt class="py-op">,</tt> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-257" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-257', 'groups', 'link-56');">groups</a></tt><tt class="py-op">)</tt> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-258" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-258', 'group', 'link-254');">group</a></tt><tt class="py-op">:</tt> </tt>
<a name="L353"></a><tt class="py-lineno">353</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-259" class="py-name" targets="Method Martel.convert_re.GroupNames.checkgroup()=Martel.convert_re.GroupNames-class.html#checkgroup,Method Martel.msre_parse.Pattern.checkgroup()=Martel.msre_parse.Pattern-class.html#checkgroup"><a title="Martel.convert_re.GroupNames.checkgroup
Martel.msre_parse.Pattern.checkgroup" class="py-name" href="#" onclick="return doclink('link-259', 'checkgroup', 'link-259');">checkgroup</a></tt><tt class="py-op">(</tt><tt id="link-260" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-260', 'group', 'link-254');">group</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-261" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-261', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"cannot refer to open group"</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-262" class="py-name" targets="Variable Martel.msre_constants.GROUPREF=Martel.msre_constants-module.html#GROUPREF,Variable Martel.msre_parse.GROUPREF=Martel.msre_parse-module.html#GROUPREF"><a title="Martel.msre_constants.GROUPREF
Martel.msre_parse.GROUPREF" class="py-name" href="#" onclick="return doclink('link-262', 'GROUPREF', 'link-262');">GROUPREF</a></tt><tt class="py-op">,</tt> <tt id="link-263" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-263', 'group', 'link-254');">group</a></tt> </tt>
<a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">ValueError</tt> </tt>
<a name="L357"></a><tt class="py-lineno">357</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-264" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-264', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-265" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-265', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt id="link-266" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-266', 'escape', 'link-158');">escape</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L359"></a><tt class="py-lineno">359</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-267" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-267', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bogus escape: %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-268" class="py-name"><a title="Martel.Dispatch.escape
Martel.Expression.escape" class="py-name" href="#" onclick="return doclink('link-268', 'escape', 'link-158');">escape</a></tt><tt class="py-op">)</tt> </tt>
</div><a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"> </tt>
<a name="_parse_sub"></a><div id="_parse_sub-def"><a name="L363"></a><tt class="py-lineno">363</tt> <a class="py-toggle" href="#" id="_parse_sub-toggle" onclick="return toggle('_parse_sub');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#_parse_sub">_parse_sub</a><tt class="py-op">(</tt><tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">state</tt><tt class="py-op">,</tt> <tt class="py-param">nested</tt><tt class="py-op">=</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse_sub-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse_sub-expanded"><a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-comment"># parse an alternation: a|b|c</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt id="link-269" class="py-name" targets="Method Bio.Crystal.Crystal.items()=Bio.Crystal.Crystal-class.html#items,Method Bio.EUtils.MultiDict._BaseMultiDict.items()=Bio.EUtils.MultiDict._BaseMultiDict-class.html#items,Variable Bio.Entrez.SerialSet.items=Bio.Entrez.SerialSet-module.html#items,Method Bio.GenBank.NCBIDictionary.items()=Bio.GenBank.NCBIDictionary-class.html#items,Method Bio.Mindy.BaseDB.DictLookup.items()=Bio.Mindy.BaseDB.DictLookup-class.html#items,Method Bio.Prosite.ExPASyDictionary.items()=Bio.Prosite.ExPASyDictionary-class.html#items,Method Bio.Prosite.Prodoc.ExPASyDictionary.items()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#items,Method Bio.PubMed.Dictionary.items()=Bio.PubMed.Dictionary-class.html#items,Method Bio.SwissProt.SProt.ExPASyDictionary.items()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#items,Method Bio.config.Registry.Registry.items()=Bio.config.Registry.Registry-class.html#items,Function Bio.listfns.items()=Bio.listfns-module.html#items,Method BioSQL.BioSeqDatabase.BioSeqDatabase.items()=BioSQL.BioSeqDatabase.BioSeqDatabase-class.html#items,Method BioSQL.BioSeqDatabase.DBServer.items()=BioSQL.BioSeqDatabase.DBServer-class.html#items,Method Martel.Parser.MartelAttributeList.items()=Martel.Parser.MartelAttributeList-class.html#items"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-269', 'items', 'link-269');">items</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L367"></a><tt class="py-lineno">367</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt id="link-270" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-270', 'items', 'link-269');">items</a></tt><tt class="py-op">.</tt><tt id="link-271" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-271', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt id="link-272" class="py-name" targets="Method Bio.Blast.NCBIStandalone._DescriptionConsumer._parse()=Bio.Blast.NCBIStandalone._DescriptionConsumer-class.html#_parse,Method Bio.Nexus.Trees.Tree._parse()=Bio.Nexus.Trees.Tree-class.html#_parse,Method Bio.PDB.PDBParser'.PDBParser._parse()=Bio.PDB.PDBParser%27.PDBParser-class.html#_parse,Method Bio.SCOP.Residues'.Residues._parse()=Bio.SCOP.Residues%27.Residues-class.html#_parse,Function Martel.msre_parse._parse()=Martel.msre_parse-module.html#_parse"><a title="Bio.Blast.NCBIStandalone._DescriptionConsumer._parse
Bio.Nexus.Trees.Tree._parse
Bio.PDB.PDBParser'.PDBParser._parse
Bio.SCOP.Residues'.Residues._parse
Martel.msre_parse._parse" class="py-name" href="#" onclick="return doclink('link-272', '_parse', 'link-272');">_parse</a></tt><tt class="py-op">(</tt><tt id="link-273" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-273', 'source', 'link-167');">source</a></tt><tt class="py-op">,</tt> <tt class="py-name">state</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L369"></a><tt class="py-lineno">369</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-274" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-274', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-275" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-275', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">nested</tt><tt class="py-op">:</tt> </tt>
<a name="L372"></a><tt class="py-lineno">372</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L373"></a><tt class="py-lineno">373</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-276" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-276', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-277" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-277', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">or</tt> <tt id="link-278" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-278', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-279" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-279', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">")"</tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-280" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-280', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"pattern not properly closed"</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-281" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-281', 'items', 'link-269');">items</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-282" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-282', 'items', 'link-269');">items</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt> <tt class="py-op">=</tt> <tt id="link-283" class="py-name"><a title="Martel.msre_parse.SubPattern" class="py-name" href="#" onclick="return doclink('link-283', 'SubPattern', 'link-82');">SubPattern</a></tt><tt class="py-op">(</tt><tt class="py-name">state</tt><tt class="py-op">)</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-comment"># check if all items share a common prefix</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt id="link-284" class="py-name" targets="Variable Bio.DocSQL.Query.prefix=Bio.DocSQL.Query-class.html#prefix"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-284', 'prefix', 'link-284');">prefix</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-285" class="py-name" targets="Method Bio.EUtils.Datatypes.DBIds.item()=Bio.EUtils.Datatypes.DBIds-class.html#item"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-285', 'item', 'link-285');">item</a></tt> <tt class="py-keyword">in</tt> <tt id="link-286" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-286', 'items', 'link-269');">items</a></tt><tt class="py-op">:</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-287" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-287', 'item', 'link-285');">item</a></tt><tt class="py-op">:</tt> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L389"></a><tt class="py-lineno">389</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-288" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-288', 'prefix', 'link-284');">prefix</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt id="link-289" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-289', 'prefix', 'link-284');">prefix</a></tt> <tt class="py-op">=</tt> <tt id="link-290" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-290', 'item', 'link-285');">item</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L391"></a><tt class="py-lineno">391</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-291" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-291', 'item', 'link-285');">item</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-292" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-292', 'prefix', 'link-284');">prefix</a></tt><tt class="py-op">:</tt> </tt>
<a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-comment"># all subitems start with a common "prefix".</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># move it out of the branch</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-293" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-293', 'item', 'link-285');">item</a></tt> <tt class="py-keyword">in</tt> <tt id="link-294" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-294', 'items', 'link-269');">items</a></tt><tt class="py-op">:</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt id="link-295" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-295', 'item', 'link-285');">item</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-296" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-296', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt id="link-297" class="py-name"><a title="Bio.DocSQL.Query.prefix" class="py-name" href="#" onclick="return doclink('link-297', 'prefix', 'link-284');">prefix</a></tt><tt class="py-op">)</tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> <tt class="py-comment"># check next one</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> </tt>
<a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> <tt class="py-comment"># check if the branch can be replaced by a character set</tt> </tt>
<a name="L403"></a><tt class="py-lineno">403</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">for</tt> <tt id="link-298" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-298', 'item', 'link-285');">item</a></tt> <tt class="py-keyword">in</tt> <tt id="link-299" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-299', 'items', 'link-269');">items</a></tt><tt class="py-op">:</tt> </tt>
<a name="L404"></a><tt class="py-lineno">404</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-300" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-300', 'item', 'link-285');">item</a></tt><tt class="py-op">)</tt> <tt class="py-op">!=</tt> <tt class="py-number">1</tt> <tt class="py-keyword">or</tt> <tt id="link-301" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-301', 'item', 'link-285');">item</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-302" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-302', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt class="py-comment"># we can store this as a character set instead of a</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># branch (the compiler may optimize this even more)</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-303" class="py-name" targets="Method Bio.Nexus.Nexus.StepMatrix.set()=Bio.Nexus.Nexus.StepMatrix-class.html#set,Method Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set()=Bio.SVDSuperimposer.SVDSuperimposer%27.SVDSuperimposer-class.html#set,Method Bio.config.DBRegistry.DBObject.set()=Bio.config.DBRegistry.DBObject-class.html#set"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-303', 'set', 'link-303');">set</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-304" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-304', 'item', 'link-285');">item</a></tt> <tt class="py-keyword">in</tt> <tt id="link-305" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-305', 'items', 'link-269');">items</a></tt><tt class="py-op">:</tt> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt id="link-306" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-306', 'set', 'link-303');">set</a></tt><tt class="py-op">.</tt><tt id="link-307" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-307', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt id="link-308" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-308', 'item', 'link-285');">item</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L412"></a><tt class="py-lineno">412</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-309" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-309', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-310" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-310', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt id="link-311" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-311', 'set', 'link-303');">set</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">subpattern</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-312" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-312', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-313" class="py-name"><a title="Martel.msre_constants.BRANCH
Martel.msre_parse.BRANCH" class="py-name" href="#" onclick="return doclink('link-313', 'BRANCH', 'link-102');">BRANCH</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt id="link-314" class="py-name"><a title="Bio.Crystal.Crystal.items
Bio.EUtils.MultiDict._BaseMultiDict.items
Bio.Entrez.SerialSet.items
Bio.GenBank.NCBIDictionary.items
Bio.Mindy.BaseDB.DictLookup.items
Bio.Prosite.ExPASyDictionary.items
Bio.Prosite.Prodoc.ExPASyDictionary.items
Bio.PubMed.Dictionary.items
Bio.SwissProt.SProt.ExPASyDictionary.items
Bio.config.Registry.Registry.items
Bio.listfns.items
BioSQL.BioSeqDatabase.BioSeqDatabase.items
BioSQL.BioSeqDatabase.DBServer.items
Martel.Parser.MartelAttributeList.items" class="py-name" href="#" onclick="return doclink('link-314', 'items', 'link-269');">items</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">subpattern</tt> </tt>
</div><a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"> </tt>
<a name="_parse"></a><div id="_parse-def"><a name="L418"></a><tt class="py-lineno">418</tt> <a class="py-toggle" href="#" id="_parse-toggle" onclick="return toggle('_parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#_parse">_parse</a><tt class="py-op">(</tt><tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">state</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_parse-expanded"><a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt class="py-comment"># parse a simple pattern</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt> <tt class="py-op">=</tt> <tt id="link-315" class="py-name"><a title="Martel.msre_parse.SubPattern" class="py-name" href="#" onclick="return doclink('link-315', 'SubPattern', 'link-82');">SubPattern</a></tt><tt class="py-op">(</tt><tt class="py-name">state</tt><tt class="py-op">)</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-316" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-316', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-317" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-317', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"|"</tt><tt class="py-op">,</tt> <tt class="py-string">")"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> <tt class="py-comment"># end of subpattern</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt id="link-318" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-318', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-319" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-319', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L429"></a><tt class="py-lineno">429</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> <tt class="py-comment"># end of pattern</tt> </tt>
