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<a href="Martel-module.html">Package Martel</a> ::
Module RecordReader
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<h1 class="epydoc">Source Code for <a href="Martel.RecordReader-module.html">Module Martel.RecordReader</a></h1>
<pre class="py-src">
<a name="L1"></a><tt class="py-lineno"> 1</tt> <tt class="py-line"><tt class="py-comment"># Copyright 2000-2001, Dalke Scientific Software, LLC</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"># Distributed under the Biopython License Agreement (see the LICENSE file).</tt> </tt>
<a name="L3"></a><tt class="py-lineno"> 3</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L4"></a><tt class="py-lineno"> 4</tt> <tt class="py-line"><tt class="py-comment"># The existing parsers are in-memory. For large data files, like</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"># swissprot, that requires too much memory.</tt> </tt>
<a name="L6"></a><tt class="py-lineno"> 6</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L7"></a><tt class="py-lineno"> 7</tt> <tt class="py-line"><tt class="py-comment"># On the other hand, the records aren't all that large (there's just a</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"># lot of them.) This module has readers which scan the input to get a</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"># record as a string.</tt> </tt>
<a name="L10"></a><tt class="py-lineno"> 10</tt> <tt class="py-line"><tt class="py-comment"></tt> </tt>
<a name="L11"></a><tt class="py-lineno"> 11</tt> <tt class="py-line"><tt class="py-keyword">import</tt> <tt class="py-name">string</tt> </tt>
<a name="L12"></a><tt class="py-lineno"> 12</tt> <tt class="py-line"><tt class="py-keyword">from</tt> <tt class="py-name">mx</tt> <tt class="py-keyword">import</tt> <tt class="py-name">TextTools</tt> <tt class="py-keyword">as</tt> <tt class="py-name">TT</tt> </tt>
<a name="L13"></a><tt class="py-lineno"> 13</tt> <tt class="py-line"> </tt>
<a name="L14"></a><tt class="py-lineno"> 14</tt> <tt class="py-line"><tt id="link-0" class="py-name" targets="Variable Martel.RecordReader.SIZEHINT=Martel.RecordReader-module.html#SIZEHINT"><a title="Martel.RecordReader.SIZEHINT" class="py-name" href="#" onclick="return doclink('link-0', 'SIZEHINT', 'link-0');">SIZEHINT</a></tt> <tt class="py-op">=</tt> <tt class="py-number">100000</tt> </tt>
<a name="L15"></a><tt class="py-lineno"> 15</tt> <tt class="py-line"> </tt>
<a name="ReaderError"></a><div id="ReaderError-def"><a name="L16"></a><tt class="py-lineno"> 16</tt> <a class="py-toggle" href="#" id="ReaderError-toggle" onclick="return toggle('ReaderError');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.RecordReader.ReaderError-class.html">ReaderError</a><tt class="py-op">(</tt><tt class="py-base-class">TypeError</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="ReaderError-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="ReaderError-expanded"><a name="L17"></a><tt class="py-lineno"> 17</tt> <tt class="py-line"> <tt class="py-keyword">pass</tt> </tt>
</div><a name="L18"></a><tt class="py-lineno"> 18</tt> <tt class="py-line"> </tt>
<a name="RecordReader"></a><div id="RecordReader-def"><a name="L19"></a><tt class="py-lineno"> 19</tt> <a class="py-toggle" href="#" id="RecordReader-toggle" onclick="return toggle('RecordReader');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.RecordReader.RecordReader-class.html">RecordReader</a><tt class="py-op">:</tt> </tt>
</div><div id="RecordReader-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="RecordReader-expanded"><a name="RecordReader.__init__"></a><div id="RecordReader.__init__-def"><a name="L20"></a><tt class="py-lineno"> 20</tt> <a class="py-toggle" href="#" id="RecordReader.__init__-toggle" onclick="return toggle('RecordReader.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.RecordReader-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">infile</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="RecordReader.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordReader.__init__-expanded"><a name="L21"></a><tt class="py-lineno"> 21</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt> <tt class="py-op">=</tt> <tt class="py-name">infile</tt> </tt>
</div><a name="RecordReader.next"></a><div id="RecordReader.next-def"><a name="L22"></a><tt class="py-lineno"> 22</tt> <a class="py-toggle" href="#" id="RecordReader.next-toggle" onclick="return toggle('RecordReader.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.RecordReader-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="RecordReader.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordReader.next-expanded"><a name="L23"></a><tt class="py-lineno"> 23</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt> </tt>
</div><a name="RecordReader.remainder"></a><div id="RecordReader.remainder-def"><a name="L24"></a><tt class="py-lineno"> 24</tt> <a class="py-toggle" href="#" id="RecordReader.remainder-toggle" onclick="return toggle('RecordReader.remainder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.RecordReader-class.html#remainder">remainder</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="RecordReader.remainder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="RecordReader.remainder-expanded"><a name="L25"></a><tt class="py-lineno"> 25</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt> </tt>
</div></div><a name="L26"></a><tt class="py-lineno"> 26</tt> <tt class="py-line"> </tt>
<a name="_startswith_tagtable_rest_of_line"></a><div id="_startswith_tagtable_rest_of_line-def"><a name="L27"></a><tt class="py-lineno"> 27</tt> <a class="py-toggle" href="#" id="_startswith_tagtable_rest_of_line-toggle" onclick="return toggle('_startswith_tagtable_rest_of_line');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader-module.html#_startswith_tagtable_rest_of_line">_startswith_tagtable_rest_of_line</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_startswith_tagtable_rest_of_line-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_startswith_tagtable_rest_of_line-expanded"><a name="L28"></a><tt class="py-lineno"> 28</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt> </tt>
<a name="L29"></a><tt class="py-lineno"> 29</tt> <tt class="py-line"> <tt class="py-comment"># Ensure the text starts with the given word</tt> </tt>
<a name="L30"></a><tt class="py-lineno"> 30</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"begin"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-1" class="py-name" targets="Function Martel.Word()=Martel-module.html#Word"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-1', 'Word', 'link-1');">Word</a></tt><tt class="py-op">,</tt> <tt id="link-2" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.text()=Bio.EUtils.POM.ElementNode-class.html#text,Method Bio.Prosite.Prodoc._RecordConsumer.text()=Bio.Prosite.Prodoc._RecordConsumer-class.html#text,Variable Martel.test.test_Iterator.text=Martel.test.test_Iterator-module.html#text,Variable Martel.test.test_ParseRecords.text=Martel.test.test_ParseRecords-module.html#text"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-2', 'text', 'link-2');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</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="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 class="py-comment"># Read to the end of line</tt> </tt>
<a name="L33"></a><tt class="py-lineno"> 33</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">invset</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</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>
<a name="L34"></a><tt class="py-lineno"> 34</tt> <tt class="py-line"> </tt>
<a name="L35"></a><tt class="py-lineno"> 35</tt> <tt class="py-line"> <tt class="py-comment"># Read the end of line</tt> </tt>
<a name="L36"></a><tt class="py-lineno"> 36</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># matches '\n' or</tt> </tt>
<a name="L37"></a><tt class="py-lineno"> 37</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">2</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-comment"># '\r' followed by</tt> </tt>
<a name="L38"></a><tt class="py-lineno"> 38</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">2</tt><tt class="py-op">,</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-comment"># optional '\n'</tt> </tt>
<a name="L39"></a><tt class="py-lineno"> 39</tt> <tt class="py-line"> </tt>
<a name="L40"></a><tt class="py-lineno"> 40</tt> <tt class="py-line"> <tt class="py-comment"># Check if EOF (allow EOF if no EOL found)</tt> </tt>
<a name="L41"></a><tt class="py-lineno"> 41</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</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-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</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>
<a name="L43"></a><tt class="py-lineno"> 43</tt> <tt class="py-line"> <tt class="py-comment"># Not EOF, so look for the next line starting with text</tt> </tt>
<a name="L44"></a><tt class="py-lineno"> 44</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"begin"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-3" class="py-name"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-3', 'Word', 'link-1');">Word</a></tt><tt class="py-op">,</tt> <tt id="link-4" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-4', 'text', 'link-2');">text</a></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">5</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>
<a name="L46"></a><tt class="py-lineno"> 46</tt> <tt class="py-line"> <tt class="py-comment"># Not what I am looking for, so read to the end of line</tt> </tt>
<a name="L47"></a><tt class="py-lineno"> 47</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">invset</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</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>
<a name="L48"></a><tt class="py-lineno"> 48</tt> <tt class="py-line"> </tt>
<a name="L49"></a><tt class="py-lineno"> 49</tt> <tt class="py-line"> <tt class="py-comment"># Read the end of line then test the next line</tt> </tt>
<a name="L50"></a><tt class="py-lineno"> 50</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</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-comment"># '\n'</tt> </tt>
<a name="L51"></a><tt class="py-lineno"> 51</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">2</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-comment"># '\r' followed by</tt> </tt>
<a name="L52"></a><tt class="py-lineno"> 52</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">4</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># optional '\n'</tt> </tt>
<a name="L53"></a><tt class="py-lineno"> 53</tt> <tt class="py-line"> <tt class="py-comment"># Allow termination at EOF</tt> </tt>
<a name="L54"></a><tt class="py-lineno"> 54</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</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-op">)</tt> </tt>
</div><a name="L56"></a><tt class="py-lineno"> 56</tt> <tt class="py-line"> </tt>
<a name="_startswith_tagtable_newline"></a><div id="_startswith_tagtable_newline-def"><a name="L57"></a><tt class="py-lineno"> 57</tt> <a class="py-toggle" href="#" id="_startswith_tagtable_newline-toggle" onclick="return toggle('_startswith_tagtable_newline');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader-module.html#_startswith_tagtable_newline">_startswith_tagtable_newline</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_startswith_tagtable_newline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_startswith_tagtable_newline-expanded"><a name="L58"></a><tt class="py-lineno"> 58</tt> <tt class="py-line"> <tt class="py-keyword">return</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"># Ensure the text starts with the given word ...</tt> </tt>
<a name="L60"></a><tt class="py-lineno"> 60</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"begin"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-5" class="py-name"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-5', 'Word', 'link-1');">Word</a></tt><tt class="py-op">,</tt> <tt id="link-6" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-6', 'text', 'link-2');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</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="L61"></a><tt class="py-lineno"> 61</tt> <tt class="py-line"> </tt>