<a name="L430"></a><tt class="py-lineno">430</tt> <tt class="py-line"> </tt>
<a name="L431"></a><tt class="py-lineno">431</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">&</tt> <tt id="link-320" class="py-name"><a title="Martel.msre_constants.SRE_FLAG_VERBOSE
Martel.msre_parse.SRE_FLAG_VERBOSE" class="py-name" href="#" onclick="return doclink('link-320', 'SRE_FLAG_VERBOSE', 'link-52');">SRE_FLAG_VERBOSE</a></tt><tt class="py-op">:</tt> </tt>
<a name="L432"></a><tt class="py-lineno">432</tt> <tt class="py-line"> <tt class="py-comment"># skip whitespace and comments</tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-keyword">in</tt> <tt id="link-321" class="py-name"><a title="Bio.Nexus.Nexus.WHITESPACE
Martel.msre_parse.WHITESPACE" class="py-name" href="#" onclick="return doclink('link-321', 'WHITESPACE', 'link-6');">WHITESPACE</a></tt><tt class="py-op">:</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"#"</tt><tt class="py-op">:</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt id="link-322" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-322', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-323" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-323', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-keyword">and</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-324" class="py-name"><a title="Martel.msre_parse.SPECIAL_CHARS" class="py-name" href="#" onclick="return doclink('link-324', 'SPECIAL_CHARS', 'link-1');">SPECIAL_CHARS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-325" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-325', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-326" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-326', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"["</tt><tt class="py-op">:</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"> <tt class="py-comment"># character set</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-327" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-327', 'set', 'link-303');">set</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-comment">## if source.match(":"):</tt> </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## pass # handle character classes</tt> </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-328" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-328', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-329" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-329', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"^"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> <tt id="link-330" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-330', 'set', 'link-303');">set</a></tt><tt class="py-op">.</tt><tt id="link-331" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-331', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-332" class="py-name" targets="Variable Martel.msre_constants.NEGATE=Martel.msre_constants-module.html#NEGATE,Variable Martel.msre_parse.NEGATE=Martel.msre_parse-module.html#NEGATE"><a title="Martel.msre_constants.NEGATE
Martel.msre_parse.NEGATE" class="py-name" href="#" onclick="return doclink('link-332', 'NEGATE', 'link-332');">NEGATE</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L452"></a><tt class="py-lineno">452</tt> <tt class="py-line"> <tt class="py-comment"># check remaining characters</tt> </tt>
<a name="L453"></a><tt class="py-lineno">453</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-333" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-333', 'start', 'link-95');">start</a></tt> <tt class="py-op">=</tt> <tt id="link-334" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-334', 'set', 'link-303');">set</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L455"></a><tt class="py-lineno">455</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt id="link-335" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-335', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-336" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-336', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"]"</tt> <tt class="py-keyword">and</tt> <tt id="link-337" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-337', 'set', 'link-303');">set</a></tt> <tt class="py-op">!=</tt> <tt id="link-338" class="py-name"><a title="Bio.GFF.easy.Location.start
Bio.Prosite.Pattern.PrositeMatch.start
Bio.Restriction._Update.RestrictionCompiler.start
Martel.LAX.LAX.start" class="py-name" href="#" onclick="return doclink('link-338', 'start', 'link-95');">start</a></tt><tt class="py-op">:</tt> </tt>
<a name="L457"></a><tt class="py-lineno">457</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L458"></a><tt class="py-lineno">458</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-keyword">and</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"\\"</tt><tt class="py-op">:</tt> </tt>
<a name="L459"></a><tt class="py-lineno">459</tt> <tt class="py-line"> <tt class="py-name">code1</tt> <tt class="py-op">=</tt> <tt id="link-339" class="py-name" targets="Function Martel.msre_parse._class_escape()=Martel.msre_parse-module.html#_class_escape"><a title="Martel.msre_parse._class_escape" class="py-name" href="#" onclick="return doclink('link-339', '_class_escape', 'link-339');">_class_escape</a></tt><tt class="py-op">(</tt><tt id="link-340" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-340', 'source', 'link-167');">source</a></tt><tt class="py-op">,</tt> <tt class="py-name">this</tt><tt class="py-op">)</tt> </tt>
<a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt><tt class="py-op">:</tt> </tt>
<a name="L461"></a><tt class="py-lineno">461</tt> <tt class="py-line"> <tt class="py-name">code1</tt> <tt class="py-op">=</tt> <tt id="link-341" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-341', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">)</tt> </tt>
<a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-342" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-342', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unexpected end of regular expression"</tt> </tt>
<a name="L464"></a><tt class="py-lineno">464</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-343" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-343', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-344" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-344', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"-"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L465"></a><tt class="py-lineno">465</tt> <tt class="py-line"> <tt class="py-comment"># potential range</tt> </tt>
<a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt id="link-345" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-345', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-346" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-346', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L467"></a><tt class="py-lineno">467</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"]"</tt><tt class="py-op">:</tt> </tt>
<a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code1</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt id="link-347" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-347', 'IN', 'link-13');">IN</a></tt><tt class="py-op">:</tt> </tt>
<a name="L469"></a><tt class="py-lineno">469</tt> <tt class="py-line"> <tt class="py-name">code1</tt> <tt class="py-op">=</tt> <tt class="py-name">code1</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt id="link-348" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-348', 'set', 'link-303');">set</a></tt><tt class="py-op">.</tt><tt id="link-349" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-349', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">code1</tt><tt class="py-op">)</tt> </tt>
<a name="L471"></a><tt class="py-lineno">471</tt> <tt class="py-line"> <tt id="link-350" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-350', 'set', 'link-303');">set</a></tt><tt class="py-op">.</tt><tt id="link-351" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-351', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-352" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-352', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-string">"-"</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L474"></a><tt class="py-lineno">474</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"\\"</tt><tt class="py-op">:</tt> </tt>
<a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-name">code2</tt> <tt class="py-op">=</tt> <tt id="link-353" class="py-name"><a title="Martel.msre_parse._class_escape" class="py-name" href="#" onclick="return doclink('link-353', '_class_escape', 'link-339');">_class_escape</a></tt><tt class="py-op">(</tt><tt id="link-354" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-354', 'source', 'link-167');">source</a></tt><tt class="py-op">,</tt> <tt class="py-name">this</tt><tt class="py-op">)</tt> </tt>
<a name="L476"></a><tt class="py-lineno">476</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt class="py-name">code2</tt> <tt class="py-op">=</tt> <tt id="link-355" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-355', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code1</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-356" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-356', 'LITERAL', 'link-8');">LITERAL</a></tt> <tt class="py-keyword">or</tt> <tt class="py-name">code2</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">!=</tt> <tt id="link-357" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-357', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">:</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-358" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-358', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bad character range"</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">code1</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">code2</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L482"></a><tt class="py-lineno">482</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hi</tt> <tt class="py-op"><</tt> <tt class="py-name">lo</tt><tt class="py-op">:</tt> </tt>
<a name="L483"></a><tt class="py-lineno">483</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-359" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-359', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bad character range"</tt> </tt>
<a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> <tt id="link-360" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-360', 'set', 'link-303');">set</a></tt><tt class="py-op">.</tt><tt id="link-361" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-361', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-362" class="py-name"><a title="Martel.msre_constants.RANGE
Martel.msre_parse.RANGE" class="py-name" href="#" onclick="return doclink('link-362', 'RANGE', 'link-122');">RANGE</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">lo</tt><tt class="py-op">,</tt> <tt class="py-name">hi</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L485"></a><tt class="py-lineno">485</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L486"></a><tt class="py-lineno">486</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code1</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt id="link-363" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-363', 'IN', 'link-13');">IN</a></tt><tt class="py-op">:</tt> </tt>
<a name="L487"></a><tt class="py-lineno">487</tt> <tt class="py-line"> <tt class="py-name">code1</tt> <tt class="py-op">=</tt> <tt class="py-name">code1</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L488"></a><tt class="py-lineno">488</tt> <tt class="py-line"> <tt id="link-364" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-364', 'set', 'link-303');">set</a></tt><tt class="py-op">.</tt><tt id="link-365" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-365', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">code1</tt><tt class="py-op">)</tt> </tt>
<a name="L489"></a><tt class="py-lineno">489</tt> <tt class="py-line"> </tt>
<a name="L490"></a><tt class="py-lineno">490</tt> <tt class="py-line"> <tt class="py-comment"># XXX: <fl> should move set optimization to compiler!</tt> </tt>
<a name="L491"></a><tt class="py-lineno">491</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-366" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-366', 'set', 'link-303');">set</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt id="link-367" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-367', 'set', 'link-303');">set</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt id="link-368" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-368', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">:</tt> </tt>
<a name="L492"></a><tt class="py-lineno">492</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-369" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-369', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt id="link-370" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-370', 'set', 'link-303');">set</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> <tt class="py-comment"># optimization</tt> </tt>
<a name="L493"></a><tt class="py-lineno">493</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-371" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-371', 'set', 'link-303');">set</a></tt><tt class="py-op">)</tt><tt class="py-op">==</tt><tt class="py-number">2</tt> <tt class="py-keyword">and</tt> <tt id="link-372" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-372', 'set', 'link-303');">set</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt id="link-373" class="py-name"><a title="Martel.msre_constants.NEGATE
Martel.msre_parse.NEGATE" class="py-name" href="#" onclick="return doclink('link-373', 'NEGATE', 'link-332');">NEGATE</a></tt> <tt class="py-keyword">and</tt> <tt id="link-374" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-374', 'set', 'link-303');">set</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt id="link-375" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-375', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">:</tt> </tt>
<a name="L494"></a><tt class="py-lineno">494</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-376" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-376', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-377" class="py-name"><a title="Martel.msre_constants.NOT_LITERAL
Martel.msre_parse.NOT_LITERAL" class="py-name" href="#" onclick="return doclink('link-377', 'NOT_LITERAL', 'link-125');">NOT_LITERAL</a></tt><tt class="py-op">,</tt> <tt id="link-378" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-378', 'set', 'link-303');">set</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> <tt class="py-comment"># optimization</tt> </tt>
<a name="L495"></a><tt class="py-lineno">495</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L496"></a><tt class="py-lineno">496</tt> <tt class="py-line"> <tt class="py-comment"># XXX: <fl> should add charmap optimization here</tt> </tt>
<a name="L497"></a><tt class="py-lineno">497</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-379" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-379', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-380" class="py-name"><a title="Martel.msre_constants.IN
Martel.msre_parse.IN" class="py-name" href="#" onclick="return doclink('link-380', 'IN', 'link-13');">IN</a></tt><tt class="py-op">,</tt> <tt id="link-381" class="py-name"><a title="Bio.Nexus.Nexus.StepMatrix.set
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.set
Bio.config.DBRegistry.DBObject.set" class="py-name" href="#" onclick="return doclink('link-381', 'set', 'link-303');">set</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L498"></a><tt class="py-lineno">498</tt> <tt class="py-line"> </tt>
<a name="L499"></a><tt class="py-lineno">499</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-keyword">and</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt id="link-382" class="py-name"><a title="Martel.msre_parse.REPEAT_CHARS" class="py-name" href="#" onclick="return doclink('link-382', 'REPEAT_CHARS', 'link-2');">REPEAT_CHARS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L500"></a><tt class="py-lineno">500</tt> <tt class="py-line"> <tt class="py-comment"># repeat previous item</tt> </tt>
<a name="L501"></a><tt class="py-lineno">501</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"?"</tt><tt class="py-op">:</tt> </tt>
<a name="L502"></a><tt class="py-lineno">502</tt> <tt class="py-line"> <tt class="py-name">min</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-number">1</tt> </tt>
<a name="L503"></a><tt class="py-lineno">503</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"*"</tt><tt class="py-op">:</tt> </tt>
<a name="L504"></a><tt class="py-lineno">504</tt> <tt class="py-line"> <tt class="py-name">min</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-383" class="py-name" targets="Variable Martel.Expression.MAXREPEAT=Martel.Expression-module.html#MAXREPEAT,Variable Martel.msre_constants.MAXREPEAT=Martel.msre_constants-module.html#MAXREPEAT,Variable Martel.msre_parse.MAXREPEAT=Martel.msre_parse-module.html#MAXREPEAT,Variable Martel.test.test_Expression.MAXREPEAT=Martel.test.test_Expression-module.html#MAXREPEAT"><a title="Martel.Expression.MAXREPEAT
Martel.msre_constants.MAXREPEAT
Martel.msre_parse.MAXREPEAT
Martel.test.test_Expression.MAXREPEAT" class="py-name" href="#" onclick="return doclink('link-383', 'MAXREPEAT', 'link-383');">MAXREPEAT</a></tt> </tt>
<a name="L505"></a><tt class="py-lineno">505</tt> <tt class="py-line"> </tt>
<a name="L506"></a><tt class="py-lineno">506</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"+"</tt><tt class="py-op">:</tt> </tt>
<a name="L507"></a><tt class="py-lineno">507</tt> <tt class="py-line"> <tt class="py-name">min</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt><tt class="py-op">,</tt> <tt id="link-384" class="py-name"><a title="Martel.Expression.MAXREPEAT
Martel.msre_constants.MAXREPEAT
Martel.msre_parse.MAXREPEAT
Martel.test.test_Expression.MAXREPEAT" class="py-name" href="#" onclick="return doclink('link-384', 'MAXREPEAT', 'link-383');">MAXREPEAT</a></tt> </tt>
<a name="L508"></a><tt class="py-lineno">508</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"{"</tt><tt class="py-op">:</tt> </tt>
<a name="L509"></a><tt class="py-lineno">509</tt> <tt class="py-line"> <tt class="py-name">here</tt> <tt class="py-op">=</tt> <tt id="link-385" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-385', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-386" class="py-name"><a title="Bio.EUtils.ReseekFile.ReseekFile.tell
Bio.File.UndoHandle.tell
Martel.msre_parse.Tokenizer.tell" class="py-name" href="#" onclick="return doclink('link-386', 'tell', 'link-233');">tell</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L510"></a><tt class="py-lineno">510</tt> <tt class="py-line"> <tt class="py-name">min</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt id="link-387" class="py-name"><a title="Martel.Expression.MAXREPEAT
Martel.msre_constants.MAXREPEAT
Martel.msre_parse.MAXREPEAT
Martel.test.test_Expression.MAXREPEAT" class="py-name" href="#" onclick="return doclink('link-387', 'MAXREPEAT', 'link-383');">MAXREPEAT</a></tt> </tt>
<a name="L511"></a><tt class="py-lineno">511</tt> <tt class="py-line"><tt class="py-comment">### Martel changes to allow a named reference for the repeat count</tt> </tt>
<a name="L512"></a><tt class="py-lineno">512</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment"># APD -- 21 Aug 2000</tt> </tt>
<a name="L513"></a><tt class="py-lineno">513</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## lo = hi = ""</tt> </tt>
<a name="L514"></a><tt class="py-lineno">514</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## while source.next in DIGITS:</tt> </tt>
<a name="L515"></a><tt class="py-lineno">515</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## lo = lo + source.get()</tt> </tt>
<a name="L516"></a><tt class="py-lineno">516</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if source.match(","):</tt> </tt>
<a name="L517"></a><tt class="py-lineno">517</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## while source.next in DIGITS:</tt> </tt>
<a name="L518"></a><tt class="py-lineno">518</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## hi = hi + source.get()</tt> </tt>
<a name="L519"></a><tt class="py-lineno">519</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## else:</tt> </tt>
<a name="L520"></a><tt class="py-lineno">520</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## hi = lo</tt> </tt>
<a name="L521"></a><tt class="py-lineno">521</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if not source.match("}"):</tt> </tt>
<a name="L522"></a><tt class="py-lineno">522</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## subpattern.append((LITERAL, ord(this)))</tt> </tt>
<a name="L523"></a><tt class="py-lineno">523</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## source.seek(here)</tt> </tt>
<a name="L524"></a><tt class="py-lineno">524</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## continue</tt> </tt>
<a name="L525"></a><tt class="py-lineno">525</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if lo:</tt> </tt>
<a name="L526"></a><tt class="py-lineno">526</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## min = atoi(lo)</tt> </tt>
<a name="L527"></a><tt class="py-lineno">527</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## if hi:</tt> </tt>
<a name="L528"></a><tt class="py-lineno">528</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## max = atoi(hi)</tt> </tt>
<a name="L529"></a><tt class="py-lineno">529</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L530"></a><tt class="py-lineno">530</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-388" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-388', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-389" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-389', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-390" class="py-name"><a title="Martel.msre_parse.DIGITS" class="py-name" href="#" onclick="return doclink('link-390', 'DIGITS', 'link-3');">DIGITS</a></tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L531"></a><tt class="py-lineno">531</tt> <tt class="py-line"> <tt id="link-391" class="py-name" targets="Function Martel.msre_parse.isname()=Martel.msre_parse-module.html#isname"><a title="Martel.msre_parse.isname" class="py-name" href="#" onclick="return doclink('link-391', 'isname', 'link-391');">isname</a></tt><tt class="py-op">(</tt><tt class="py-name">lo</tt> <tt class="py-op">+</tt> <tt id="link-392" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-392', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-393" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-393', 'next', 'link-131');">next</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L532"></a><tt class="py-lineno">532</tt> <tt class="py-line"> <tt class="py-name">lo</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> <tt class="py-op">+</tt> <tt id="link-394" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-394', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-395" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-395', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L533"></a><tt class="py-lineno">533</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-396" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-396', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-397" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-397', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">","</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L534"></a><tt class="py-lineno">534</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-398" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-398', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-399" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-399', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-400" class="py-name"><a title="Martel.msre_parse.DIGITS" class="py-name" href="#" onclick="return doclink('link-400', 'DIGITS', 'link-3');">DIGITS</a></tt> <tt class="py-keyword">or</tt> \ </tt>
<a name="L535"></a><tt class="py-lineno">535</tt> <tt class="py-line"> <tt id="link-401" class="py-name"><a title="Martel.msre_parse.isname" class="py-name" href="#" onclick="return doclink('link-401', 'isname', 'link-391');">isname</a></tt><tt class="py-op">(</tt><tt class="py-name">hi</tt> <tt class="py-op">+</tt> <tt id="link-402" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-402', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-403" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-403', 'next', 'link-131');">next</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L536"></a><tt class="py-lineno">536</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> <tt class="py-op">+</tt> <tt id="link-404" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-404', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-405" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-405', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L537"></a><tt class="py-lineno">537</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L538"></a><tt class="py-lineno">538</tt> <tt class="py-line"> <tt class="py-name">hi</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> </tt>
<a name="L539"></a><tt class="py-lineno">539</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-406" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-406', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-407" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-407', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"}"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L540"></a><tt class="py-lineno">540</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-408" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-408', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-409" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-409', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">ord</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L541"></a><tt class="py-lineno">541</tt> <tt class="py-line"> <tt id="link-410" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-410', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-411" class="py-name" targets="Method Bio.EUtils.ReseekFile.ReseekFile.seek()=Bio.EUtils.ReseekFile.ReseekFile-class.html#seek,Method Bio.File.UndoHandle.seek()=Bio.File.UndoHandle-class.html#seek,Method Martel.msre_parse.Tokenizer.seek()=Martel.msre_parse.Tokenizer-class.html#seek"><a title="Bio.EUtils.ReseekFile.ReseekFile.seek
Bio.File.UndoHandle.seek
Martel.msre_parse.Tokenizer.seek" class="py-name" href="#" onclick="return doclink('link-411', 'seek', 'link-411');">seek</a></tt><tt class="py-op">(</tt><tt class="py-name">here</tt><tt class="py-op">)</tt> </tt>
<a name="L542"></a><tt class="py-lineno">542</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L543"></a><tt class="py-lineno">543</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">lo</tt><tt class="py-op">:</tt> </tt>
<a name="L544"></a><tt class="py-lineno">544</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-412" class="py-name"><a title="Martel.msre_parse.is_firstchar" class="py-name" href="#" onclick="return doclink('link-412', 'is_firstchar', 'link-148');">is_firstchar</a></tt><tt class="py-op">(</tt><tt class="py-name">lo</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L545"></a><tt class="py-lineno">545</tt> <tt class="py-line"> <tt class="py-name">min</tt> <tt class="py-op">=</tt> <tt class="py-name">lo</tt> </tt>
<a name="L546"></a><tt class="py-lineno">546</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L547"></a><tt class="py-lineno">547</tt> <tt class="py-line"> <tt class="py-name">min</tt> <tt class="py-op">=</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt class="py-name">lo</tt><tt class="py-op">)</tt> </tt>
<a name="L548"></a><tt class="py-lineno">548</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">hi</tt><tt class="py-op">:</tt> </tt>
<a name="L549"></a><tt class="py-lineno">549</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-413" class="py-name"><a title="Martel.msre_parse.is_firstchar" class="py-name" href="#" onclick="return doclink('link-413', 'is_firstchar', 'link-148');">is_firstchar</a></tt><tt class="py-op">(</tt><tt class="py-name">hi</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L550"></a><tt class="py-lineno">550</tt> <tt class="py-line"> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-name">hi</tt> </tt>
<a name="L551"></a><tt class="py-lineno">551</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L552"></a><tt class="py-lineno">552</tt> <tt class="py-line"> <tt class="py-name">max</tt> <tt class="py-op">=</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt class="py-name">hi</tt><tt class="py-op">)</tt> </tt>
<a name="L553"></a><tt class="py-lineno">553</tt> <tt class="py-line"> </tt>
<a name="L554"></a><tt class="py-lineno">554</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-414" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-414', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">lo</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-415" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-415', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">hi</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt id="link-416" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-416', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-number">0</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L555"></a><tt class="py-lineno">555</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">max</tt> <tt class="py-op"><</tt> <tt class="py-name">min</tt><tt class="py-op">:</tt> </tt>
<a name="L556"></a><tt class="py-lineno">556</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-417" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-417', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bad repeat interval"</tt> </tt>
<a name="L557"></a><tt class="py-lineno">557</tt> <tt class="py-line"><tt class="py-comment">### End of Martel named group repeat changes</tt> </tt>
<a name="L558"></a><tt class="py-lineno">558</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L559"></a><tt class="py-lineno">559</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-418" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-418', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"not supported"</tt> </tt>
<a name="L560"></a><tt class="py-lineno">560</tt> <tt class="py-line"> <tt class="py-comment"># figure out which item to repeat</tt> </tt>
<a name="L561"></a><tt class="py-lineno">561</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">subpattern</tt><tt class="py-op">:</tt> </tt>
<a name="L562"></a><tt class="py-lineno">562</tt> <tt class="py-line"> <tt id="link-419" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-419', 'item', 'link-285');">item</a></tt> <tt class="py-op">=</tt> <tt class="py-name">subpattern</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L563"></a><tt class="py-lineno">563</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L564"></a><tt class="py-lineno">564</tt> <tt class="py-line"> <tt id="link-420" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-420', 'item', 'link-285');">item</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L565"></a><tt class="py-lineno">565</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-421" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-421', 'item', 'link-285');">item</a></tt> <tt class="py-keyword">or</tt> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-422" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-422', 'item', 'link-285');">item</a></tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt id="link-423" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-423', 'item', 'link-285');">item</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt id="link-424" class="py-name"><a title="Martel.msre_constants.AT
Martel.msre_parse.AT" class="py-name" href="#" onclick="return doclink('link-424', 'AT', 'link-20');">AT</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L566"></a><tt class="py-lineno">566</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-425" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-425', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"nothing to repeat"</tt> </tt>
<a name="L567"></a><tt class="py-lineno">567</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-426" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-426', 'item', 'link-285');">item</a></tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt id="link-427" class="py-name"><a title="Martel.msre_constants.MIN_REPEAT