<a name="L62"></a><tt class="py-lineno"> 62</tt> <tt class="py-line"> <tt class="py-comment"># ... followed by the end of line</tt> </tt>
<a name="L63"></a><tt class="py-lineno"> 63</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">+</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># matches '\n' or</tt> </tt>
<a name="L64"></a><tt class="py-lineno"> 64</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">2</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-comment"># '\r' followed by</tt> </tt>
<a name="L65"></a><tt class="py-lineno"> 65</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">2</tt><tt class="py-op">,</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-comment"># optional '\n'</tt> </tt>
<a name="L66"></a><tt class="py-lineno"> 66</tt> <tt class="py-line"> </tt>
<a name="L67"></a><tt class="py-lineno"> 67</tt> <tt class="py-line"> <tt class="py-comment"># Check if EOF instead of a newline (allow EOF if found)</tt> </tt>
<a name="L68"></a><tt class="py-lineno"> 68</tt> <tt class="py-line"> <tt class="py-comment"># Otherwise, this means the line starts with the text but</tt> </tt>
<a name="L69"></a><tt class="py-lineno"> 69</tt> <tt class="py-line"> <tt class="py-comment"># doesn't have a successive newline.</tt> </tt>
<a name="L70"></a><tt class="py-lineno"> 70</tt> <tt class="py-line"> <tt class="py-comment"># XXX BUG! When looking for "A\n" should not fail on "AA\n"!</tt> </tt>
<a name="L71"></a><tt class="py-lineno"> 71</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L72"></a><tt class="py-lineno"> 72</tt> <tt class="py-line"> </tt>
<a name="L73"></a><tt class="py-lineno"> 73</tt> <tt class="py-line"> <tt class="py-comment"># Look for the next line starting with text</tt> </tt>
<a name="L74"></a><tt class="py-lineno"> 74</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"begin"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-7" class="py-name"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-7', 'Word', 'link-1');">Word</a></tt><tt class="py-op">,</tt> <tt id="link-8" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-8', 'text', 'link-2');">text</a></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">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L75"></a><tt class="py-lineno"> 75</tt> <tt class="py-line"> </tt>
<a name="L76"></a><tt class="py-lineno"> 76</tt> <tt class="py-line"> <tt class="py-comment"># Not what I am looking for, so read to the end of line</tt> </tt>
<a name="L77"></a><tt class="py-lineno"> 77</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">invset</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</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>
<a name="L78"></a><tt class="py-lineno"> 78</tt> <tt class="py-line"> </tt>
<a name="L79"></a><tt class="py-lineno"> 79</tt> <tt class="py-line"> <tt class="py-comment"># Read the end of line then test the next line</tt> </tt>
<a name="L80"></a><tt class="py-lineno"> 80</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</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-comment"># '\n'</tt> </tt>
<a name="L81"></a><tt class="py-lineno"> 81</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">2</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-comment"># '\r' followed by</tt> </tt>
<a name="L82"></a><tt class="py-lineno"> 82</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">4</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># optional '\n'</tt> </tt>
<a name="L83"></a><tt class="py-lineno"> 83</tt> <tt class="py-line"> <tt class="py-comment"># Allow termination at EOF</tt> </tt>
<a name="L84"></a><tt class="py-lineno"> 84</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L85"></a><tt class="py-lineno"> 85</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L86"></a><tt class="py-lineno"> 86</tt> <tt class="py-line"> </tt>
<a name="L87"></a><tt class="py-lineno"> 87</tt> <tt class="py-line"> </tt>
<a name="_find_begin_positions"></a><div id="_find_begin_positions-def"><a name="L88"></a><tt class="py-lineno"> 88</tt> <a class="py-toggle" href="#" id="_find_begin_positions-toggle" onclick="return toggle('_find_begin_positions');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader-module.html#_find_begin_positions">_find_begin_positions</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">tagtable</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_find_begin_positions-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_find_begin_positions-expanded"><a name="L89"></a><tt class="py-lineno"> 89</tt> <tt class="py-line"> <tt class="py-name">success</tt><tt class="py-op">,</tt> <tt class="py-name">tags</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-9" class="py-name" targets="Variable Martel.Time.tag=Martel.Time-module.html#tag"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-9', 'tag', 'link-9');">tag</a></tt><tt class="py-op">(</tt><tt id="link-10" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-10', 'text', 'link-2');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">tagtable</tt><tt class="py-op">)</tt> </tt>
<a name="L90"></a><tt class="py-lineno"> 90</tt> <tt class="py-line"> <tt class="py-comment"># print "XXX", success, tags, pos, len(text)</tt> </tt>
<a name="L91"></a><tt class="py-lineno"> 91</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">success</tt><tt class="py-op">:</tt> </tt>
<a name="L92"></a><tt class="py-lineno"> 92</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-11" class="py-name" targets="Class Martel.RecordReader.ReaderError=Martel.RecordReader.ReaderError-class.html"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-11', 'ReaderError', 'link-11');">ReaderError</a></tt><tt class="py-op">(</tt><tt class="py-string">"invalid format starting with %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-12" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-12', 'text', 'link-2');">text</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">50</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L93"></a><tt class="py-lineno"> 93</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pos</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-13" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-13', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L94"></a><tt class="py-lineno"> 94</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-14" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-14', 'ReaderError', 'link-11');">ReaderError</a></tt><tt class="py-op">,</tt> \ </tt>
<a name="L95"></a><tt class="py-lineno"> 95</tt> <tt class="py-line"> <tt class="py-string">"could not parse to end of text (ended at %d of %d)"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L96"></a><tt class="py-lineno"> 96</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-15" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-15', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L97"></a><tt class="py-lineno"> 97</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">[</tt><tt id="link-16" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-16', 'tag', 'link-9');">tag</a></tt><tt class="py-op">[</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-17" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-17', 'tag', 'link-9');">tag</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">tags</tt><tt class="py-op">]</tt> </tt>
</div><a name="L98"></a><tt class="py-lineno"> 98</tt> <tt class="py-line"> </tt>
<a name="L99"></a><tt class="py-lineno"> 99</tt> <tt class="py-line"> </tt>
<a name="StartsWith"></a><div id="StartsWith-def"><a name="L100"></a><tt class="py-lineno">100</tt> <a class="py-toggle" href="#" id="StartsWith-toggle" onclick="return toggle('StartsWith');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.RecordReader.StartsWith-class.html">StartsWith</a><tt class="py-op">(</tt><tt class="py-base-class">RecordReader</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StartsWith-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="StartsWith-expanded"><a name="StartsWith.__init__"></a><div id="StartsWith.__init__-def"><a name="L101"></a><tt class="py-lineno">101</tt> <a class="py-toggle" href="#" id="StartsWith.__init__-toggle" onclick="return toggle('StartsWith.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.StartsWith-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">infile</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">sizehint</tt> <tt class="py-op">=</tt> <tt id="link-18" class="py-name"><a title="Martel.RecordReader.SIZEHINT" class="py-name" href="#" onclick="return doclink('link-18', 'SIZEHINT', 'link-0');">SIZEHINT</a></tt><tt class="py-op">,</tt> <tt class="py-param">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="StartsWith.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StartsWith.__init__-expanded"><a name="L102"></a><tt class="py-lineno">102</tt> <tt class="py-line"> <tt id="link-19" class="py-name" targets="Module Martel.RecordReader=Martel.RecordReader-module.html,Class Martel.RecordReader.RecordReader=Martel.RecordReader.RecordReader-class.html"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-19', 'RecordReader', 'link-19');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-20" class="py-name" targets="Method Bio.Affy.CelFile.CelConsumer.__init__()=Bio.Affy.CelFile.CelConsumer-class.html#__init__,Method Bio.Affy.CelFile.CelParser.__init__()=Bio.Affy.CelFile.CelParser-class.html#__init__,Method Bio.Affy.CelFile.CelRecord.__init__()=Bio.Affy.CelFile.CelRecord-class.html#__init__,Method Bio.Ais.Immune.__init__()=Bio.Ais.Immune-class.html#__init__,Method Bio.Ais.Lymphocyte.__init__()=Bio.Ais.Lymphocyte-class.html#__init__,Method Bio.Align.AlignInfo.PSSM.__init__()=Bio.Align.AlignInfo.PSSM-class.html#__init__,Method Bio.Align.AlignInfo.SummaryInfo.__init__()=Bio.Align.AlignInfo.SummaryInfo-class.html#__init__,Method Bio.Align.FormatConvert.FormatConverter.__init__()=Bio.Align.FormatConvert.FormatConverter-class.html#__init__,Method Bio.Align.Generic.Alignment.__init__()=Bio.Align.Generic.Alignment-class.html#__init__,Method Bio.AlignAce.Applications.AlignAceCommandline.__init__()=Bio.AlignAce.Applications.AlignAceCommandline-class.html#__init__,Method Bio.AlignAce.Applications.CompareAceCommandline.__init__()=Bio.AlignAce.Applications.CompareAceCommandline-class.html#__init__,Method Bio.AlignAce.Motif.Motif.__init__()=Bio.AlignAce.Motif.Motif-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceConsumer.__init__()=Bio.AlignAce.Parser.AlignAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.AlignAceParser.__init__()=Bio.AlignAce.Parser.AlignAceParser-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceConsumer.__init__()=Bio.AlignAce.Parser.CompareAceConsumer-class.html#__init__,Method Bio.AlignAce.Parser.CompareAceParser.__init__()=Bio.AlignAce.Parser.CompareAceParser-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentIterator.__init__()=Bio.AlignIO.Interfaces.AlignmentIterator-class.html#__init__,Method Bio.AlignIO.Interfaces.AlignmentWriter.__init__()=Bio.AlignIO.Interfaces.AlignmentWriter-class.html#__init__,Method Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__()=Bio.AlignIO.Interfaces.SequentialAlignmentWriter-class.html#__init__,Method Bio.Alphabet.AlphabetEncoder.__init__()=Bio.Alphabet.AlphabetEncoder-class.html#__init__,Method Bio.Alphabet.Gapped.__init__()=Bio.Alphabet.Gapped-class.html#__init__,Method Bio.Alphabet.HasStopCodon.__init__()=Bio.Alphabet.HasStopCodon-class.html#__init__,Method Bio.Application.AbstractCommandline.__init__()=Bio.Application.AbstractCommandline-class.html#__init__,Method Bio.Application.ApplicationResult.__init__()=Bio.Application.ApplicationResult-class.html#__init__,Method Bio.Application._AbstractParameter.__init__()=Bio.Application._AbstractParameter-class.html#__init__,Method Bio.Blast.Applications.BlastallCommandline.__init__()=Bio.Blast.Applications.BlastallCommandline-class.html#__init__,Method Bio.Blast.Applications.FastacmdCommandline.__init__()=Bio.Blast.Applications.FastacmdCommandline-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastErrorParser.__init__()=Bio.Blast.NCBIStandalone.BlastErrorParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.BlastParser.__init__()=Bio.Blast.NCBIStandalone.BlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone.Iterator.__init__()=Bio.Blast.NCBIStandalone.Iterator-class.html#__init__,Method Bio.Blast.NCBIStandalone.PSIBlastParser.__init__()=Bio.Blast.NCBIStandalone.PSIBlastParser-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastConsumer-class.html#__init__,Method Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__()=Bio.Blast.NCBIStandalone._BlastErrorConsumer-class.html#__init__,Method 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Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-20', '__init__', 'link-20');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">infile</tt><tt class="py-op">)</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 id="link-21" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-21', 'text', 'link-2');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-22" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-22', 'text', 'link-2');">text</a></tt> </tt>
<a name="L104"></a><tt class="py-lineno">104</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-name">sizehint</tt> </tt>
<a name="L105"></a><tt class="py-lineno">105</tt> <tt class="py-line"> </tt>
<a name="L106"></a><tt class="py-lineno">106</tt> <tt class="py-line"> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-23" class="py-name" targets="Method Bio.EUtils.POM.ElementNode.find()=Bio.EUtils.POM.ElementNode-class.html#find,Method Bio.NeuralNetwork.Gene.Motif.MotifFinder.find()=Bio.NeuralNetwork.Gene.Motif.MotifFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find()=Bio.NeuralNetwork.Gene.Schema.SchemaFinder-class.html#find,Method Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find()=Bio.NeuralNetwork.Gene.Signature.SignatureFinder-class.html#find,Method Bio.biblio.Biblio.find()=Bio.biblio.Biblio-class.html#find,Function Bio.triefind.find()=Bio.triefind-module.html#find"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-23', 'find', 'link-23');">find</a></tt><tt class="py-op">(</tt><tt id="link-24" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-24', 'text', 'link-2');">text</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</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">if</tt> <tt class="py-name">pos</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="L108"></a><tt class="py-lineno">108</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pos</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-25" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-25', 'text', 'link-2');">text</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="L109"></a><tt class="py-lineno">109</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"'\\n' can only exist at the end of the string"</tt> </tt>
<a name="L110"></a><tt class="py-lineno">110</tt> <tt class="py-line"> <tt id="link-26" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-26', 'text', 'link-2');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-27" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-27', 'text', 'link-2');">text</a></tt><tt class="py-op">[</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="L111"></a><tt class="py-lineno">111</tt> <tt class="py-line"> <tt class="py-name">has_newline</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L112"></a><tt class="py-lineno">112</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L113"></a><tt class="py-lineno">113</tt> <tt class="py-line"> <tt class="py-name">has_newline</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L114"></a><tt class="py-lineno">114</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-28" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-28', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"StartsWith text size is too short"</tt> </tt>
<a name="L115"></a><tt class="py-lineno">115</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-29" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-29', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">sizehint</tt> <tt class="py-op">-</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> \ </tt>
<a name="L116"></a><tt class="py-lineno">116</tt> <tt class="py-line"> <tt class="py-string">"StartsWith text size larger than sizehint allows"</tt> </tt>
<a name="L117"></a><tt class="py-lineno">117</tt> <tt class="py-line"> </tt>
<a name="L118"></a><tt class="py-lineno">118</tt> <tt class="py-line"> </tt>
<a name="L119"></a><tt class="py-lineno">119</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">has_newline</tt><tt class="py-op">:</tt> </tt>
<a name="L120"></a><tt class="py-lineno">120</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"there's a bug in the '\\n' option"</tt> </tt>
<a name="L121"></a><tt class="py-lineno">121</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt> <tt class="py-op">=</tt> <tt id="link-30" class="py-name" targets="Function Martel.RecordReader._startswith_tagtable_newline()=Martel.RecordReader-module.html#_startswith_tagtable_newline"><a title="Martel.RecordReader._startswith_tagtable_newline" class="py-name" href="#" onclick="return doclink('link-30', '_startswith_tagtable_newline', 'link-30');">_startswith_tagtable_newline</a></tt><tt class="py-op">(</tt><tt id="link-31" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-31', 'text', 'link-2');">text</a></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">else</tt><tt class="py-op">:</tt> </tt>
<a name="L123"></a><tt class="py-lineno">123</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt> <tt class="py-op">=</tt> <tt id="link-32" class="py-name" targets="Function Martel.RecordReader._startswith_tagtable_rest_of_line()=Martel.RecordReader-module.html#_startswith_tagtable_rest_of_line"><a title="Martel.RecordReader._startswith_tagtable_rest_of_line" class="py-name" href="#" onclick="return doclink('link-32', '_startswith_tagtable_rest_of_line', 'link-32');">_startswith_tagtable_rest_of_line</a></tt><tt class="py-op">(</tt><tt id="link-33" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-33', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L124"></a><tt class="py-lineno">124</tt> <tt class="py-line"> </tt>
<a name="L125"></a><tt class="py-lineno">125</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L126"></a><tt class="py-lineno">126</tt> <tt class="py-line"> </tt>
<a name="L127"></a><tt class="py-lineno">127</tt> <tt class="py-line"> <tt class="py-comment"># Start parsing here. This guarantees the first line is in</tt> </tt>
<a name="L128"></a><tt class="py-lineno">128</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># the right format.</tt> </tt>
<a name="L129"></a><tt class="py-lineno">129</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 class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-34" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-34', 'text', 'link-2');">text</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="L130"></a><tt class="py-lineno">130</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">+=</tt> <tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-35" class="py-name" targets="Method Bio.AlignAce.Motif.Motif.read()=Bio.AlignAce.Motif.Motif-class.html#read,Function Bio.AlignIO.read()=Bio.AlignIO-module.html#read,Function Bio.Cluster.read()=Bio.Cluster-module.html#read,Method Bio.EUtils.ReseekFile.ReseekFile.read()=Bio.EUtils.ReseekFile.ReseekFile-class.html#read,Function Bio.Entrez.read()=Bio.Entrez-module.html#read,Method Bio.File.SGMLHandle.read()=Bio.File.SGMLHandle-class.html#read,Method Bio.File.UndoHandle.read()=Bio.File.UndoHandle-class.html#read,Method Bio.FilteredReader.FilteredReader.read()=Bio.FilteredReader.FilteredReader-class.html#read,Method Bio.NeuralNetwork.Gene.Pattern.PatternIO.read()=Bio.NeuralNetwork.Gene.Pattern.PatternIO-class.html#read,Method Bio.Nexus.Nexus.Nexus.read()=Bio.Nexus.Nexus.Nexus-class.html#read,Function Bio.Prosite.Prodoc.read()=Bio.Prosite.Prodoc-module.html#read,Function Bio.Prosite.read()=Bio.Prosite-module.html#read,Method Bio.SGMLExtractor.SGMLExtractorHandle.read()=Bio.SGMLExtractor.SGMLExtractorHandle-class.html#read,Function Bio.SeqIO.read()=Bio.SeqIO-module.html#read,Function Bio.SwissProt.read()=Bio.SwissProt-module.html#read"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-35', 'read', 'link-35');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">sizehint</tt><tt class="py-op">)</tt> </tt>
<a name="L131"></a><tt class="py-lineno">131</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">:</tt> </tt>
<a name="L132"></a><tt class="py-lineno">132</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt id="link-36" class="py-name" targets="Function Martel.RecordReader._find_begin_positions()=Martel.RecordReader-module.html#_find_begin_positions"><a title="Martel.RecordReader._find_begin_positions" class="py-name" href="#" onclick="return doclink('link-36', '_find_begin_positions', 'link-36');">_find_begin_positions</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">,</tt> </tt>
<a name="L133"></a><tt class="py-lineno">133</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">)</tt> </tt>
<a name="L134"></a><tt class="py-lineno">134</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L135"></a><tt class="py-lineno">135</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</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="L136"></a><tt class="py-lineno">136</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-37" 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-37', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L137"></a><tt class="py-lineno">137</tt> <tt class="py-line"> </tt>
<a name="StartsWith.next"></a><div id="StartsWith.next-def"><a name="L138"></a><tt class="py-lineno">138</tt> <a class="py-toggle" href="#" id="StartsWith.next-toggle" onclick="return toggle('StartsWith.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.StartsWith-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="StartsWith.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StartsWith.next-expanded"><a name="L139"></a><tt class="py-lineno">139</tt> <tt class="py-line"> <tt class="py-comment"># Are any precomputed positions remaining?</tt> </tt>
<a name="L140"></a><tt class="py-lineno">140</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 id="link-38" 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-38', 'index', 'link-37');">index</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</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">positions</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L141"></a><tt class="py-lineno">141</tt> <tt class="py-line"> <tt class="py-comment"># Yes, so return the text in the range</tt> </tt>
<a name="L142"></a><tt class="py-lineno">142</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt id="link-39" 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-39', 's', 'link-39');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-40" 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-40', 'index', 'link-37');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt> </tt>
<a name="L143"></a><tt class="py-lineno">143</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-41" 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-41', 'index', 'link-37');">index</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="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-42" 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-42', 'index', 'link-37');">index</a></tt> <tt class="py-op">+=</tt> <tt class="py-number">1</tt> </tt>
<a name="L145"></a><tt class="py-lineno">145</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-43" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-43', 's', 'link-39');">s</a></tt> </tt>
<a name="L146"></a><tt class="py-lineno">146</tt> <tt class="py-line"> </tt>
<a name="L147"></a><tt class="py-lineno">147</tt> <tt class="py-line"> <tt class="py-comment"># The last record may be incomplete, so reset the</tt> </tt>
<a name="L148"></a><tt class="py-lineno">148</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># lookahead to be just that text</tt> </tt>
<a name="L149"></a><tt class="py-lineno">149</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</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="L150"></a><tt class="py-lineno">150</tt> <tt class="py-line"> </tt>
<a name="L151"></a><tt class="py-lineno">151</tt> <tt class="py-line"> <tt class="py-comment"># Read past at least the start of the second record or to the</tt> </tt>
<a name="L152"></a><tt class="py-lineno">152</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># end of file.</tt> </tt>