Martel.msre_parse.MIN_REPEAT" class="py-name" href="#" onclick="return doclink('link-427', 'MIN_REPEAT', 'link-116');">MIN_REPEAT</a></tt><tt class="py-op">,</tt> <tt id="link-428" class="py-name"><a title="Martel.msre_constants.MAX_REPEAT
Martel.msre_parse.MAX_REPEAT" class="py-name" href="#" onclick="return doclink('link-428', 'MAX_REPEAT', 'link-117');">MAX_REPEAT</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L568"></a><tt class="py-lineno">568</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-429" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-429', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"multiple repeat"</tt> </tt>
<a name="L569"></a><tt class="py-lineno">569</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-430" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-430', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-431" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-431', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"?"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L570"></a><tt class="py-lineno">570</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-432" class="py-name"><a title="Martel.msre_constants.MIN_REPEAT
Martel.msre_parse.MIN_REPEAT" class="py-name" href="#" onclick="return doclink('link-432', 'MIN_REPEAT', 'link-116');">MIN_REPEAT</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt><tt class="py-op">,</tt> <tt id="link-433" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-433', 'item', 'link-285');">item</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L571"></a><tt class="py-lineno">571</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L572"></a><tt class="py-lineno">572</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt><tt id="link-434" class="py-name"><a title="Martel.msre_constants.MAX_REPEAT
Martel.msre_parse.MAX_REPEAT" class="py-name" href="#" onclick="return doclink('link-434', 'MAX_REPEAT', 'link-117');">MAX_REPEAT</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">min</tt><tt class="py-op">,</tt> <tt class="py-name">max</tt><tt class="py-op">,</tt> <tt id="link-435" class="py-name"><a title="Bio.EUtils.Datatypes.DBIds.item" class="py-name" href="#" onclick="return doclink('link-435', 'item', 'link-285');">item</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L573"></a><tt class="py-lineno">573</tt> <tt class="py-line"> </tt>
<a name="L574"></a><tt class="py-lineno">574</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"."</tt><tt class="py-op">:</tt> </tt>
<a name="L575"></a><tt class="py-lineno">575</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-436" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-436', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-437" class="py-name"><a title="Bio.EUtils.POM.ANY
Martel.msre_constants.ANY
Martel.msre_parse.ANY" class="py-name" href="#" onclick="return doclink('link-437', 'ANY', 'link-121');">ANY</a></tt><tt class="py-op">,</tt> <tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L576"></a><tt class="py-lineno">576</tt> <tt class="py-line"> </tt>
<a name="L577"></a><tt class="py-lineno">577</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"("</tt><tt class="py-op">:</tt> </tt>
<a name="L578"></a><tt class="py-lineno">578</tt> <tt class="py-line"> <tt id="link-438" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-438', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L579"></a><tt class="py-lineno">579</tt> <tt class="py-line"> <tt id="link-439" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-439', 'name', 'link-59');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L580"></a><tt class="py-lineno">580</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-440" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-440', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-441" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-441', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"?"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L581"></a><tt class="py-lineno">581</tt> <tt class="py-line"> <tt id="link-442" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-442', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L582"></a><tt class="py-lineno">582</tt> <tt class="py-line"> <tt class="py-comment"># options</tt> </tt>
<a name="L583"></a><tt class="py-lineno">583</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-443" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-443', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-444" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-444', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"P"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L584"></a><tt class="py-lineno">584</tt> <tt class="py-line"> <tt class="py-comment"># python extensions</tt> </tt>
<a name="L585"></a><tt class="py-lineno">585</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-445" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-445', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-446" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-446', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"<"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L586"></a><tt class="py-lineno">586</tt> <tt class="py-line"> <tt class="py-comment"># named group: skip forward to end of name</tt> </tt>
<a name="L587"></a><tt class="py-lineno">587</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-447" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-447', 'name', 'link-59');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L588"></a><tt class="py-lineno">588</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L589"></a><tt class="py-lineno">589</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt id="link-448" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-448', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-449" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-449', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L590"></a><tt class="py-lineno">590</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L591"></a><tt class="py-lineno">591</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-450" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-450', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unterminated name"</tt> </tt>
<a name="L592"></a><tt class="py-lineno">592</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-op">==</tt> <tt class="py-string">">"</tt><tt class="py-op">:</tt> </tt>
<a name="L593"></a><tt class="py-lineno">593</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L594"></a><tt class="py-lineno">594</tt> <tt class="py-line"> <tt id="link-451" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-451', 'name', 'link-59');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-452" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-452', 'name', 'link-59');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-name">char</tt> </tt>
<a name="L595"></a><tt class="py-lineno">595</tt> <tt class="py-line"> <tt id="link-453" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-453', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L596"></a><tt class="py-lineno">596</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-454" class="py-name" targets="Function Martel.msre_parse.isname_with_attrs()=Martel.msre_parse-module.html#isname_with_attrs"><a title="Martel.msre_parse.isname_with_attrs" class="py-name" href="#" onclick="return doclink('link-454', 'isname_with_attrs', 'link-454');">isname_with_attrs</a></tt><tt class="py-op">(</tt><tt id="link-455" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-455', 'name', 'link-59');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L597"></a><tt class="py-lineno">597</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-456" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-456', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bad character in group name"</tt> </tt>
<a name="L598"></a><tt class="py-lineno">598</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-457" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-457', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-458" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-458', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L599"></a><tt class="py-lineno">599</tt> <tt class="py-line"> <tt class="py-comment"># named backreference</tt> </tt>
<a name="L600"></a><tt class="py-lineno">600</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-459" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-459', 'name', 'link-59');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L601"></a><tt class="py-lineno">601</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L602"></a><tt class="py-lineno">602</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt id="link-460" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-460', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-461" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-461', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L603"></a><tt class="py-lineno">603</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L604"></a><tt class="py-lineno">604</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-462" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-462', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unterminated name"</tt> </tt>
<a name="L605"></a><tt class="py-lineno">605</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-op">==</tt> <tt class="py-string">")"</tt><tt class="py-op">:</tt> </tt>
<a name="L606"></a><tt class="py-lineno">606</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L607"></a><tt class="py-lineno">607</tt> <tt class="py-line"> <tt id="link-463" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-463', 'name', 'link-59');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-464" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-464', 'name', 'link-59');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-name">char</tt> </tt>
<a name="L608"></a><tt class="py-lineno">608</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-465" class="py-name"><a title="Martel.msre_parse.isname" class="py-name" href="#" onclick="return doclink('link-465', 'isname', 'link-391');">isname</a></tt><tt class="py-op">(</tt><tt id="link-466" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-466', 'name', 'link-59');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L609"></a><tt class="py-lineno">609</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-467" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-467', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bad character in group name"</tt> </tt>
<a name="L610"></a><tt class="py-lineno">610</tt> <tt class="py-line"> <tt class="py-name">gid</tt> <tt class="py-op">=</tt> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt class="py-name">groupdict</tt><tt class="py-op">.</tt><tt id="link-468" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-468', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt id="link-469" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-469', 'name', 'link-59');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L611"></a><tt class="py-lineno">611</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">gid</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L612"></a><tt class="py-lineno">612</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-470" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-470', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unknown group name"</tt> </tt>
<a name="L613"></a><tt class="py-lineno">613</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-471" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-471', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-472" class="py-name"><a title="Martel.msre_constants.GROUPREF
Martel.msre_parse.GROUPREF" class="py-name" href="#" onclick="return doclink('link-472', 'GROUPREF', 'link-262');">GROUPREF</a></tt><tt class="py-op">,</tt> <tt class="py-name">gid</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L614"></a><tt class="py-lineno">614</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L615"></a><tt class="py-lineno">615</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L616"></a><tt class="py-lineno">616</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt id="link-473" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-473', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-474" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-474', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L617"></a><tt class="py-lineno">617</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L618"></a><tt class="py-lineno">618</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-475" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-475', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unexpected end of pattern"</tt> </tt>
<a name="L619"></a><tt class="py-lineno">619</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-476" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-476', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unknown specifier: ?P%s"</tt> <tt class="py-op">%</tt> <tt class="py-name">char</tt> </tt>
<a name="L620"></a><tt class="py-lineno">620</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-477" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-477', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-478" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-478', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">":"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L621"></a><tt class="py-lineno">621</tt> <tt class="py-line"> <tt class="py-comment"># non-capturing group</tt> </tt>
<a name="L622"></a><tt class="py-lineno">622</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-479" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-479', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt class="py-number">2</tt> </tt>
<a name="L623"></a><tt class="py-lineno">623</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-480" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-480', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-481" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-481', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"#"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L624"></a><tt class="py-lineno">624</tt> <tt class="py-line"> <tt class="py-comment"># comment</tt> </tt>
<a name="L625"></a><tt class="py-lineno">625</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L626"></a><tt class="py-lineno">626</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-482" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-482', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-483" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-483', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt> <tt class="py-keyword">or</tt> <tt id="link-484" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-484', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-485" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-485', 'next', 'link-131');">next</a></tt> <tt class="py-op">==</tt> <tt class="py-string">")"</tt><tt class="py-op">:</tt> </tt>
<a name="L627"></a><tt class="py-lineno">627</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L628"></a><tt class="py-lineno">628</tt> <tt class="py-line"> <tt id="link-486" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-486', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-487" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-487', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L629"></a><tt class="py-lineno">629</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-488" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-488', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-489" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-489', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">")"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L630"></a><tt class="py-lineno">630</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-490" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-490', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unbalanced parenthesis"</tt> </tt>
<a name="L631"></a><tt class="py-lineno">631</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L632"></a><tt class="py-lineno">632</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-491" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-491', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-492" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-492', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">,</tt> <tt class="py-string">"!"</tt><tt class="py-op">,</tt> <tt class="py-string">"<"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L633"></a><tt class="py-lineno">633</tt> <tt class="py-line"> <tt class="py-comment"># lookahead assertions</tt> </tt>
<a name="L634"></a><tt class="py-lineno">634</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt id="link-493" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-493', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-494" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-494', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L635"></a><tt class="py-lineno">635</tt> <tt class="py-line"> <tt class="py-name">dir</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L636"></a><tt class="py-lineno">636</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-op">==</tt> <tt class="py-string">"<"</tt><tt class="py-op">:</tt> </tt>
<a name="L637"></a><tt class="py-lineno">637</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-495" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-495', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-496" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-496', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-op">(</tt><tt class="py-string">"="</tt><tt class="py-op">,</tt> <tt class="py-string">"!"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L638"></a><tt class="py-lineno">638</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-497" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-497', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"syntax error"</tt> </tt>
<a name="L639"></a><tt class="py-lineno">639</tt> <tt class="py-line"> <tt class="py-name">dir</tt> <tt class="py-op">=</tt> <tt class="py-op">-</tt><tt class="py-number">1</tt> <tt class="py-comment"># lookbehind</tt> </tt>
<a name="L640"></a><tt class="py-lineno">640</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt id="link-498" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-498', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-499" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-499', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L641"></a><tt class="py-lineno">641</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-500" class="py-name" targets="Function Martel.msre_parse._parse_sub()=Martel.msre_parse-module.html#_parse_sub"><a title="Martel.msre_parse._parse_sub" class="py-name" href="#" onclick="return doclink('link-500', '_parse_sub', 'link-500');">_parse_sub</a></tt><tt class="py-op">(</tt><tt id="link-501" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-501', 'source', 'link-167');">source</a></tt><tt class="py-op">,</tt> <tt class="py-name">state</tt><tt class="py-op">)</tt> </tt>
<a name="L642"></a><tt class="py-lineno">642</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-502" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-502', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-503" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-503', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">")"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L643"></a><tt class="py-lineno">643</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-504" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-504', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unbalanced parenthesis"</tt> </tt>
<a name="L644"></a><tt class="py-lineno">644</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-op">==</tt> <tt class="py-string">"="</tt><tt class="py-op">:</tt> </tt>
<a name="L645"></a><tt class="py-lineno">645</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-505" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-505', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-506" class="py-name" targets="Variable Martel.msre_constants.ASSERT=Martel.msre_constants-module.html#ASSERT,Variable Martel.msre_parse.ASSERT=Martel.msre_parse-module.html#ASSERT"><a title="Martel.msre_constants.ASSERT
Martel.msre_parse.ASSERT" class="py-name" href="#" onclick="return doclink('link-506', 'ASSERT', 'link-506');">ASSERT</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">dir</tt><tt class="py-op">,</tt> <tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L646"></a><tt class="py-lineno">646</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L647"></a><tt class="py-lineno">647</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-507" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-507', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-508" class="py-name" targets="Variable Martel.msre_constants.ASSERT_NOT=Martel.msre_constants-module.html#ASSERT_NOT,Variable Martel.msre_parse.ASSERT_NOT=Martel.msre_parse-module.html#ASSERT_NOT"><a title="Martel.msre_constants.ASSERT_NOT
Martel.msre_parse.ASSERT_NOT" class="py-name" href="#" onclick="return doclink('link-508', 'ASSERT_NOT', 'link-508');">ASSERT_NOT</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt class="py-name">dir</tt><tt class="py-op">,</tt> <tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L648"></a><tt class="py-lineno">648</tt> <tt class="py-line"> <tt class="py-keyword">continue</tt> </tt>
<a name="L649"></a><tt class="py-lineno">649</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L650"></a><tt class="py-lineno">650</tt> <tt class="py-line"> <tt class="py-comment"># flags</tt> </tt>
<a name="L651"></a><tt class="py-lineno">651</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-509" class="py-name"><a title="Martel.msre_parse.FLAGS" class="py-name" href="#" onclick="return doclink('link-509', 'FLAGS', 'link-47');">FLAGS</a></tt><tt class="py-op">.</tt><tt id="link-510" class="py-name" targets="Method Bio.Crystal.Crystal.has_key()=Bio.Crystal.Crystal-class.html#has_key,Method Bio.EUtils.POM.ElementNode.has_key()=Bio.EUtils.POM.ElementNode-class.html#has_key,Method Bio.GenBank.NCBIDictionary.has_key()=Bio.GenBank.NCBIDictionary-class.html#has_key,Method Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key()=Bio.PDB.AbstractPropertyMap.AbstractPropertyMap-class.html#has_key,Method Bio.PDB.FragmentMapper'.FragmentMapper.has_key()=Bio.PDB.FragmentMapper%27.FragmentMapper-class.html#has_key,Method Bio.Prosite.ExPASyDictionary.has_key()=Bio.Prosite.ExPASyDictionary-class.html#has_key,Method Bio.Prosite.Prodoc.ExPASyDictionary.has_key()=Bio.Prosite.Prodoc.ExPASyDictionary-class.html#has_key,Method Bio.PubMed.Dictionary.has_key()=Bio.PubMed.Dictionary-class.html#has_key,Method Bio.SwissProt.SProt.ExPASyDictionary.has_key()=Bio.SwissProt.SProt.ExPASyDictionary-class.html#has_key,Method Martel.Parser.MartelAttributeList.has_key()=Martel.Parser.MartelAttributeList-class.html#has_key"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-510', 'has_key', 'link-510');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-511" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-511', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-512" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-512', 'next', 'link-131');">next</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L652"></a><tt class="py-lineno">652</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-513" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-513', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unexpected end of pattern"</tt> </tt>
<a name="L653"></a><tt class="py-lineno">653</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt id="link-514" class="py-name"><a title="Martel.msre_parse.FLAGS" class="py-name" href="#" onclick="return doclink('link-514', 'FLAGS', 'link-47');">FLAGS</a></tt><tt class="py-op">.</tt><tt id="link-515" class="py-name"><a title="Bio.Crystal.Crystal.has_key
Bio.EUtils.POM.ElementNode.has_key
Bio.GenBank.NCBIDictionary.has_key
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.has_key
Bio.PDB.FragmentMapper'.FragmentMapper.has_key
Bio.Prosite.ExPASyDictionary.has_key
Bio.Prosite.Prodoc.ExPASyDictionary.has_key
Bio.PubMed.Dictionary.has_key
Bio.SwissProt.SProt.ExPASyDictionary.has_key
Martel.Parser.MartelAttributeList.has_key" class="py-name" href="#" onclick="return doclink('link-515', 'has_key', 'link-510');">has_key</a></tt><tt class="py-op">(</tt><tt id="link-516" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-516', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-517" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-517', 'next', 'link-131');">next</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L654"></a><tt class="py-lineno">654</tt> <tt class="py-line"> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">=</tt> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">|</tt> <tt id="link-518" class="py-name"><a title="Martel.msre_parse.FLAGS" class="py-name" href="#" onclick="return doclink('link-518', 'FLAGS', 'link-47');">FLAGS</a></tt><tt class="py-op">[</tt><tt id="link-519" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-519', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-520" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-520', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt><tt class="py-op">]</tt> </tt>
<a name="L655"></a><tt class="py-lineno">655</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-521" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-521', 'group', 'link-254');">group</a></tt><tt class="py-op">:</tt> </tt>
<a name="L656"></a><tt class="py-lineno">656</tt> <tt class="py-line"> <tt class="py-comment"># parse group contents</tt> </tt>
<a name="L657"></a><tt class="py-lineno">657</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt id="link-522" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-522', 'group', 'link-254');">group</a></tt> <tt class="py-op">==</tt> <tt class="py-number">2</tt><tt class="py-op">:</tt> </tt>
<a name="L658"></a><tt class="py-lineno">658</tt> <tt class="py-line"> <tt class="py-comment"># anonymous group</tt> </tt>
<a name="L659"></a><tt class="py-lineno">659</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-523" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-523', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L660"></a><tt class="py-lineno">660</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L661"></a><tt class="py-lineno">661</tt> <tt class="py-line"> <tt id="link-524" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-524', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-525" class="py-name" targets="Method Martel.convert_re.GroupNames.opengroup()=Martel.convert_re.GroupNames-class.html#opengroup,Method Martel.msre_parse.Pattern.opengroup()=Martel.msre_parse.Pattern-class.html#opengroup"><a title="Martel.convert_re.GroupNames.opengroup
Martel.msre_parse.Pattern.opengroup" class="py-name" href="#" onclick="return doclink('link-525', 'opengroup', 'link-525');">opengroup</a></tt><tt class="py-op">(</tt><tt id="link-526" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-526', 'name', 'link-59');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L662"></a><tt class="py-lineno">662</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-527" class="py-name"><a title="Martel.msre_parse._parse_sub" class="py-name" href="#" onclick="return doclink('link-527', '_parse_sub', 'link-500');">_parse_sub</a></tt><tt class="py-op">(</tt><tt id="link-528" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-528', 'source', 'link-167');">source</a></tt><tt class="py-op">,</tt> <tt class="py-name">state</tt><tt class="py-op">)</tt> </tt>
<a name="L663"></a><tt class="py-lineno">663</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-529" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-529', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-530" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-530', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">")"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L664"></a><tt class="py-lineno">664</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-531" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-531', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unbalanced parenthesis"</tt> </tt>
<a name="L665"></a><tt class="py-lineno">665</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-532" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-532', 'group', 'link-254');">group</a></tt> <tt class="py-keyword">is</tt> <tt class="py-keyword">not</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L666"></a><tt class="py-lineno">666</tt> <tt class="py-line"> <tt class="py-name">state</tt><tt class="py-op">.</tt><tt id="link-533" class="py-name" targets="Method Martel.convert_re.GroupNames.closegroup()=Martel.convert_re.GroupNames-class.html#closegroup,Method Martel.msre_parse.Pattern.closegroup()=Martel.msre_parse.Pattern-class.html#closegroup"><a title="Martel.convert_re.GroupNames.closegroup
Martel.msre_parse.Pattern.closegroup" class="py-name" href="#" onclick="return doclink('link-533', 'closegroup', 'link-533');">closegroup</a></tt><tt class="py-op">(</tt><tt id="link-534" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-534', 'group', 'link-254');">group</a></tt><tt class="py-op">)</tt> </tt>
<a name="L667"></a><tt class="py-lineno">667</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-535" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-535', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-536" class="py-name"><a title="Martel.msre_constants.SUBPATTERN
Martel.msre_parse.SUBPATTERN" class="py-name" href="#" onclick="return doclink('link-536', 'SUBPATTERN', 'link-112');">SUBPATTERN</a></tt><tt class="py-op">,</tt> <tt class="py-op">(</tt><tt id="link-537" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-537', 'group', 'link-254');">group</a></tt><tt class="py-op">,</tt> <tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L668"></a><tt class="py-lineno">668</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L669"></a><tt class="py-lineno">669</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L670"></a><tt class="py-lineno">670</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt id="link-538" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-538', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-539" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-539', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L671"></a><tt class="py-lineno">671</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L672"></a><tt class="py-lineno">672</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-540" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-540', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unexpected end of pattern"</tt> </tt>
<a name="L673"></a><tt class="py-lineno">673</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-op">==</tt> <tt class="py-string">")"</tt><tt class="py-op">:</tt> </tt>
<a name="L674"></a><tt class="py-lineno">674</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L675"></a><tt class="py-lineno">675</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-541" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-541', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unknown extension"</tt> </tt>
<a name="L676"></a><tt class="py-lineno">676</tt> <tt class="py-line"> </tt>
<a name="L677"></a><tt class="py-lineno">677</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"^"</tt><tt class="py-op">:</tt> </tt>
<a name="L678"></a><tt class="py-lineno">678</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-542" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-542', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-543" class="py-name"><a title="Martel.msre_constants.AT
Martel.msre_parse.AT" class="py-name" href="#" onclick="return doclink('link-543', 'AT', 'link-20');">AT</a></tt><tt class="py-op">,</tt> <tt id="link-544" class="py-name" targets="Variable Martel.msre_constants.AT_BEGINNING=Martel.msre_constants-module.html#AT_BEGINNING,Variable Martel.msre_parse.AT_BEGINNING=Martel.msre_parse-module.html#AT_BEGINNING"><a title="Martel.msre_constants.AT_BEGINNING
Martel.msre_parse.AT_BEGINNING" class="py-name" href="#" onclick="return doclink('link-544', 'AT_BEGINNING', 'link-544');">AT_BEGINNING</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L679"></a><tt class="py-lineno">679</tt> <tt class="py-line"> </tt>
<a name="L680"></a><tt class="py-lineno">680</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"$"</tt><tt class="py-op">:</tt> </tt>
<a name="L681"></a><tt class="py-lineno">681</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-545" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-545', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-546" class="py-name"><a title="Martel.msre_constants.AT