<a name="L153"></a><tt class="py-lineno">153</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</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="L154"></a><tt class="py-lineno">154</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="L155"></a><tt class="py-lineno">155</tt> <tt class="py-line"> <tt id="link-44" 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-44', 'data', 'link-44');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-45" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-45', 'read', 'link-35');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</tt><tt class="py-op">)</tt> </tt>
<a name="L156"></a><tt class="py-lineno">156</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-46" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-46', 'data', 'link-44');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L157"></a><tt class="py-lineno">157</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L158"></a><tt class="py-lineno">158</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">+</tt> <tt id="link-47" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-47', 'data', 'link-44');">data</a></tt> </tt>
<a name="L159"></a><tt class="py-lineno">159</tt> <tt class="py-line"> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt id="link-48" class="py-name"><a title="Martel.RecordReader._find_begin_positions" class="py-name" href="#" onclick="return doclink('link-48', '_find_begin_positions', 'link-36');">_find_begin_positions</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt><tt class="py-op">)</tt> </tt>
<a name="L160"></a><tt class="py-lineno">160</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</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="L161"></a><tt class="py-lineno">161</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L162"></a><tt class="py-lineno">162</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</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="L163"></a><tt class="py-lineno">163</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-name">positions</tt> </tt>
<a name="L164"></a><tt class="py-lineno">164</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-49" 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-49', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L165"></a><tt class="py-lineno">165</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">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">positions</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-name">positions</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="L166"></a><tt class="py-lineno">166</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">:</tt> </tt>
<a name="L167"></a><tt class="py-lineno">167</tt> <tt class="py-line"> <tt class="py-comment"># No data (either empty file or at EOF)</tt> </tt>
<a name="L168"></a><tt class="py-lineno">168</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</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="L169"></a><tt class="py-lineno">169</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-50" 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-50', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L170"></a><tt class="py-lineno">170</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L171"></a><tt class="py-lineno">171</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L172"></a><tt class="py-lineno">172</tt> <tt class="py-line"> <tt class="py-comment"># Read to the end of file and it's the last record</tt> </tt>
<a name="L173"></a><tt class="py-lineno">173</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt> <tt class="py-op">==</tt> <tt class="py-number">1</tt> </tt>
<a name="L174"></a><tt class="py-lineno">174</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</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="L175"></a><tt class="py-lineno">175</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-51" 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-51', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L176"></a><tt class="py-lineno">176</tt> <tt class="py-line"> <tt id="link-52" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-52', 's', 'link-39');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> </tt>
<a name="L177"></a><tt class="py-lineno">177</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L178"></a><tt class="py-lineno">178</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-53" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-53', 's', 'link-39');">s</a></tt> </tt>
</div><a name="L179"></a><tt class="py-lineno">179</tt> <tt class="py-line"> </tt>
<a name="StartsWith.remainder"></a><div id="StartsWith.remainder-def"><a name="L180"></a><tt class="py-lineno">180</tt> <a class="py-toggle" href="#" id="StartsWith.remainder-toggle" onclick="return toggle('StartsWith.remainder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.StartsWith-class.html#remainder">remainder</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="StartsWith.remainder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="StartsWith.remainder-expanded"><a name="L181"></a><tt class="py-lineno">181</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">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-54" 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-54', 'index', 'link-37');">index</a></tt><tt class="py-op">]</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L182"></a><tt class="py-lineno">182</tt> <tt class="py-line"> </tt>
<a name="_endswith_tagtable_newline"></a><div id="_endswith_tagtable_newline-def"><a name="L183"></a><tt class="py-lineno">183</tt> <a class="py-toggle" href="#" id="_endswith_tagtable_newline-toggle" onclick="return toggle('_endswith_tagtable_newline');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader-module.html#_endswith_tagtable_newline">_endswith_tagtable_newline</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_endswith_tagtable_newline-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_endswith_tagtable_newline-expanded"><a name="L184"></a><tt class="py-lineno">184</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt> </tt>
<a name="L185"></a><tt class="py-lineno">185</tt> <tt class="py-line"> <tt class="py-comment"># Is the current line the end of record marker?</tt> </tt>
<a name="L186"></a><tt class="py-lineno">186</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-55" class="py-name"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-55', 'Word', 'link-1');">Word</a></tt><tt class="py-op">,</tt> <tt id="link-56" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-56', 'text', 'link-2');">text</a></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-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L187"></a><tt class="py-lineno">187</tt> <tt class="py-line"> </tt>
<a name="L188"></a><tt class="py-lineno">188</tt> <tt class="py-line"> <tt class="py-comment"># Make sure it ends the line</tt> </tt>
<a name="L189"></a><tt class="py-lineno">189</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-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-comment"># matches '\n'</tt> </tt>
<a name="L190"></a><tt class="py-lineno">190</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">4</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="L191"></a><tt class="py-lineno">191</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L192"></a><tt class="py-lineno">192</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Skip</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-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L193"></a><tt class="py-lineno">193</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Skip</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">5</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L194"></a><tt class="py-lineno">194</tt> <tt class="py-line"> </tt>
<a name="L195"></a><tt class="py-lineno">195</tt> <tt class="py-line"> <tt class="py-comment"># Not the end of record marker, so read to the end of line</tt> </tt>
<a name="L196"></a><tt class="py-lineno">196</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">invset</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</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>
<a name="L197"></a><tt class="py-lineno">197</tt> <tt class="py-line"> </tt>
<a name="L198"></a><tt class="py-lineno">198</tt> <tt class="py-line"> <tt class="py-comment"># Check if EOF</tt> </tt>
<a name="L199"></a><tt class="py-lineno">199</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</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-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L200"></a><tt class="py-lineno">200</tt> <tt class="py-line"> </tt>
<a name="L201"></a><tt class="py-lineno">201</tt> <tt class="py-line"> <tt class="py-comment"># Not EOF, so scarf any newlines</tt> </tt>
<a name="L202"></a><tt class="py-lineno">202</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-57" 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-57', 'set', 'link-57');">set</a></tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</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>
<a name="L203"></a><tt class="py-lineno">203</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L204"></a><tt class="py-lineno">204</tt> <tt class="py-line"> </tt>
<a name="_endswith_tagtable_rest_of_line"></a><div id="_endswith_tagtable_rest_of_line-def"><a name="L205"></a><tt class="py-lineno">205</tt> <a class="py-toggle" href="#" id="_endswith_tagtable_rest_of_line-toggle" onclick="return toggle('_endswith_tagtable_rest_of_line');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader-module.html#_endswith_tagtable_rest_of_line">_endswith_tagtable_rest_of_line</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_endswith_tagtable_rest_of_line-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_endswith_tagtable_rest_of_line-expanded"><a name="L206"></a><tt class="py-lineno">206</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-op">(</tt> </tt>
<a name="L207"></a><tt class="py-lineno">207</tt> <tt class="py-line"> <tt class="py-comment"># Is the current line the end of record marker?</tt> </tt>
<a name="L208"></a><tt class="py-lineno">208</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-58" class="py-name"><a title="Martel.Word" class="py-name" href="#" onclick="return doclink('link-58', 'Word', 'link-1');">Word</a></tt><tt class="py-op">,</tt> <tt id="link-59" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-59', 'text', 'link-2');">text</a></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">1</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>
<a name="L210"></a><tt class="py-lineno">210</tt> <tt class="py-line"> <tt class="py-comment"># Read whatever else is on that line (could be nothing)</tt> </tt>
<a name="L211"></a><tt class="py-lineno">211</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">invset</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</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>
<a name="L212"></a><tt class="py-lineno">212</tt> <tt class="py-line"> </tt>
<a name="L213"></a><tt class="py-lineno">213</tt> <tt class="py-line"> <tt class="py-comment"># Get the end of line</tt> </tt>
<a name="L214"></a><tt class="py-lineno">214</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</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-comment"># matches '\n'</tt> </tt>
<a name="L215"></a><tt class="py-lineno">215</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">4</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="L216"></a><tt class="py-lineno">216</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L217"></a><tt class="py-lineno">217</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Skip</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-number">1</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L218"></a><tt class="py-lineno">218</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Skip</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">6</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>
<a name="L219"></a><tt class="py-lineno">219</tt> <tt class="py-line"> </tt>
<a name="L220"></a><tt class="py-lineno">220</tt> <tt class="py-line"> <tt class="py-comment"># Check if EOF (only tests when the end of record line has no \n)</tt> </tt>
<a name="L221"></a><tt class="py-lineno">221</tt> <tt class="py-line"> <tt class="py-comment"># Only time this should fail is with a bug in TT.</tt> </tt>
<a name="L222"></a><tt class="py-lineno">222</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"end"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L223"></a><tt class="py-lineno">223</tt> <tt class="py-line"> </tt>
<a name="L224"></a><tt class="py-lineno">224</tt> <tt class="py-line"> <tt class="py-comment"># Not the end of record marker, so read to the end of line</tt> </tt>
<a name="L225"></a><tt class="py-lineno">225</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">invset</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</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>
<a name="L226"></a><tt class="py-lineno">226</tt> <tt class="py-line"> </tt>
<a name="L227"></a><tt class="py-lineno">227</tt> <tt class="py-line"> <tt class="py-comment"># Check if EOF</tt> </tt>
<a name="L228"></a><tt class="py-lineno">228</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</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-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L229"></a><tt class="py-lineno">229</tt> <tt class="py-line"> </tt>
<a name="L230"></a><tt class="py-lineno">230</tt> <tt class="py-line"> <tt class="py-comment"># Not EOF, so scarf any newlines and try again</tt> </tt>
<a name="L231"></a><tt class="py-lineno">231</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-60" 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-60', 'set', 'link-57');">set</a></tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchFail</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">10</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> </tt>
<a name="L232"></a><tt class="py-lineno">232</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
</div><a name="L233"></a><tt class="py-lineno">233</tt> <tt class="py-line"> </tt>
<a name="L234"></a><tt class="py-lineno">234</tt> <tt class="py-line"> </tt>
<a name="_find_end_positions"></a><div id="_find_end_positions-def"><a name="L235"></a><tt class="py-lineno">235</tt> <a class="py-toggle" href="#" id="_find_end_positions-toggle" onclick="return toggle('_find_end_positions');">-</a><tt class="py-line"><tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader-module.html#_find_end_positions">_find_end_positions</a><tt class="py-op">(</tt><tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">tagtable</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="_find_end_positions-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="_find_end_positions-expanded"><a name="L236"></a><tt class="py-lineno">236</tt> <tt class="py-line"> <tt class="py-name">success</tt><tt class="py-op">,</tt> <tt class="py-name">tags</tt><tt class="py-op">,</tt> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt id="link-61" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-61', 'tag', 'link-9');">tag</a></tt><tt class="py-op">(</tt><tt id="link-62" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-62', 'text', 'link-2');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">tagtable</tt><tt class="py-op">)</tt> </tt>
<a name="L237"></a><tt class="py-lineno">237</tt> <tt class="py-line"> <tt class="py-comment">#print "XXX", success, tags, pos, len(text), repr(text)</tt> </tt>
<a name="L238"></a><tt class="py-lineno">238</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">success</tt><tt class="py-op">:</tt> </tt>
<a name="L239"></a><tt class="py-lineno">239</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-63" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-63', 'ReaderError', 'link-11');">ReaderError</a></tt><tt class="py-op">(</tt><tt class="py-string">"invalid format starting with %s"</tt> <tt class="py-op">%</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt id="link-64" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-64', 'text', 'link-2');">text</a></tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">50</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L240"></a><tt class="py-lineno">240</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pos</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-65" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-65', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L241"></a><tt class="py-lineno">241</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-66" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-66', 'ReaderError', 'link-11');">ReaderError</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-string">"could not parse to end of text (ended at %d of %d)"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L243"></a><tt class="py-lineno">243</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-67" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-67', 'text', 'link-2');">text</a></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-op">[</tt><tt id="link-68" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-68', 'tag', 'link-9');">tag</a></tt><tt class="py-op">[</tt><tt class="py-number">2</tt><tt class="py-op">]</tt> <tt class="py-keyword">for</tt> <tt id="link-69" class="py-name"><a title="Martel.Time.tag" class="py-name" href="#" onclick="return doclink('link-69', 'tag', 'link-9');">tag</a></tt> <tt class="py-keyword">in</tt> <tt class="py-name">tags</tt><tt class="py-op">]</tt> </tt>
</div><a name="L245"></a><tt class="py-lineno">245</tt> <tt class="py-line"> </tt>
<a name="EndsWith"></a><div id="EndsWith-def"><a name="L246"></a><tt class="py-lineno">246</tt> <a class="py-toggle" href="#" id="EndsWith-toggle" onclick="return toggle('EndsWith');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.RecordReader.EndsWith-class.html">EndsWith</a><tt class="py-op">(</tt><tt class="py-base-class">RecordReader</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="EndsWith-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="EndsWith-expanded"><a name="EndsWith.__init__"></a><div id="EndsWith.__init__-def"><a name="L247"></a><tt class="py-lineno">247</tt> <a class="py-toggle" href="#" id="EndsWith.__init__-toggle" onclick="return toggle('EndsWith.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.EndsWith-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">infile</tt><tt class="py-op">,</tt> <tt class="py-param">text</tt><tt class="py-op">,</tt> <tt class="py-param">sizehint</tt> <tt class="py-op">=</tt> <tt id="link-70" class="py-name"><a title="Martel.RecordReader.SIZEHINT" class="py-name" href="#" onclick="return doclink('link-70', 'SIZEHINT', 'link-0');">SIZEHINT</a></tt><tt class="py-op">,</tt> <tt class="py-param">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="EndsWith.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EndsWith.__init__-expanded"><a name="L248"></a><tt class="py-lineno">248</tt> <tt class="py-line"> <tt id="link-71" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-71', 'RecordReader', 'link-19');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-72" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
Bio.GA.Mutation.Simple.SinglePositionMutation.__init__
Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
Bio.GFF.easy.LocationFromString.__init__
Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
Bio.Gobase.RecordParser.__init__
Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
Bio.MEME.Parser.MASTRecord.__init__
Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
Bio.MetaTool._Scanner.__init__
Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
Bio.Mindy.BerkeleyDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.BaseFlatDB.__init__
Bio.Mindy.FlatDB.BisectFile.__init__
Bio.Mindy.FlatDB.DiskFlatDB.__init__
Bio.Mindy.FlatDB.MemoryFlatDB.__init__
Bio.Mindy.FlatDB.PrimaryNamespace.__init__
Bio.Mindy.FlatDB.PrimaryTable.__init__
Bio.Mindy.FlatDB.SecondaryNamespace.__init__
Bio.Mindy.FlatDB.SecondaryTable.__init__
Bio.Mindy.Location.Location.__init__
Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
Bio.Mindy.SimpleSeqRecord.FunctionIndexer.__init__
Bio.Mindy.SimpleSeqRecord.SimpleIndexer.__init__
Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
Bio.NBRF.RecordParser.__init__
Bio.NBRF._RecordConsumer.__init__
Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
Bio.NetCatch.NetCatch.__init__
Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.HiddenLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.InputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Layer.OutputLayer.__init__
Bio.NeuralNetwork.BackPropagation.Network.BasicNetwork.__init__
Bio.NeuralNetwork.Gene.Motif.MotifCoder.__init__
Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.RandomMotifGenerator.__init__
Bio.NeuralNetwork.Gene.Schema.Schema.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFactory.__init__
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.__init__
Bio.NeuralNetwork.Gene.Schema.SimpleFinisher.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.__init__
Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
Bio.NeuralNetwork.Training.ExampleManager.__init__
Bio.NeuralNetwork.Training.TrainingExample.__init__
Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
Bio.Nexus.Nexus.Nexus.__init__
Bio.Nexus.Nexus.StepMatrix.__init__
Bio.Nexus.Nodes.Chain.__init__
Bio.Nexus.Nodes.Node.__init__
Bio.Nexus.Trees.NodeData.__init__
Bio.Nexus.Trees.Tree.__init__
Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractResiduePropertyMap.__init__
Bio.PDB.Atom.Atom.__init__
Bio.PDB.Atom.DisorderedAtom.__init__
Bio.PDB.Chain.Chain.__init__
Bio.PDB.DSSP'.DSSP.__init__
Bio.PDB.Dice.ChainSelector.__init__
Bio.PDB.Entity.DisorderedEntityWrapper.__init__
Bio.PDB.Entity.Entity.__init__
Bio.PDB.FragmentMapper'.Fragment.__init__
Bio.PDB.FragmentMapper'.FragmentMapper.__init__
Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
Bio.PDB.HSExposure.HSExposureCB.__init__
Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
Bio.PDB.NACCESS.NACCESS_atomic.__init__
Bio.PDB.NeighborSearch.NeighborSearch.__init__
Bio.PDB.PDBIO'.PDBIO.__init__
Bio.PDB.PDBList'.PDBList.__init__
Bio.PDB.PDBParser'.PDBParser.__init__
Bio.PDB.PSEA.PSEA.__init__
Bio.PDB.Polypeptide.CaPPBuilder.__init__
Bio.PDB.Polypeptide.PPBuilder.__init__
Bio.PDB.Polypeptide._PPBuilder.__init__
Bio.PDB.Residue.DisorderedResidue.__init__
Bio.PDB.Residue.Residue.__init__
Bio.PDB.ResidueDepth'.ResidueDepth.__init__
Bio.PDB.Structure.Structure.__init__
Bio.PDB.StructureAlignment'.StructureAlignment.__init__
Bio.PDB.StructureBuilder.StructureBuilder.__init__
Bio.PDB.Superimposer'.Superimposer.__init__
Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
Bio.ParserSupport.SGMLStrippingConsumer.__init__
Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
Bio.Parsers.spark.GenericParser.__init__
Bio.Parsers.spark.GenericScanner.__init__
Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
Bio.Pathway.Rep.Graph.Graph.__init__
Bio.Pathway.Rep.HashSet.HashSet.__init__
Bio.Pathway.Rep.MultiGraph.MultiGraph.__init__
Bio.Pathway.System.__init__
Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
Bio.PopGen.Async.FileRetriever.__init__
Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
Bio.PopGen.FDist.Async.SplitFDist.__init__
Bio.PopGen.FDist.Controller.FDistController.__init__
Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-72', '__init__', 'link-20');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L249"></a><tt class="py-lineno">249</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-73" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-73', 'text', 'link-2');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-74" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-74', 'text', 'link-2');">text</a></tt> </tt>
<a name="L250"></a><tt class="py-lineno">250</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-name">sizehint</tt> </tt>
<a name="L251"></a><tt class="py-lineno">251</tt> <tt class="py-line"> </tt>
<a name="L252"></a><tt class="py-lineno">252</tt> <tt class="py-line"> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">string</tt><tt class="py-op">.</tt><tt id="link-75" class="py-name"><a title="Bio.EUtils.POM.ElementNode.find
Bio.NeuralNetwork.Gene.Motif.MotifFinder.find
Bio.NeuralNetwork.Gene.Schema.SchemaFinder.find
Bio.NeuralNetwork.Gene.Signature.SignatureFinder.find
Bio.biblio.Biblio.find
Bio.triefind.find" class="py-name" href="#" onclick="return doclink('link-75', 'find', 'link-23');">find</a></tt><tt class="py-op">(</tt><tt id="link-76" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-76', 'text', 'link-2');">text</a></tt><tt class="py-op">,</tt> <tt class="py-string">"\n"</tt><tt class="py-op">)</tt> </tt>