Martel.msre_parse.AT" class="py-name" href="#" onclick="return doclink('link-546', 'AT', 'link-20');">AT</a></tt><tt class="py-op">,</tt> <tt id="link-547" class="py-name" targets="Variable Martel.msre_constants.AT_END=Martel.msre_constants-module.html#AT_END,Variable Martel.msre_parse.AT_END=Martel.msre_parse-module.html#AT_END"><a title="Martel.msre_constants.AT_END
Martel.msre_parse.AT_END" class="py-name" href="#" onclick="return doclink('link-547', 'AT_END', 'link-547');">AT_END</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L682"></a><tt class="py-lineno">682</tt> <tt class="py-line"> </tt>
<a name="L683"></a><tt class="py-lineno">683</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">this</tt> <tt class="py-keyword">and</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"\\"</tt><tt class="py-op">:</tt> </tt>
<a name="L684"></a><tt class="py-lineno">684</tt> <tt class="py-line"> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt id="link-548" class="py-name" targets="Function Martel.msre_parse._escape()=Martel.msre_parse-module.html#_escape"><a title="Martel.msre_parse._escape" class="py-name" href="#" onclick="return doclink('link-548', '_escape', 'link-548');">_escape</a></tt><tt class="py-op">(</tt><tt id="link-549" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-549', 'source', 'link-167');">source</a></tt><tt class="py-op">,</tt> <tt class="py-name">this</tt><tt class="py-op">,</tt> <tt class="py-name">state</tt><tt class="py-op">)</tt> </tt>
<a name="L685"></a><tt class="py-lineno">685</tt> <tt class="py-line"> <tt class="py-name">subpattern</tt><tt class="py-op">.</tt><tt id="link-550" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-550', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">code</tt><tt class="py-op">)</tt> </tt>
<a name="L686"></a><tt class="py-lineno">686</tt> <tt class="py-line"> </tt>
<a name="L687"></a><tt class="py-lineno">687</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L688"></a><tt class="py-lineno">688</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-551" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-551', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"parser error"</tt> </tt>
<a name="L689"></a><tt class="py-lineno">689</tt> <tt class="py-line"> </tt>
<a name="L690"></a><tt class="py-lineno">690</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">subpattern</tt> </tt>
</div><a name="L691"></a><tt class="py-lineno">691</tt> <tt class="py-line"> </tt>
<a name="parse"></a><div id="parse-def"><a name="L692"></a><tt class="py-lineno">692</tt> <a class="py-toggle" href="#" id="parse-toggle" onclick="return toggle('parse');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#parse">parse</a><tt class="py-op">(</tt><tt class="py-param">str</tt><tt class="py-op">,</tt> <tt class="py-param">flags</tt><tt class="py-op">=</tt><tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-param">pattern</tt><tt class="py-op">=</tt><tt class="py-name">None</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse-expanded"><a name="L693"></a><tt class="py-lineno">693</tt> <tt class="py-line"> <tt class="py-comment"># parse 're' pattern into list of (opcode, argument) tuples</tt> </tt>
<a name="L694"></a><tt class="py-lineno">694</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L695"></a><tt class="py-lineno">695</tt> <tt class="py-line"> <tt id="link-552" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-552', 'source', 'link-167');">source</a></tt> <tt class="py-op">=</tt> <tt id="link-553" class="py-name" targets="Class Martel.msre_parse.Tokenizer=Martel.msre_parse.Tokenizer-class.html"><a title="Martel.msre_parse.Tokenizer" class="py-name" href="#" onclick="return doclink('link-553', 'Tokenizer', 'link-553');">Tokenizer</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">)</tt> </tt>
<a name="L696"></a><tt class="py-lineno">696</tt> <tt class="py-line"> </tt>
<a name="L697"></a><tt class="py-lineno">697</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-554" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-554', 'pattern', 'link-67');">pattern</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L698"></a><tt class="py-lineno">698</tt> <tt class="py-line"> <tt id="link-555" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-555', 'pattern', 'link-67');">pattern</a></tt> <tt class="py-op">=</tt> <tt id="link-556" class="py-name" targets="Module Bio.NeuralNetwork.Gene.Pattern=Bio.NeuralNetwork.Gene.Pattern-module.html,Module Bio.Prosite.Pattern=Bio.Prosite.Pattern-module.html,Class Martel.msre_parse.Pattern=Martel.msre_parse.Pattern-class.html"><a title="Bio.NeuralNetwork.Gene.Pattern
Bio.Prosite.Pattern
Martel.msre_parse.Pattern" class="py-name" href="#" onclick="return doclink('link-556', 'Pattern', 'link-556');">Pattern</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L699"></a><tt class="py-lineno">699</tt> <tt class="py-line"> <tt id="link-557" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-557', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">=</tt> <tt class="py-name">flags</tt> </tt>
<a name="L700"></a><tt class="py-lineno">700</tt> <tt class="py-line"> <tt id="link-558" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-558', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">.</tt><tt class="py-name">str</tt> <tt class="py-op">=</tt> <tt class="py-name">str</tt> </tt>
<a name="L701"></a><tt class="py-lineno">701</tt> <tt class="py-line"> </tt>
<a name="L702"></a><tt class="py-lineno">702</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt id="link-559" class="py-name"><a title="Martel.msre_parse._parse_sub" class="py-name" href="#" onclick="return doclink('link-559', '_parse_sub', 'link-500');">_parse_sub</a></tt><tt class="py-op">(</tt><tt id="link-560" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-560', 'source', 'link-167');">source</a></tt><tt class="py-op">,</tt> <tt id="link-561" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-561', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">,</tt> <tt class="py-number">0</tt><tt class="py-op">)</tt> </tt>
<a name="L703"></a><tt class="py-lineno">703</tt> <tt class="py-line"> </tt>
<a name="L704"></a><tt class="py-lineno">704</tt> <tt class="py-line"> <tt class="py-name">tail</tt> <tt class="py-op">=</tt> <tt id="link-562" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-562', 'source', 'link-167');">source</a></tt><tt class="py-op">.</tt><tt id="link-563" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-563', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L705"></a><tt class="py-lineno">705</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">tail</tt> <tt class="py-op">==</tt> <tt class="py-string">")"</tt><tt class="py-op">:</tt> </tt>
<a name="L706"></a><tt class="py-lineno">706</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-564" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-564', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unbalanced parenthesis"</tt> </tt>
<a name="L707"></a><tt class="py-lineno">707</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">tail</tt><tt class="py-op">:</tt> </tt>
<a name="L708"></a><tt class="py-lineno">708</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-565" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-565', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bogus characters at end of regular expression"</tt> </tt>
<a name="L709"></a><tt class="py-lineno">709</tt> <tt class="py-line"> </tt>
<a name="L710"></a><tt class="py-lineno">710</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">flags</tt> <tt class="py-op">&</tt> <tt id="link-566" class="py-name" targets="Variable Martel.msre_constants.SRE_FLAG_DEBUG=Martel.msre_constants-module.html#SRE_FLAG_DEBUG,Variable Martel.msre_parse.SRE_FLAG_DEBUG=Martel.msre_parse-module.html#SRE_FLAG_DEBUG"><a title="Martel.msre_constants.SRE_FLAG_DEBUG
Martel.msre_parse.SRE_FLAG_DEBUG" class="py-name" href="#" onclick="return doclink('link-566', 'SRE_FLAG_DEBUG', 'link-566');">SRE_FLAG_DEBUG</a></tt><tt class="py-op">:</tt> </tt>
<a name="L711"></a><tt class="py-lineno">711</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-567" class="py-name"><a title="Bio.DocSQL.Query.dump
Martel.msre_parse.SubPattern.dump
Martel.test.support.Storage.dump
Martel.test.test_swissprot38.dump" class="py-name" href="#" onclick="return doclink('link-567', 'dump', 'link-76');">dump</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L712"></a><tt class="py-lineno">712</tt> <tt class="py-line"> </tt>
<a name="L713"></a><tt class="py-lineno">713</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-op">(</tt><tt class="py-name">flags</tt> <tt class="py-op">&</tt> <tt id="link-568" class="py-name"><a title="Martel.msre_constants.SRE_FLAG_VERBOSE
Martel.msre_parse.SRE_FLAG_VERBOSE" class="py-name" href="#" onclick="return doclink('link-568', 'SRE_FLAG_VERBOSE', 'link-52');">SRE_FLAG_VERBOSE</a></tt><tt class="py-op">)</tt> <tt class="py-keyword">and</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-569" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-569', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">.</tt><tt class="py-name">flags</tt> <tt class="py-op">&</tt> <tt id="link-570" class="py-name"><a title="Martel.msre_constants.SRE_FLAG_VERBOSE
Martel.msre_parse.SRE_FLAG_VERBOSE" class="py-name" href="#" onclick="return doclink('link-570', 'SRE_FLAG_VERBOSE', 'link-52');">SRE_FLAG_VERBOSE</a></tt><tt class="py-op">:</tt> </tt>
<a name="L714"></a><tt class="py-lineno">714</tt> <tt class="py-line"> <tt class="py-comment"># the VERBOSE flag was switched on inside the pattern. to be</tt> </tt>
<a name="L715"></a><tt class="py-lineno">715</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># on the safe side, we'll parse the whole thing again...</tt> </tt>
<a name="L716"></a><tt class="py-lineno">716</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">return</tt> <tt id="link-571" class="py-name" targets="Method Bio.Affy.CelFile.CelParser.parse()=Bio.Affy.CelFile.CelParser-class.html#parse,Method Bio.AlignAce.Parser.AlignAceParser.parse()=Bio.AlignAce.Parser.AlignAceParser-class.html#parse,Method Bio.AlignAce.Parser.CompareAceParser.parse()=Bio.AlignAce.Parser.CompareAceParser-class.html#parse,Function Bio.AlignIO.parse()=Bio.AlignIO-module.html#parse,Method Bio.Blast.NCBIStandalone.BlastErrorParser.parse()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#parse,Method Bio.Blast.NCBIStandalone.BlastParser.parse()=Bio.Blast.NCBIStandalone.BlastParser-class.html#parse,Method Bio.Blast.NCBIStandalone.PSIBlastParser.parse()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#parse,Method Bio.Blast.NCBIWWW.BlastParser.parse()=Bio.Blast.NCBIWWW.BlastParser-class.html#parse,Method Bio.Blast.NCBIXML.BlastParser.parse()=Bio.Blast.NCBIXML.BlastParser-class.html#parse,Function Bio.Blast.NCBIXML.parse()=Bio.Blast.NCBIXML-module.html#parse,Method Bio.CDD.RecordParser.parse()=Bio.CDD.RecordParser-class.html#parse,Method Bio.Compass.RecordParser.parse()=Bio.Compass.RecordParser-class.html#parse,Function Bio.Decode.parse()=Bio.Decode-module.html#parse,Method Bio.ECell.RecordParser.parse()=Bio.ECell.RecordParser-class.html#parse,Method Bio.EUtils.POM.POMDocument.parse()=Bio.EUtils.POM.POMDocument-class.html#parse,Module Bio.EUtils.parse=Bio.EUtils.parse-module.html,Method Bio.Emboss.Primer.Primer3Parser.parse()=Bio.Emboss.Primer.Primer3Parser-class.html#parse,Method Bio.Emboss.Primer.PrimerSearchParser.parse()=Bio.Emboss.Primer.PrimerSearchParser-class.html#parse,Method Bio.Enzyme.RecordParser.parse()=Bio.Enzyme.RecordParser-class.html#parse,Method Bio.Fasta.RecordParser.parse()=Bio.Fasta.RecordParser-class.html#parse,Method Bio.Fasta.SequenceParser.parse()=Bio.Fasta.SequenceParser-class.html#parse,Method Bio.GenBank.FeatureParser.parse()=Bio.GenBank.FeatureParser-class.html#parse,Function Bio.GenBank.LocationParser.parse()=Bio.GenBank.LocationParser-module.html#parse,Method Bio.GenBank.RecordParser.parse()=Bio.GenBank.RecordParser-class.html#parse,Method Bio.GenBank.Scanner.InsdcScanner.parse()=Bio.GenBank.Scanner.InsdcScanner-class.html#parse,Function Bio.Geo.parse()=Bio.Geo-module.html#parse,Method Bio.Gobase.RecordParser.parse()=Bio.Gobase.RecordParser-class.html#parse,Method Bio.IntelliGenetics.RecordParser.parse()=Bio.IntelliGenetics.RecordParser-class.html#parse,Method Bio.InterPro.InterProParser.parse()=Bio.InterPro.InterProParser-class.html#parse,Function Bio.KEGG.Compound.parse()=Bio.KEGG.Compound-module.html#parse,Function Bio.KEGG.Enzyme.parse()=Bio.KEGG.Enzyme-module.html#parse,Function Bio.KEGG.Map.parse()=Bio.KEGG.Map-module.html#parse,Method Bio.LocusLink.RecordParser.parse()=Bio.LocusLink.RecordParser-class.html#parse,Method Bio.LocusLink.web_parse.LocusLinkParser.parse()=Bio.LocusLink.web_parse.LocusLinkParser-class.html#parse,Method Bio.MEME.Parser.MASTParser.parse()=Bio.MEME.Parser.MASTParser-class.html#parse,Method Bio.MEME.Parser.MEMEParser.parse()=Bio.MEME.Parser.MEMEParser-class.html#parse,Method Bio.Medline.RecordParser.parse()=Bio.Medline.RecordParser-class.html#parse,Method Bio.MetaTool.RecordParser.parse()=Bio.MetaTool.RecordParser-class.html#parse,Method Bio.NBRF.RecordParser.parse()=Bio.NBRF.RecordParser-class.html#parse,Method Bio.Ndb.NdbParser.parse()=Bio.Ndb.NdbParser-class.html#parse,Method Bio.ParserSupport.AbstractParser.parse()=Bio.ParserSupport.AbstractParser-class.html#parse,Method Bio.Parsers.spark.GenericParser.parse()=Bio.Parsers.spark.GenericParser-class.html#parse,Method Bio.PopGen.FDist.RecordParser.parse()=Bio.PopGen.FDist.RecordParser-class.html#parse,Method Bio.PopGen.GenePop.RecordParser.parse()=Bio.PopGen.GenePop.RecordParser-class.html#parse,Function Bio.PopGen.GenePop.parse()=Bio.PopGen.GenePop-module.html#parse,Method Bio.Prosite.Prodoc.RecordParser.parse()=Bio.Prosite.Prodoc.RecordParser-class.html#parse,Function Bio.Prosite.Prodoc.parse()=Bio.Prosite.Prodoc-module.html#parse,Method Bio.Prosite.RecordParser.parse()=Bio.Prosite.RecordParser-class.html#parse,Function Bio.Prosite.parse()=Bio.Prosite-module.html#parse,Method Bio.Rebase.RecordParser.parse()=Bio.Rebase.RecordParser-class.html#parse,Method Bio.SCOP.Cla.Parser.parse()=Bio.SCOP.Cla.Parser-class.html#parse,Function Bio.SCOP.Cla.parse()=Bio.SCOP.Cla-module.html#parse,Method Bio.SCOP.Des.Parser.parse()=Bio.SCOP.Des.Parser-class.html#parse,Function Bio.SCOP.Des.parse()=Bio.SCOP.Des-module.html#parse,Method Bio.SCOP.Dom.Parser.parse()=Bio.SCOP.Dom.Parser-class.html#parse,Function Bio.SCOP.Dom.parse()=Bio.SCOP.Dom-module.html#parse,Method Bio.SCOP.Hie.Parser.parse()=Bio.SCOP.Hie.Parser-class.html#parse,Function Bio.SCOP.Hie.parse()=Bio.SCOP.Hie-module.html#parse,Method Bio.SCOP.Raf.Parser.parse()=Bio.SCOP.Raf.Parser-class.html#parse,Function Bio.SCOP.Raf.parse()=Bio.SCOP.Raf-module.html#parse,Method Bio.Saf.RecordParser.parse()=Bio.Saf.RecordParser-class.html#parse,Function Bio.SeqIO.parse()=Bio.SeqIO-module.html#parse,Method Bio.Sequencing.Ace.ACEParser.parse()=Bio.Sequencing.Ace.ACEParser-class.html#parse,Method Bio.Sequencing.Ace.RecordParser.parse()=Bio.Sequencing.Ace.RecordParser-class.html#parse,Method Bio.Sequencing.Phd.RecordParser.parse()=Bio.Sequencing.Phd.RecordParser-class.html#parse,Method Bio.SwissProt.KeyWList.ListParser.parse()=Bio.SwissProt.KeyWList.ListParser-class.html#parse,Function Bio.SwissProt.KeyWList.parse()=Bio.SwissProt.KeyWList-module.html#parse,Method Bio.SwissProt.SProt.RecordParser.parse()=Bio.SwissProt.SProt.RecordParser-class.html#parse,Method Bio.SwissProt.SProt.SequenceParser.parse()=Bio.SwissProt.SProt.SequenceParser-class.html#parse,Function Bio.SwissProt.parse()=Bio.SwissProt-module.html#parse,Method Bio.UniGene.RecordParser.parse()=Bio.UniGene.RecordParser-class.html#parse,Function Bio.Wise.psw.parse()=Bio.Wise.psw-module.html#parse,Method Martel.Parser.HeaderFooterParser.parse()=Martel.Parser.HeaderFooterParser-class.html#parse,Method Martel.Parser.Parser.parse()=Martel.Parser.Parser-class.html#parse,Method Martel.Parser.RecordParser.parse()=Martel.Parser.RecordParser-class.html#parse,Function Martel.msre_parse.parse()=Martel.msre_parse-module.html#parse"><a title="Bio.Affy.CelFile.CelParser.parse
Bio.AlignAce.Parser.AlignAceParser.parse
Bio.AlignAce.Parser.CompareAceParser.parse
Bio.AlignIO.parse
Bio.Blast.NCBIStandalone.BlastErrorParser.parse
Bio.Blast.NCBIStandalone.BlastParser.parse
Bio.Blast.NCBIStandalone.PSIBlastParser.parse
Bio.Blast.NCBIWWW.BlastParser.parse
Bio.Blast.NCBIXML.BlastParser.parse
Bio.Blast.NCBIXML.parse
Bio.CDD.RecordParser.parse
Bio.Compass.RecordParser.parse
Bio.Decode.parse
Bio.ECell.RecordParser.parse
Bio.EUtils.POM.POMDocument.parse
Bio.EUtils.parse
Bio.Emboss.Primer.Primer3Parser.parse
Bio.Emboss.Primer.PrimerSearchParser.parse