<a name="L253"></a><tt class="py-lineno">253</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pos</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="L254"></a><tt class="py-lineno">254</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">pos</tt> <tt class="py-op">!=</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-77" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-77', 'text', 'link-2');">text</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="L255"></a><tt class="py-lineno">255</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"'\\n' can only exist at the end of the string"</tt> </tt>
<a name="L256"></a><tt class="py-lineno">256</tt> <tt class="py-line"> <tt id="link-78" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-78', 'text', 'link-2');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-79" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-79', 'text', 'link-2');">text</a></tt><tt class="py-op">[</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="L257"></a><tt class="py-lineno">257</tt> <tt class="py-line"> <tt class="py-name">has_newline</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L258"></a><tt class="py-lineno">258</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L259"></a><tt class="py-lineno">259</tt> <tt class="py-line"> <tt class="py-name">has_newline</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L260"></a><tt class="py-lineno">260</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt id="link-80" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-80', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt> <tt class="py-op"><</tt> <tt class="py-name">sizehint</tt> <tt class="py-op">-</tt> <tt class="py-number">2</tt><tt class="py-op">,</tt> \ </tt>
<a name="L261"></a><tt class="py-lineno">261</tt> <tt class="py-line"> <tt class="py-string">"EndsWith text size larger than sizehint allows"</tt> </tt>
<a name="L262"></a><tt class="py-lineno">262</tt> <tt class="py-line"> </tt>
<a name="L263"></a><tt class="py-lineno">263</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">has_newline</tt><tt class="py-op">:</tt> </tt>
<a name="L264"></a><tt class="py-lineno">264</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt> <tt class="py-op">=</tt> <tt id="link-81" class="py-name" targets="Function Martel.RecordReader._endswith_tagtable_newline()=Martel.RecordReader-module.html#_endswith_tagtable_newline"><a title="Martel.RecordReader._endswith_tagtable_newline" class="py-name" href="#" onclick="return doclink('link-81', '_endswith_tagtable_newline', 'link-81');">_endswith_tagtable_newline</a></tt><tt class="py-op">(</tt><tt id="link-82" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-82', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L265"></a><tt class="py-lineno">265</tt> <tt class="py-line"> <tt class="py-keyword">else</tt><tt class="py-op">:</tt> </tt>
<a name="L266"></a><tt class="py-lineno">266</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</tt> <tt class="py-op">=</tt> <tt id="link-83" class="py-name" targets="Function Martel.RecordReader._endswith_tagtable_rest_of_line()=Martel.RecordReader-module.html#_endswith_tagtable_rest_of_line"><a title="Martel.RecordReader._endswith_tagtable_rest_of_line" class="py-name" href="#" onclick="return doclink('link-83', '_endswith_tagtable_rest_of_line', 'link-83');">_endswith_tagtable_rest_of_line</a></tt><tt class="py-op">(</tt><tt id="link-84" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-84', 'text', 'link-2');">text</a></tt><tt class="py-op">)</tt> </tt>
<a name="L267"></a><tt class="py-lineno">267</tt> <tt class="py-line"> </tt>
<a name="L268"></a><tt class="py-lineno">268</tt> <tt class="py-line"> </tt>
<a name="L269"></a><tt class="py-lineno">269</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L270"></a><tt class="py-lineno">270</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L271"></a><tt class="py-lineno">271</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-85" 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-85', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L272"></a><tt class="py-lineno">272</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L273"></a><tt class="py-lineno">273</tt> <tt class="py-line"> </tt>
<a name="EndsWith.next"></a><div id="EndsWith.next-def"><a name="L274"></a><tt class="py-lineno">274</tt> <a class="py-toggle" href="#" id="EndsWith.next-toggle" onclick="return toggle('EndsWith.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.EndsWith-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="EndsWith.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EndsWith.next-expanded"><a name="L275"></a><tt class="py-lineno">275</tt> <tt class="py-line"> <tt class="py-comment"># Are any precomputed positions remaining?</tt> </tt>
<a name="L276"></a><tt class="py-lineno">276</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 id="link-86" 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-86', 'index', 'link-37');">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">positions</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L277"></a><tt class="py-lineno">277</tt> <tt class="py-line"> <tt class="py-comment"># Yes, so return that text</tt> </tt>
<a name="L278"></a><tt class="py-lineno">278</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">newpos</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-87" 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-87', 'index', 'link-37');">index</a></tt><tt class="py-op">]</tt> </tt>
<a name="L279"></a><tt class="py-lineno">279</tt> <tt class="py-line"> <tt id="link-88" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-88', 's', 'link-39');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt><tt class="py-name">newpos</tt><tt class="py-op">]</tt> </tt>
<a name="L280"></a><tt class="py-lineno">280</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">newpos</tt> </tt>
<a name="L281"></a><tt class="py-lineno">281</tt> <tt class="py-line"> <tt class="py-name">self</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-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-90" 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-90', 'index', 'link-37');">index</a></tt> <tt class="py-op">+</tt> <tt class="py-number">1</tt> </tt>
<a name="L282"></a><tt class="py-lineno">282</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-91" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-91', 's', 'link-39');">s</a></tt> </tt>
<a name="L283"></a><tt class="py-lineno">283</tt> <tt class="py-line"> </tt>
<a name="L284"></a><tt class="py-lineno">284</tt> <tt class="py-line"> <tt class="py-comment"># No available information, so use what remains to seed the</tt> </tt>
<a name="L285"></a><tt class="py-lineno">285</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># next level.</tt> </tt>
<a name="L286"></a><tt class="py-lineno">286</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
<a name="L287"></a><tt class="py-lineno">287</tt> <tt class="py-line"> </tt>
<a name="L288"></a><tt class="py-lineno">288</tt> <tt class="py-line"> <tt id="link-92" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-92', 'data', 'link-44');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L289"></a><tt class="py-lineno">289</tt> <tt class="py-line"> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L290"></a><tt class="py-lineno">290</tt> <tt class="py-line"> <tt class="py-comment"># Add text until I've found a record or there is no more data</tt> </tt>
<a name="L291"></a><tt class="py-lineno">291</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="L292"></a><tt class="py-lineno">292</tt> <tt class="py-line"> <tt id="link-93" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-93', 'data', 'link-44');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-94" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-94', 'read', 'link-35');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</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-keyword">not</tt> <tt id="link-95" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-95', 'data', 'link-44');">data</a></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">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">positions</tt><tt class="py-op">:</tt> </tt>
<a name="L295"></a><tt class="py-lineno">295</tt> <tt class="py-line"> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt id="link-96" class="py-name" targets="Function Martel.RecordReader._find_end_positions()=Martel.RecordReader-module.html#_find_end_positions"><a title="Martel.RecordReader._find_end_positions" class="py-name" href="#" onclick="return doclink('link-96', '_find_end_positions', 'link-96');">_find_end_positions</a></tt><tt class="py-op">(</tt><tt class="py-name">lookahead</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</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">break</tt> </tt>
<a name="L297"></a><tt class="py-lineno">297</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">+</tt> <tt id="link-97" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-97', 'data', 'link-44');">data</a></tt> </tt>
<a name="L298"></a><tt class="py-lineno">298</tt> <tt class="py-line"> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt id="link-98" class="py-name"><a title="Martel.RecordReader._find_end_positions" class="py-name" href="#" onclick="return doclink('link-98', '_find_end_positions', 'link-96');">_find_end_positions</a></tt><tt class="py-op">(</tt><tt class="py-name">lookahead</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</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 class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</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="L300"></a><tt class="py-lineno">300</tt> <tt class="py-line"> <tt class="py-keyword">del</tt> <tt class="py-name">positions</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="L301"></a><tt class="py-lineno">301</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L302"></a><tt class="py-lineno">302</tt> <tt class="py-line"> </tt>
<a name="L303"></a><tt class="py-lineno">303</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L304"></a><tt class="py-lineno">304</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-name">positions</tt> </tt>
<a name="L305"></a><tt class="py-lineno">305</tt> <tt class="py-line"> </tt>
<a name="L306"></a><tt class="py-lineno">306</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">positions</tt><tt class="py-op">:</tt> </tt>
<a name="L307"></a><tt class="py-lineno">307</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="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-99', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L308"></a><tt class="py-lineno">308</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">positions</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">]</tt> </tt>
<a name="L309"></a><tt class="py-lineno">309</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-name">positions</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="L310"></a><tt class="py-lineno">310</tt> <tt class="py-line"> <tt class="py-keyword">elif</tt> <tt class="py-keyword">not</tt> <tt class="py-name">lookahead</tt><tt class="py-op">:</tt> </tt>
<a name="L311"></a><tt class="py-lineno">311</tt> <tt class="py-line"> <tt class="py-comment"># No data (either empty file or at EOF)</tt> </tt>
<a name="L312"></a><tt class="py-lineno">312</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L313"></a><tt class="py-lineno">313</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-100" 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-100', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L314"></a><tt class="py-lineno">314</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L315"></a><tt class="py-lineno">315</tt> <tt class="py-line"> </tt>
<a name="L316"></a><tt class="py-lineno">316</tt> <tt class="py-line"> <tt class="py-comment"># This is likely an unterminated record. However, it could be</tt> </tt>
<a name="L317"></a><tt class="py-lineno">317</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># that there is no terminal end-of-line character so check for</tt> </tt>
<a name="L318"></a><tt class="py-lineno">318</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># that case.</tt> </tt>
<a name="L319"></a><tt class="py-lineno">319</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">if</tt> <tt class="py-name">lookahead</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-keyword">not</tt> <tt class="py-keyword">in</tt> <tt class="py-string">"\r\n"</tt><tt class="py-op">:</tt> </tt>
<a name="L320"></a><tt class="py-lineno">320</tt> <tt class="py-line"> <tt class="py-name">special_case</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L321"></a><tt class="py-lineno">321</tt> <tt class="py-line"> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt id="link-101" class="py-name"><a title="Martel.RecordReader._find_end_positions" class="py-name" href="#" onclick="return doclink('link-101', '_find_end_positions', 'link-96');">_find_end_positions</a></tt><tt class="py-op">(</tt><tt class="py-name">special_case</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">tagtable</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">positions</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">assert</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</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-string">"this case should not occur"</tt> </tt>
<a name="L324"></a><tt class="py-lineno">324</tt> <tt class="py-line"> <tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">positions</tt><tt class="py-op">[</tt><tt class="py-number">0</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">assert</tt> <tt class="py-name">pos</tt> <tt class="py-op">==</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">special_case</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-string">"wrong sizes: %d and %d"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L326"></a><tt class="py-lineno">326</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">pos</tt><tt class="py-op">,</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">special_case</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
<a name="L327"></a><tt class="py-lineno">327</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L328"></a><tt class="py-lineno">328</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L329"></a><tt class="py-lineno">329</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L330"></a><tt class="py-lineno">330</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-102" 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-102', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L331"></a><tt class="py-lineno">331</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L332"></a><tt class="py-lineno">332</tt> <tt class="py-line"> </tt>
<a name="L333"></a><tt class="py-lineno">333</tt> <tt class="py-line"> <tt class="py-comment"># Really could not find a terminator</tt> </tt>
<a name="L334"></a><tt class="py-lineno">334</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-103" 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-103', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L335"></a><tt class="py-lineno">335</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L336"></a><tt class="py-lineno">336</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt id="link-104" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-104', 'ReaderError', 'link-11');">ReaderError</a></tt><tt class="py-op">(</tt><tt class="py-string">"Last record not terminated: at %s ..."</tt> <tt class="py-op">%</tt> </tt>
<a name="L337"></a><tt class="py-lineno">337</tt> <tt class="py-line"> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">50</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L338"></a><tt class="py-lineno">338</tt> <tt class="py-line"> </tt>
<a name="EndsWith.remainder"></a><div id="EndsWith.remainder-def"><a name="L339"></a><tt class="py-lineno">339</tt> <a class="py-toggle" href="#" id="EndsWith.remainder-toggle" onclick="return toggle('EndsWith.remainder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.EndsWith-class.html#remainder">remainder</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="EndsWith.remainder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="EndsWith.remainder-expanded"><a name="L340"></a><tt class="py-lineno">340</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">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
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<a name="L342"></a><tt class="py-lineno">342</tt> <tt class="py-line"> </tt>
<a name="L343"></a><tt class="py-lineno">343</tt> <tt class="py-line"> </tt>
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Bio.PopGen.FDist.Record.__init__
Bio.PopGen.FDist.RecordParser.__init__
Bio.PopGen.FDist._RecordConsumer.__init__
Bio.PopGen.GenePop.Record.__init__
Bio.PopGen.GenePop.RecordParser.__init__
Bio.PopGen.GenePop._RecordConsumer.__init__
Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
Bio.PopGen.SimCoal.Controller.SimCoalController.__init__
Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
Bio.Prosite.Prodoc.Dictionary.__init__
Bio.Prosite.Prodoc.ExPASyDictionary.__init__
Bio.Prosite.Prodoc.Iterator.__init__
Bio.Prosite.Prodoc.Record.__init__
Bio.Prosite.Prodoc.RecordParser.__init__
Bio.Prosite.Prodoc.Reference.__init__
Bio.Prosite.Prodoc._RecordConsumer.__init__
Bio.Prosite.Record.__init__
Bio.Prosite.RecordParser.__init__
Bio.Prosite._RecordConsumer.__init__
Bio.PubMed.Dictionary.__init__
Bio.Rebase.Dictionary.__init__
Bio.Rebase.Iterator.__init__
Bio.Rebase.Record.__init__
Bio.Rebase.RecordParser.__init__
Bio.Rebase._RecordConsumer.__init__
Bio.Restriction.PrintFormat.PrintFormat.__init__
Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
Bio.Restriction._Update.RestrictionCompiler.TypeCompiler.__init__
Bio.Restriction._Update.RestrictionCompiler.newenzyme.__init__
Bio.Restriction._Update.Update.ConnectionError.__init__
Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
Bio.Restriction._Update.Update.RebaseUpdate.__init__
Bio.SCOP.Astral.__init__
Bio.SCOP.Cla.Index.__init__
Bio.SCOP.Cla.Iterator.__init__
Bio.SCOP.Cla.Parser.__init__
Bio.SCOP.Cla.Record.__init__
Bio.SCOP.Des.Iterator.__init__
Bio.SCOP.Des.Parser.__init__
Bio.SCOP.Des.Record.__init__
Bio.SCOP.Dom.Iterator.__init__
Bio.SCOP.Dom.Record.__init__
Bio.SCOP.Domain.__init__
Bio.SCOP.FileIndex.FileIndex.__init__
Bio.SCOP.FileIndex.defaultdict.__init__
Bio.SCOP.Hie.Iterator.__init__
Bio.SCOP.Hie.Parser.__init__
Bio.SCOP.Hie.Record.__init__
Bio.SCOP.Node.__init__
Bio.SCOP.Raf.Iterator.__init__
Bio.SCOP.Raf.Parser.__init__
Bio.SCOP.Raf.Res.__init__
Bio.SCOP.Raf.SeqMap.__init__
Bio.SCOP.Raf.SeqMapIndex.__init__
Bio.SCOP.Residues'.Residues.__init__
Bio.SCOP.Scop.__init__
Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
Bio.Search.HomologySeq.__init__
Bio.Search.Query.__init__
Bio.Search.Search.__init__
Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
Bio.Sequencing.Ace.RecordParser.__init__
Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
Bio.StdHandler.Feature.__init__
Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
Bio.StdHandler.Handle_features.__init__
Bio.StdHandler.Handle_hsp.__init__
Bio.StdHandler.RecognizeHandler.__init__
Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
Bio.SwissProt.KeyWList._Scanner.__init__
Bio.SwissProt.SProt.Dictionary.__init__
Bio.SwissProt.SProt.ExPASyDictionary.__init__
Bio.SwissProt.SProt.Iterator.__init__
Bio.SwissProt.SProt.Record.__init__
Bio.SwissProt.SProt.RecordParser.__init__
Bio.SwissProt.SProt.Reference.__init__
Bio.SwissProt.SProt.SequenceParser.__init__
Bio.SwissProt.SProt._RecordConsumer.__init__
Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
Bio.Wise.psw.ColumnUnit.__init__
Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
Bio.builders.SeqRecord.sequence.BuildSeqRecord.__init__
Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
Bio.config.DBRegistry.DBObject.__init__
Bio.config.DBRegistry.DBRegistry.__init__
Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
Martel.Dispatch.DispatchHandler.__init__
Martel.Dispatch.Dispatcher.__init__
Martel.Dispatch.Multicall.__init__
Martel.Dispatch.RemapEnd.__init__
Martel.Dispatch.RemapStart.__init__
Martel.Expression.Alt.__init__
Martel.Expression.Any.__init__
Martel.Expression.Assert.__init__
Martel.Expression.Debug.__init__
Martel.Expression.FastFeature.__init__
Martel.Expression.Group.__init__
Martel.Expression.GroupRef.__init__
Martel.Expression.HeaderFooter.__init__
Martel.Expression.Literal.__init__
Martel.Expression.MaxRepeat.__init__
Martel.Expression.NullOp.__init__
Martel.Expression.ParseRecords.__init__
Martel.Expression.PassThrough.__init__
Martel.Expression.Seq.__init__
Martel.Expression.Str.__init__
Martel.Generate.CheckAssert.__init__
Martel.Generate.CheckAssertNot.__init__
Martel.Generate.CheckGroupRef.__init__
Martel.Generate.GeneratorState.__init__
Martel.Generate.HandleRepeatCount.__init__
Martel.Generate.SetGroupValue.__init__
Martel.Generate._call_call.__init__
Martel.Generate._call_calltag.__init__
Martel.Generate.print_debug.__init__
Martel.Generate.print_info.__init__
Martel.IterParser.IterHeaderFooter.__init__
Martel.IterParser.IterRecords.__init__
Martel.Iterator.EventStream.__init__
Martel.Iterator.HeaderFooterEventStream.__init__
Martel.Iterator.Iterate.__init__
Martel.Iterator.Iterator.__init__
Martel.Iterator.IteratorHeaderFooter.__init__
Martel.Iterator.IteratorRecords.__init__
Martel.Iterator.RecordEventStream.__init__
Martel.Iterator.StoreEvents.__init__
Martel.LAX.ElementInfo.__init__
Martel.LAX.LAX.__init__
Martel.Parser.HeaderFooterParser.__init__
Martel.Parser.Parser.__init__
Martel.Parser.ParserIncompleteException.__init__
Martel.Parser.ParserPositionException.__init__
Martel.Parser.RecordParser.__init__
Martel.RecordReader.CountLines.__init__
Martel.RecordReader.EndsWith.__init__
Martel.RecordReader.Everything.__init__
Martel.RecordReader.Nothing.__init__
Martel.RecordReader.RecordReader.__init__
Martel.RecordReader.StartsWith.__init__
Martel.RecordReader.Until.__init__
Martel.convert_re.GroupNames.__init__
Martel.msre_parse.Pattern.__init__
Martel.msre_parse.SubPattern.__init__
Martel.msre_parse.Tokenizer.__init__
Martel.test.support.CheckGood.__init__
Martel.test.support.Dump.__init__
Martel.test.support.Storage.__init__
Martel.test.test_Parser.CountErrors.__init__
Martel.test.test_Parser.CountRecords.__init__
Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-107', '__init__', 'link-20');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L347"></a><tt class="py-lineno">347</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-108" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-108', 'text', 'link-2');">text</a></tt> <tt class="py-op">=</tt> <tt id="link-109" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-109', 'text', 'link-2');">text</a></tt> </tt>
<a name="L348"></a><tt class="py-lineno">348</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L349"></a><tt class="py-lineno">349</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-name">sizehint</tt> </tt>
<a name="L350"></a><tt class="py-lineno">350</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">found</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L351"></a><tt class="py-lineno">351</tt> <tt class="py-line"> </tt>
<a name="L352"></a><tt class="py-lineno">352</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt id="link-110" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-110', 'text', 'link-2');">text</a></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-string">"\n"</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">raise</tt> <tt class="py-name">NotImplementedError</tt><tt class="py-op">,</tt> <tt class="py-string">"Until reader does not support '\\n'"</tt> </tt>
<a name="L354"></a><tt class="py-lineno">354</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-string">"\n"</tt> <tt class="py-keyword">in</tt> <tt id="link-111" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-111', 'text', 'link-2');">text</a></tt><tt class="py-op">:</tt> </tt>
<a name="L355"></a><tt class="py-lineno">355</tt> <tt class="py-line"> <tt class="py-keyword">raise</tt> <tt class="py-name">AssertionError</tt><tt class="py-op">,</tt> <tt class="py-string">"'\\n' can only exist at the end of the string"</tt> </tt>
</div><a name="L356"></a><tt class="py-lineno">356</tt> <tt class="py-line"> </tt>