Bio.Enzyme.RecordParser.parse
Bio.Fasta.RecordParser.parse
Bio.Fasta.SequenceParser.parse
Bio.GenBank.FeatureParser.parse
Bio.GenBank.LocationParser.parse
Bio.GenBank.RecordParser.parse
Bio.GenBank.Scanner.InsdcScanner.parse
Bio.Geo.parse
Bio.Gobase.RecordParser.parse
Bio.IntelliGenetics.RecordParser.parse
Bio.InterPro.InterProParser.parse
Bio.KEGG.Compound.parse
Bio.KEGG.Enzyme.parse
Bio.KEGG.Map.parse
Bio.LocusLink.RecordParser.parse
Bio.LocusLink.web_parse.LocusLinkParser.parse
Bio.MEME.Parser.MASTParser.parse
Bio.MEME.Parser.MEMEParser.parse
Bio.Medline.RecordParser.parse
Bio.MetaTool.RecordParser.parse
Bio.NBRF.RecordParser.parse
Bio.Ndb.NdbParser.parse
Bio.ParserSupport.AbstractParser.parse
Bio.Parsers.spark.GenericParser.parse
Bio.PopGen.FDist.RecordParser.parse
Bio.PopGen.GenePop.RecordParser.parse
Bio.PopGen.GenePop.parse
Bio.Prosite.Prodoc.RecordParser.parse
Bio.Prosite.Prodoc.parse
Bio.Prosite.RecordParser.parse
Bio.Prosite.parse
Bio.Rebase.RecordParser.parse
Bio.SCOP.Cla.Parser.parse
Bio.SCOP.Cla.parse
Bio.SCOP.Des.Parser.parse
Bio.SCOP.Des.parse
Bio.SCOP.Dom.Parser.parse
Bio.SCOP.Dom.parse
Bio.SCOP.Hie.Parser.parse
Bio.SCOP.Hie.parse
Bio.SCOP.Raf.Parser.parse
Bio.SCOP.Raf.parse
Bio.Saf.RecordParser.parse
Bio.SeqIO.parse
Bio.Sequencing.Ace.ACEParser.parse
Bio.Sequencing.Ace.RecordParser.parse
Bio.Sequencing.Phd.RecordParser.parse
Bio.SwissProt.KeyWList.ListParser.parse
Bio.SwissProt.KeyWList.parse
Bio.SwissProt.SProt.RecordParser.parse
Bio.SwissProt.SProt.SequenceParser.parse
Bio.SwissProt.parse
Bio.UniGene.RecordParser.parse
Bio.Wise.psw.parse
Martel.Parser.HeaderFooterParser.parse
Martel.Parser.Parser.parse
Martel.Parser.RecordParser.parse
Martel.msre_parse.parse" class="py-name" href="#" onclick="return doclink('link-571', 'parse', 'link-571');">parse</a></tt><tt class="py-op">(</tt><tt class="py-name">str</tt><tt class="py-op">,</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-572" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-572', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">.</tt><tt class="py-name">flags</tt><tt class="py-op">)</tt> </tt>
<a name="L717"></a><tt class="py-lineno">717</tt> <tt class="py-line"> </tt>
<a name="L718"></a><tt class="py-lineno">718</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">p</tt> </tt>
</div><a name="L719"></a><tt class="py-lineno">719</tt> <tt class="py-line"> </tt>
<a name="parse_template"></a><div id="parse_template-def"><a name="L720"></a><tt class="py-lineno">720</tt> <a class="py-toggle" href="#" id="parse_template-toggle" onclick="return toggle('parse_template');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#parse_template">parse_template</a><tt class="py-op">(</tt><tt class="py-param">source</tt><tt class="py-op">,</tt> <tt class="py-param">pattern</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="parse_template-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="parse_template-expanded"><a name="L721"></a><tt class="py-lineno">721</tt> <tt class="py-line"> <tt class="py-comment"># parse 're' replacement string into list of literals and</tt> </tt>
<a name="L722"></a><tt class="py-lineno">722</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># group references</tt> </tt>
<a name="L723"></a><tt class="py-lineno">723</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-573" class="py-name" targets="Variable Martel.test.test_swissprot38.s=Martel.test.test_swissprot38-module.html#s"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-573', 's', 'link-573');">s</a></tt> <tt class="py-op">=</tt> <tt id="link-574" class="py-name"><a title="Martel.msre_parse.Tokenizer" class="py-name" href="#" onclick="return doclink('link-574', 'Tokenizer', 'link-553');">Tokenizer</a></tt><tt class="py-op">(</tt><tt id="link-575" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-575', 'source', 'link-167');">source</a></tt><tt class="py-op">)</tt> </tt>
<a name="L724"></a><tt class="py-lineno">724</tt> <tt class="py-line"> <tt class="py-name">p</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L725"></a><tt class="py-lineno">725</tt> <tt class="py-line"> <tt class="py-name">a</tt> <tt class="py-op">=</tt> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-576" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-576', 'append', 'link-62');">append</a></tt> </tt>
<a name="L726"></a><tt class="py-lineno">726</tt> <tt class="py-line"> <tt class="py-keyword">def</tt> <tt class="py-def-name">literal</tt><tt class="py-op">(</tt><tt class="py-param">literal</tt><tt class="py-op">,</tt> <tt class="py-param">p</tt><tt class="py-op">=</tt><tt class="py-name">p</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L727"></a><tt class="py-lineno">727</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">p</tt> <tt class="py-keyword">and</tt> <tt class="py-name">p</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt id="link-577" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-577', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">:</tt> </tt>
<a name="L728"></a><tt class="py-lineno">728</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-578" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-578', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">p</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-op">+</tt> <tt class="py-name">literal</tt> </tt>
<a name="L729"></a><tt class="py-lineno">729</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L730"></a><tt class="py-lineno">730</tt> <tt class="py-line"> <tt class="py-name">p</tt><tt class="py-op">.</tt><tt id="link-579" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-579', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-580" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-580', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">literal</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L731"></a><tt class="py-lineno">731</tt> <tt class="py-line"> <tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt id="link-581" class="py-name"><a title="Bio.GenBank._FeatureConsumer.source
Bio.GenBank._RecordConsumer.source
Bio.Medline._RecordConsumer.source
Bio.Pathway.Network.source
Bio.Rebase._RecordConsumer.source" class="py-name" href="#" onclick="return doclink('link-581', 'source', 'link-167');">source</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L732"></a><tt class="py-lineno">732</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-582" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-582', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-name">sep</tt><tt class="py-op">)</tt> <tt class="py-keyword">is</tt> <tt id="link-583" class="py-name"><a title="Bio.GenBank.LocationParser.Integer.type
Bio.GenBank.LocationParser.Symbol.type
Bio.GenBank.LocationParser.UnsignedInteger.type" class="py-name" href="#" onclick="return doclink('link-583', 'type', 'link-79');">type</a></tt><tt class="py-op">(</tt><tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L733"></a><tt class="py-lineno">733</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt class="py-name">chr</tt> </tt>
<a name="L734"></a><tt class="py-lineno">734</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L735"></a><tt class="py-lineno">735</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt class="py-name">unichr</tt> </tt>
<a name="L736"></a><tt class="py-lineno">736</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L737"></a><tt class="py-lineno">737</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt id="link-584" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-584', 's', 'link-573');">s</a></tt><tt class="py-op">.</tt><tt id="link-585" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-585', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L738"></a><tt class="py-lineno">738</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L739"></a><tt class="py-lineno">739</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> <tt class="py-comment"># end of replacement string</tt> </tt>
<a name="L740"></a><tt class="py-lineno">740</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-keyword">and</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-op">==</tt> <tt class="py-string">"\\"</tt><tt class="py-op">:</tt> </tt>
<a name="L741"></a><tt class="py-lineno">741</tt> <tt class="py-line"> <tt class="py-comment"># group</tt> </tt>
<a name="L742"></a><tt class="py-lineno">742</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">this</tt> <tt class="py-op">==</tt> <tt class="py-string">"\\g"</tt><tt class="py-op">:</tt> </tt>
<a name="L743"></a><tt class="py-lineno">743</tt> <tt class="py-line"> <tt id="link-586" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-586', 'name', 'link-59');">name</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L744"></a><tt class="py-lineno">744</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-587" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-587', 's', 'link-573');">s</a></tt><tt class="py-op">.</tt><tt id="link-588" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-588', 'match', 'link-156');">match</a></tt><tt class="py-op">(</tt><tt class="py-string">"<"</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L745"></a><tt class="py-lineno">745</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L746"></a><tt class="py-lineno">746</tt> <tt class="py-line"> <tt class="py-name">char</tt> <tt class="py-op">=</tt> <tt id="link-589" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-589', 's', 'link-573');">s</a></tt><tt class="py-op">.</tt><tt id="link-590" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-590', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L747"></a><tt class="py-lineno">747</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L748"></a><tt class="py-lineno">748</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-591" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-591', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"unterminated group name"</tt> </tt>
<a name="L749"></a><tt class="py-lineno">749</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">char</tt> <tt class="py-op">==</tt> <tt class="py-string">">"</tt><tt class="py-op">:</tt> </tt>
<a name="L750"></a><tt class="py-lineno">750</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L751"></a><tt class="py-lineno">751</tt> <tt class="py-line"> <tt id="link-592" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-592', 'name', 'link-59');">name</a></tt> <tt class="py-op">=</tt> <tt id="link-593" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-593', 'name', 'link-59');">name</a></tt> <tt class="py-op">+</tt> <tt class="py-name">char</tt> </tt>
<a name="L752"></a><tt class="py-lineno">752</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-594" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-594', 'name', 'link-59');">name</a></tt><tt class="py-op">:</tt> </tt>
<a name="L753"></a><tt class="py-lineno">753</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-595" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-595', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bad group name"</tt> </tt>
<a name="L754"></a><tt class="py-lineno">754</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L755"></a><tt class="py-lineno">755</tt> <tt class="py-line"> <tt id="link-596" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-596', 'index', 'link-87');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt id="link-597" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-597', 'name', 'link-59');">name</a></tt><tt class="py-op">)</tt> </tt>
<a name="L756"></a><tt class="py-lineno">756</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">ValueError</tt><tt class="py-op">:</tt> </tt>
<a name="L757"></a><tt class="py-lineno">757</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-598" class="py-name"><a title="Martel.msre_parse.isname" class="py-name" href="#" onclick="return doclink('link-598', 'isname', 'link-391');">isname</a></tt><tt class="py-op">(</tt><tt id="link-599" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-599', 'name', 'link-59');">name</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L758"></a><tt class="py-lineno">758</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-600" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-600', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"bad character in group name"</tt> </tt>
<a name="L759"></a><tt class="py-lineno">759</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L760"></a><tt class="py-lineno">760</tt> <tt class="py-line"> <tt id="link-601" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-601', 'index', 'link-87');">index</a></tt> <tt class="py-op">=</tt> <tt id="link-602" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-602', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">.</tt><tt class="py-name">groupindex</tt><tt class="py-op">[</tt><tt id="link-603" class="py-name"><a title="Bio.Encodings.IUPACEncoding.name" class="py-name" href="#" onclick="return doclink('link-603', 'name', 'link-59');">name</a></tt><tt class="py-op">]</tt> </tt>
<a name="L761"></a><tt class="py-lineno">761</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L762"></a><tt class="py-lineno">762</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt><tt class="py-op">,</tt> <tt class="py-string">"unknown group name"</tt> </tt>
<a name="L763"></a><tt class="py-lineno">763</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-604" class="py-name" targets="Variable Martel.msre_constants.MARK=Martel.msre_constants-module.html#MARK,Variable Martel.msre_parse.MARK=Martel.msre_parse-module.html#MARK"><a title="Martel.msre_constants.MARK
Martel.msre_parse.MARK" class="py-name" href="#" onclick="return doclink('link-604', 'MARK', 'link-604');">MARK</a></tt><tt class="py-op">,</tt> <tt id="link-605" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-605', 'index', 'link-87');">index</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L764"></a><tt class="py-lineno">764</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-number">1</tt> <tt class="py-keyword">and</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">in</tt> <tt id="link-606" class="py-name"><a title="Martel.msre_parse.DIGITS" class="py-name" href="#" onclick="return doclink('link-606', 'DIGITS', 'link-3');">DIGITS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L765"></a><tt class="py-lineno">765</tt> <tt class="py-line"> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt class="py-name">None</tt> </tt>
<a name="L766"></a><tt class="py-lineno">766</tt> <tt class="py-line"> <tt class="py-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L767"></a><tt class="py-lineno">767</tt> <tt class="py-line"> <tt id="link-607" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-607', 'group', 'link-254');">group</a></tt> <tt class="py-op">=</tt> <tt id="link-608" class="py-name"><a title="Martel._group
Martel.msre_parse._group" class="py-name" href="#" onclick="return doclink('link-608', '_group', 'link-255');">_group</a></tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">,</tt> <tt id="link-609" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-609', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">.</tt><tt id="link-610" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-610', 'groups', 'link-56');">groups</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt> </tt>
<a name="L768"></a><tt class="py-lineno">768</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-611" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-611', 'group', 'link-254');">group</a></tt><tt class="py-op">:</tt> </tt>
<a name="L769"></a><tt class="py-lineno">769</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-op">(</tt><tt id="link-612" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-612', 's', 'link-573');">s</a></tt><tt class="py-op">.</tt><tt id="link-613" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-613', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">not</tt> <tt class="py-keyword">in</tt> <tt id="link-614" class="py-name"><a title="Martel.msre_parse.DIGITS" class="py-name" href="#" onclick="return doclink('link-614', 'DIGITS', 'link-3');">DIGITS</a></tt> <tt class="py-keyword">or</tt> </tt>
<a name="L770"></a><tt class="py-lineno">770</tt> <tt class="py-line"> <tt class="py-keyword">not</tt> <tt id="link-615" class="py-name"><a title="Martel._group
Martel.msre_parse._group" class="py-name" href="#" onclick="return doclink('link-615', '_group', 'link-255');">_group</a></tt><tt class="py-op">(</tt><tt class="py-name">this</tt> <tt class="py-op">+</tt> <tt id="link-616" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-616', 's', 'link-573');">s</a></tt><tt class="py-op">.</tt><tt id="link-617" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-617', 'next', 'link-131');">next</a></tt><tt class="py-op">,</tt> <tt id="link-618" class="py-name"><a title="Bio.Prosite._RecordConsumer.pattern" class="py-name" href="#" onclick="return doclink('link-618', 'pattern', 'link-67');">pattern</a></tt><tt class="py-op">.</tt><tt id="link-619" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-619', 'groups', 'link-56');">groups</a></tt><tt class="py-op">+</tt><tt class="py-number">1</tt><tt class="py-op">)</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L771"></a><tt class="py-lineno">771</tt> <tt class="py-line"> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt id="link-620" class="py-name"><a title="Martel.msre_constants.MARK
Martel.msre_parse.MARK" class="py-name" href="#" onclick="return doclink('link-620', 'MARK', 'link-604');">MARK</a></tt><tt class="py-op">,</tt> <tt id="link-621" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-621', 'group', 'link-254');">group</a></tt> </tt>
<a name="L772"></a><tt class="py-lineno">772</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L773"></a><tt class="py-lineno">773</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt id="link-622" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-622', 's', 'link-573');">s</a></tt><tt class="py-op">.</tt><tt id="link-623" class="py-name"><a title="Bio.AlignIO.ClustalIO.ClustalIterator.next
Bio.AlignIO.EmbossIO.EmbossIterator.next
Bio.AlignIO.FastaIO.FastaM10Iterator.next
Bio.AlignIO.Interfaces.AlignmentIterator.next
Bio.AlignIO.PhylipIO.PhylipIterator.next
Bio.AlignIO.StockholmIO.StockholmIterator.next
Bio.Blast.NCBIStandalone.Iterator.next
Bio.Blast.ParseBlastTable.BlastTableReader.next
Bio.CDD.Iterator.next
Bio.Compass.Iterator.next
Bio.DocSQL.IterationCursor.next
Bio.ECell.Iterator.next
Bio.Enzyme.Iterator.next
Bio.Fasta.Iterator.next
Bio.GenBank.Iterator.next
Bio.Gobase.Iterator.next
Bio.IntelliGenetics.IntelliGeneticsReader.next
Bio.IntelliGenetics.Iterator.next
Bio.LocusLink.Iterator.next
Bio.Medline.Iterator.next
Bio.MetaTool.Iterator.next
Bio.NBRF.Iterator.next
Bio.Nexus.Nexus.CharBuffer.next
Bio.Prosite.Iterator.next
Bio.Prosite.Prodoc.Iterator.next
Bio.Rebase.Iterator.next
Bio.SCOP.Cla.Iterator.next
Bio.SCOP.Des.Iterator.next
Bio.SCOP.Dom.Iterator.next
Bio.SCOP.Hie.Iterator.next
Bio.SCOP.Raf.Iterator.next
Bio.Saf.Iterator.next
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.next
Bio.SeqIO.Interfaces.SequenceIterator.next
Bio.Sequencing.Ace.Iterator.next
Bio.Sequencing.Phd.Iterator.next
Bio.SwissProt.SProt.Iterator.next
Bio.UniGene.Iterator.next
Martel.Iterator.EventStream.next
Martel.Iterator.HeaderFooterEventStream.next
Martel.Iterator.Iterate.next
Martel.Iterator.RecordEventStream.next
Martel.RecordReader.CountLines.next
Martel.RecordReader.EndsWith.next
Martel.RecordReader.Everything.next
Martel.RecordReader.Nothing.next
Martel.RecordReader.RecordReader.next
Martel.RecordReader.StartsWith.next
Martel.RecordReader.Until.next" class="py-name" href="#" onclick="return doclink('link-623', 'next', 'link-131');">next</a></tt> <tt class="py-keyword">in</tt> <tt id="link-624" class="py-name"><a title="Martel.msre_parse.OCTDIGITS" class="py-name" href="#" onclick="return doclink('link-624', 'OCTDIGITS', 'link-4');">OCTDIGITS</a></tt><tt class="py-op">:</tt> </tt>
<a name="L774"></a><tt class="py-lineno">774</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt class="py-name">this</tt> <tt class="py-op">+</tt> <tt id="link-625" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-625', 's', 'link-573');">s</a></tt><tt class="py-op">.</tt><tt id="link-626" class="py-name"><a title="Bio.Crystal.Crystal.get
Bio.Data.CodonTable.AmbiguousForwardTable.get
Bio.EUtils.MultiDict._BaseMultiDict.get
Bio.EUtils.POM.ElementNode.get
Bio.GenBank.NCBIDictionary.get
Bio.Mindy.BaseDB.DictLookup.get
Bio.Prosite.ExPASyDictionary.get
Bio.Prosite.Prodoc.ExPASyDictionary.get
Bio.PubMed.Dictionary.get
Bio.Restriction.Restriction.RestrictionBatch.get
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.get
Bio.SeqUtils.MissingTable.get
Bio.SwissProt.SProt.ExPASyDictionary.get
Bio.config.DBRegistry.DBGroup.get
Bio.config.DBRegistry.DBObject.get
Bio.config.Registry.Registry.get
Martel.Parser.MartelAttributeList.get
Martel.msre_parse.Tokenizer.get" class="py-name" href="#" onclick="return doclink('link-626', 'get', 'link-161');">get</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L775"></a><tt class="py-lineno">775</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L776"></a><tt class="py-lineno">776</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L777"></a><tt class="py-lineno">777</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">code</tt><tt class="py-op">:</tt> </tt>
<a name="L778"></a><tt class="py-lineno">778</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L779"></a><tt class="py-lineno">779</tt> <tt class="py-line"> <tt class="py-name">code</tt> <tt class="py-op">=</tt> <tt id="link-627" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-627', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">,</tt> <tt class="py-name">char</tt><tt class="py-op">(</tt><tt class="py-name">atoi</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">[</tt><tt class="py-op">-</tt><tt class="py-number">6</tt><tt class="py-op">:</tt><tt class="py-op">]</tt><tt class="py-op">,</tt> <tt class="py-number">8</tt><tt class="py-op">)</tt> <tt class="py-op">&</tt> <tt class="py-number">0xff</tt><tt class="py-op">)</tt> </tt>
<a name="L780"></a><tt class="py-lineno">780</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">code</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> <tt class="py-keyword">is</tt> <tt id="link-628" class="py-name"><a title="Martel.msre_constants.LITERAL
Martel.msre_parse.LITERAL" class="py-name" href="#" onclick="return doclink('link-628', 'LITERAL', 'link-8');">LITERAL</a></tt><tt class="py-op">:</tt> </tt>
<a name="L781"></a><tt class="py-lineno">781</tt> <tt class="py-line"> <tt class="py-name">literal</tt><tt class="py-op">(</tt><tt class="py-name">code</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L782"></a><tt class="py-lineno">782</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L783"></a><tt class="py-lineno">783</tt> <tt class="py-line"> <tt class="py-name">a</tt><tt class="py-op">(</tt><tt class="py-name">code</tt><tt class="py-op">)</tt> </tt>
<a name="L784"></a><tt class="py-lineno">784</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L785"></a><tt class="py-lineno">785</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L786"></a><tt class="py-lineno">786</tt> <tt class="py-line"> <tt class="py-name">this</tt> <tt class="py-op">=</tt> <tt class="py-name">char</tt><tt class="py-op">(</tt><tt id="link-629" class="py-name"><a title="Martel.msre_parse.ESCAPES" class="py-name" href="#" onclick="return doclink('link-629', 'ESCAPES', 'link-7');">ESCAPES</a></tt><tt class="py-op">[</tt><tt class="py-name">this</tt><tt class="py-op">]</tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt><tt class="py-op">)</tt> </tt>
<a name="L787"></a><tt class="py-lineno">787</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">KeyError</tt><tt class="py-op">:</tt> </tt>
<a name="L788"></a><tt class="py-lineno">788</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
<a name="L789"></a><tt class="py-lineno">789</tt> <tt class="py-line"> <tt class="py-name">literal</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">)</tt> </tt>
<a name="L790"></a><tt class="py-lineno">790</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L791"></a><tt class="py-lineno">791</tt> <tt class="py-line"> <tt class="py-name">literal</tt><tt class="py-op">(</tt><tt class="py-name">this</tt><tt class="py-op">)</tt> </tt>
<a name="L792"></a><tt class="py-lineno">792</tt> <tt class="py-line"> <tt class="py-comment"># convert template to groups and literals lists</tt> </tt>
<a name="L793"></a><tt class="py-lineno">793</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-630" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-630', 'i', 'link-74');">i</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L794"></a><tt class="py-lineno">794</tt> <tt class="py-line"> <tt id="link-631" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-631', 'groups', 'link-56');">groups</a></tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L795"></a><tt class="py-lineno">795</tt> <tt class="py-line"> <tt class="py-name">literals</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L796"></a><tt class="py-lineno">796</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt class="py-name">c</tt><tt class="py-op">,</tt> <tt id="link-632" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-632', 's', 'link-573');">s</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">p</tt><tt class="py-op">:</tt> </tt>
<a name="L797"></a><tt class="py-lineno">797</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">c</tt> <tt class="py-keyword">is</tt> <tt id="link-633" class="py-name"><a title="Martel.msre_constants.MARK
Martel.msre_parse.MARK" class="py-name" href="#" onclick="return doclink('link-633', 'MARK', 'link-604');">MARK</a></tt><tt class="py-op">:</tt> </tt>
<a name="L798"></a><tt class="py-lineno">798</tt> <tt class="py-line"> <tt id="link-634" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-634', 'groups', 'link-56');">groups</a></tt><tt class="py-op">.</tt><tt id="link-635" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-635', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-op">(</tt><tt id="link-636" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-636', 'i', 'link-74');">i</a></tt><tt class="py-op">,</tt> <tt id="link-637" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-637', 's', 'link-573');">s</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L799"></a><tt class="py-lineno">799</tt> <tt class="py-line"> <tt class="py-name">literals</tt><tt class="py-op">.</tt><tt id="link-638" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-638', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">)</tt> </tt>
<a name="L800"></a><tt class="py-lineno">800</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L801"></a><tt class="py-lineno">801</tt> <tt class="py-line"> <tt class="py-name">literals</tt><tt class="py-op">.</tt><tt id="link-639" class="py-name"><a title="Bio.Crystal.Chain.append
Bio.EUtils.POM.ElementNode.append
Bio.EUtils.sourcegen.SourceFile.append
Bio.SCOP.Raf.SeqMap.append
Bio.Seq.MutableSeq.append
Bio.Wise.psw.Alignment.append
Bio.Wise.psw.AlignmentColumn.append
Martel.msre_parse.SubPattern.append" class="py-name" href="#" onclick="return doclink('link-639', 'append', 'link-62');">append</a></tt><tt class="py-op">(</tt><tt id="link-640" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-640', 's', 'link-573');">s</a></tt><tt class="py-op">)</tt> </tt>
<a name="L802"></a><tt class="py-lineno">802</tt> <tt class="py-line"> <tt id="link-641" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-641', 'i', 'link-74');">i</a></tt> <tt class="py-op">=</tt> <tt id="link-642" class="py-name"><a title="Bio.PDB.Polypeptide.i" class="py-name" href="#" onclick="return doclink('link-642', 'i', 'link-74');">i</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L803"></a><tt class="py-lineno">803</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-643" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-643', 'groups', 'link-56');">groups</a></tt><tt class="py-op">,</tt> <tt class="py-name">literals</tt> </tt>
</div><a name="L804"></a><tt class="py-lineno">804</tt> <tt class="py-line"> </tt>
<a name="expand_template"></a><div id="expand_template-def"><a name="L805"></a><tt class="py-lineno">805</tt> <a class="py-toggle" href="#" id="expand_template-toggle" onclick="return toggle('expand_template');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.msre_parse-module.html#expand_template">expand_template</a><tt class="py-op">(</tt><tt class="py-param">template</tt><tt class="py-op">,</tt> <tt class="py-param">match</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="expand_template-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="expand_template-expanded"><a name="L806"></a><tt class="py-lineno">806</tt> <tt class="py-line"> <tt class="py-name">g</tt> <tt class="py-op">=</tt> <tt id="link-644" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-644', 'match', 'link-156');">match</a></tt><tt class="py-op">.</tt><tt id="link-645" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-645', 'group', 'link-254');">group</a></tt> </tt>
<a name="L807"></a><tt class="py-lineno">807</tt> <tt class="py-line"> <tt class="py-name">sep</tt> <tt class="py-op">=</tt> <tt id="link-646" class="py-name"><a title="Bio.Parsers.spark.GenericASTMatcher.match
Bio.Prosite.Pattern.Prosite.match
Bio.triefind.match
Martel.msre_parse.Tokenizer.match" class="py-name" href="#" onclick="return doclink('link-646', 'match', 'link-156');">match</a></tt><tt class="py-op">.</tt><tt class="py-name">string</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L808"></a><tt class="py-lineno">808</tt> <tt class="py-line"> <tt id="link-647" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-647', 'groups', 'link-56');">groups</a></tt><tt class="py-op">,</tt> <tt class="py-name">literals</tt> <tt class="py-op">=</tt> <tt class="py-name">template</tt> </tt>
<a name="L809"></a><tt class="py-lineno">809</tt> <tt class="py-line"> <tt class="py-name">literals</tt> <tt class="py-op">=</tt> <tt class="py-name">literals</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L810"></a><tt class="py-lineno">810</tt> <tt class="py-line"> <tt class="py-keyword">try</tt><tt class="py-op">:</tt> </tt>
<a name="L811"></a><tt class="py-lineno">811</tt> <tt class="py-line"> <tt class="py-keyword">for</tt> <tt id="link-648" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-648', 'index', 'link-87');">index</a></tt><tt class="py-op">,</tt> <tt id="link-649" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-649', 'group', 'link-254');">group</a></tt> <tt class="py-keyword">in</tt> <tt id="link-650" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.groups" class="py-name" href="#" onclick="return doclink('link-650', 'groups', 'link-56');">groups</a></tt><tt class="py-op">:</tt> </tt>
<a name="L812"></a><tt class="py-lineno">812</tt> <tt class="py-line"> <tt class="py-name">literals</tt><tt class="py-op">[</tt><tt id="link-651" class="py-name"><a title="Bio.Crystal.Chain.index
Bio.EUtils.POM.ElementNode.index
Bio.SCOP.Raf.SeqMap.index
Bio.Seq.MutableSeq.index" class="py-name" href="#" onclick="return doclink('link-651', 'index', 'link-87');">index</a></tt><tt class="py-op">]</tt> <tt class="py-op">=</tt> <tt id="link-652" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-652', 's', 'link-573');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">g</tt><tt class="py-op">(</tt><tt id="link-653" class="py-name"><a title="Bio.Prosite.Pattern.PrositeMatch.group" class="py-name" href="#" onclick="return doclink('link-653', 'group', 'link-254');">group</a></tt><tt class="py-op">)</tt> </tt>
<a name="L813"></a><tt class="py-lineno">813</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-654" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-654', 's', 'link-573');">s</a></tt> <tt class="py-keyword">is</tt> <tt class="py-name">None</tt><tt class="py-op">:</tt> </tt>
<a name="L814"></a><tt class="py-lineno">814</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">IndexError</tt> </tt>
<a name="L815"></a><tt class="py-lineno">815</tt> <tt class="py-line"> <tt class="py-keyword">except</tt> <tt class="py-name">IndexError</tt><tt class="py-op">:</tt> </tt>
<a name="L816"></a><tt class="py-lineno">816</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-655" class="py-name"><a title="Bio.Parsers.spark.GenericParser.error
Bio.Parsers.spark.GenericScanner.error
Martel.Iterator.StoreEvents.error
Martel.msre_constants.error
Martel.test.support.Dump.error
Martel.test.test_Parser.CountErrors.error
Martel.test.test_optimize.GetErrorPos.error" class="py-name" href="#" onclick="return doclink('link-655', 'error', 'link-134');">error</a></tt><tt class="py-op">,</tt> <tt class="py-string">"empty group"</tt> </tt>
<a name="L817"></a><tt class="py-lineno">817</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt class="py-name">join</tt><tt class="py-op">(</tt><tt class="py-name">literals</tt><tt class="py-op">,</tt> <tt class="py-name">sep</tt><tt class="py-op">)</tt> </tt>
</div><a name="L818"></a><tt class="py-lineno">818</tt> <tt class="py-line"> </tt><script type="text/javascript">
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