<a name="Until.next"></a><div id="Until.next-def"><a name="L357"></a><tt class="py-lineno">357</tt> <a class="py-toggle" href="#" id="Until.next-toggle" onclick="return toggle('Until.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.Until-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="Until.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Until.next-expanded"><a name="L358"></a><tt class="py-lineno">358</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">found</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">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L360"></a><tt class="py-lineno">360</tt> <tt class="py-line"> </tt>
<a name="L361"></a><tt class="py-lineno">361</tt> <tt class="py-line"> <tt class="py-comment"># Use the StartsWith reader to get to the end of this record.</tt> </tt>
<a name="L362"></a><tt class="py-lineno">362</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Need to fake the first line..</tt> </tt>
<a name="L363"></a><tt class="py-lineno">363</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-name">fake</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-112" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-112', 'text', 'link-2');">text</a></tt> <tt class="py-op">+</tt> <tt class="py-string">"\n"</tt> </tt>
<a name="L364"></a><tt class="py-lineno">364</tt> <tt class="py-line"> <tt class="py-name">reader</tt> <tt class="py-op">=</tt> <tt id="link-113" class="py-name" targets="Class Martel.RecordReader.StartsWith=Martel.RecordReader.StartsWith-class.html"><a title="Martel.RecordReader.StartsWith" class="py-name" href="#" onclick="return doclink('link-113', 'StartsWith', 'link-113');">StartsWith</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-114" class="py-name"><a title="Bio.EUtils.POM.ElementNode.text
Bio.Prosite.Prodoc._RecordConsumer.text
Martel.test.test_Iterator.text
Martel.test.test_ParseRecords.text" class="py-name" href="#" onclick="return doclink('link-114', 'text', 'link-2');">text</a></tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</tt><tt class="py-op">,</tt> </tt>
<a name="L365"></a><tt class="py-lineno">365</tt> <tt class="py-line"> <tt class="py-name">fake</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">)</tt> </tt>
<a name="L366"></a><tt class="py-lineno">366</tt> <tt class="py-line"> <tt class="py-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-115" 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-115', 'next', 'link-115');">next</a></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-name">rec</tt> <tt class="py-op">=</tt> <tt class="py-name">rec</tt><tt class="py-op">[</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">fake</tt><tt class="py-op">)</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> <tt class="py-comment"># remove the fake data</tt> </tt>
<a name="L368"></a><tt class="py-lineno">368</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">reader</tt><tt class="py-op">.</tt><tt id="link-116" class="py-name" targets="Variable Bio.Affy.CelFile.remainder=Bio.Affy.CelFile-module.html#remainder,Variable Bio.LogisticRegression.remainder=Bio.LogisticRegression-module.html#remainder,Variable Bio.MarkovModel.remainder=Bio.MarkovModel-module.html#remainder,Variable Bio.MaxEntropy.remainder=Bio.MaxEntropy-module.html#remainder,Variable Bio.NaiveBayes.remainder=Bio.NaiveBayes-module.html#remainder,Variable Bio.Statistics.lowess.remainder=Bio.Statistics.lowess-module.html#remainder,Variable Bio.distance.remainder=Bio.distance-module.html#remainder,Variable Bio.kNN.remainder=Bio.kNN-module.html#remainder,Method Martel.RecordReader.CountLines.remainder()=Martel.RecordReader.CountLines-class.html#remainder,Method Martel.RecordReader.EndsWith.remainder()=Martel.RecordReader.EndsWith-class.html#remainder,Method Martel.RecordReader.Everything.remainder()=Martel.RecordReader.Everything-class.html#remainder,Method Martel.RecordReader.Nothing.remainder()=Martel.RecordReader.Nothing-class.html#remainder,Method Martel.RecordReader.RecordReader.remainder()=Martel.RecordReader.RecordReader-class.html#remainder,Method Martel.RecordReader.StartsWith.remainder()=Martel.RecordReader.StartsWith-class.html#remainder,Method Martel.RecordReader.Until.remainder()=Martel.RecordReader.Until-class.html#remainder"><a title="Bio.Affy.CelFile.remainder
Bio.LogisticRegression.remainder
Bio.MarkovModel.remainder
Bio.MaxEntropy.remainder
Bio.NaiveBayes.remainder
Bio.Statistics.lowess.remainder
Bio.distance.remainder
Bio.kNN.remainder
Martel.RecordReader.CountLines.remainder
Martel.RecordReader.EndsWith.remainder
Martel.RecordReader.Everything.remainder
Martel.RecordReader.Nothing.remainder
Martel.RecordReader.RecordReader.remainder
Martel.RecordReader.StartsWith.remainder
Martel.RecordReader.Until.remainder" class="py-name" href="#" onclick="return doclink('link-116', 'remainder', 'link-116');">remainder</a></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-name">self</tt><tt class="py-op">.</tt><tt class="py-name">found</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L370"></a><tt class="py-lineno">370</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">rec</tt> </tt>
</div><a name="L371"></a><tt class="py-lineno">371</tt> <tt class="py-line"> </tt>
<a name="Until.remainder"></a><div id="Until.remainder-def"><a name="L372"></a><tt class="py-lineno">372</tt> <a class="py-toggle" href="#" id="Until.remainder-toggle" onclick="return toggle('Until.remainder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.Until-class.html#remainder">remainder</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="Until.remainder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Until.remainder-expanded"><a name="L373"></a><tt class="py-lineno">373</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">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> </tt>
</div></div><a name="L374"></a><tt class="py-lineno">374</tt> <tt class="py-line"> </tt>
<a name="L375"></a><tt class="py-lineno">375</tt> <tt class="py-line"><tt class="py-comment"># Tag the last byte of every newline</tt> </tt>
<a name="L376"></a><tt class="py-lineno">376</tt> <tt class="py-line"><tt class="py-comment"></tt><tt id="link-117" class="py-name" targets="Variable Martel.RecordReader._tag_lines_tagtable=Martel.RecordReader-module.html#_tag_lines_tagtable"><a title="Martel.RecordReader._tag_lines_tagtable" class="py-name" href="#" onclick="return doclink('link-117', '_tag_lines_tagtable', 'link-117');">_tag_lines_tagtable</a></tt> <tt class="py-op">=</tt> <tt class="py-op">(</tt> </tt>
<a name="L377"></a><tt class="py-lineno">377</tt> <tt class="py-line"> <tt class="py-comment"># Skip non-newline characters</tt> </tt>
<a name="L378"></a><tt class="py-lineno">378</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">AllInSet</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">invset</tt><tt class="py-op">(</tt><tt class="py-string">'\r\n'</tt><tt class="py-op">)</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>
<a name="L379"></a><tt class="py-lineno">379</tt> <tt class="py-line"> </tt>
<a name="L380"></a><tt class="py-lineno">380</tt> <tt class="py-line"> <tt class="py-comment"># Check if newline</tt> </tt>
<a name="L381"></a><tt class="py-lineno">381</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"newline"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-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-comment"># can be '\n'</tt> </tt>
<a name="L382"></a><tt class="py-lineno">382</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">3</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-comment"># or start a '\r' followed by ..</tt> </tt>
<a name="L383"></a><tt class="py-lineno">383</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"newline"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Is</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-number">1</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">3</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># .. an optional '\n'</tt> </tt>
<a name="L384"></a><tt class="py-lineno">384</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-string">"newline"</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Skip</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">4</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">4</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># get here with just an '\r'</tt> </tt>
<a name="L385"></a><tt class="py-lineno">385</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">None</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">EOF</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">Here</tt><tt class="py-op">,</tt> <tt class="py-op">-</tt><tt class="py-number">5</tt><tt class="py-op">,</tt> <tt class="py-name">TT</tt><tt class="py-op">.</tt><tt class="py-name">MatchOk</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-comment"># stop at end of text</tt> </tt>
<a name="L386"></a><tt class="py-lineno">386</tt> <tt class="py-line"> <tt class="py-op">)</tt> </tt>
<a name="L387"></a><tt class="py-lineno">387</tt> <tt class="py-line"> </tt>
<a name="L388"></a><tt class="py-lineno">388</tt> <tt class="py-line"> </tt>
<a name="CountLines"></a><div id="CountLines-def"><a name="L389"></a><tt class="py-lineno">389</tt> <a class="py-toggle" href="#" id="CountLines-toggle" onclick="return toggle('CountLines');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.RecordReader.CountLines-class.html">CountLines</a><tt class="py-op">(</tt><tt class="py-base-class">RecordReader</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountLines-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="CountLines-expanded"><a name="L390"></a><tt class="py-lineno">390</tt> <tt class="py-line"> <tt class="py-docstring">"""Read a specified (fixed) number of lines"""</tt> </tt>
<a name="CountLines.__init__"></a><div id="CountLines.__init__-def"><a name="L391"></a><tt class="py-lineno">391</tt> <a class="py-toggle" href="#" id="CountLines.__init__-toggle" onclick="return toggle('CountLines.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.CountLines-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">infile</tt><tt class="py-op">,</tt> <tt class="py-param">count</tt><tt class="py-op">,</tt> <tt class="py-param">sizehint</tt> <tt class="py-op">=</tt> <tt id="link-118" class="py-name"><a title="Martel.RecordReader.SIZEHINT" class="py-name" href="#" onclick="return doclink('link-118', 'SIZEHINT', 'link-0');">SIZEHINT</a></tt><tt class="py-op">,</tt> <tt class="py-param">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="CountLines.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountLines.__init__-expanded"><a name="L392"></a><tt class="py-lineno">392</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt id="link-119" class="py-name" targets="Method Bio.Crystal.Chain.count()=Bio.Crystal.Chain-class.html#count,Method Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count()=Bio.NeuralNetwork.Gene.Pattern.PatternRepository-class.html#count,Method Bio.Seq.MutableSeq.count()=Bio.Seq.MutableSeq-class.html#count,Method Bio.Seq.Seq.count()=Bio.Seq.Seq-class.html#count,Function Bio.listfns.count()=Bio.listfns-module.html#count"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-119', 'count', 'link-119');">count</a></tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"CountLines reader must read at least one line"</tt> </tt>
<a name="L393"></a><tt class="py-lineno">393</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"Must read at least a character at a time"</tt> </tt>
<a name="L394"></a><tt class="py-lineno">394</tt> <tt class="py-line"> <tt class="py-keyword">assert</tt> <tt class="py-name">sizehint</tt> <tt class="py-op">></tt> <tt class="py-number">0</tt><tt class="py-op">,</tt> <tt class="py-string">"sizehint must be positive"</tt> </tt>
<a name="L395"></a><tt class="py-lineno">395</tt> <tt class="py-line"> <tt id="link-120" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-120', 'RecordReader', 'link-19');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-121" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
Bio.Blast.Record.Parameters.__init__
Bio.Blast.Record.Round.__init__
Bio.CAPS.CAPSMap.__init__
Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
Bio.Clustalw.ClustalAlignment.__init__
Bio.Clustalw.MultipleAlignCL.__init__
Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
Bio.Compass.Record.__init__
Bio.Compass.RecordParser.__init__
Bio.Compass._Consumer.__init__
Bio.Crystal.Chain.__init__
Bio.Crystal.Crystal.__init__
Bio.Crystal.CrystalError.__init__
Bio.Crystal.Error.__init__
Bio.Crystal.Hetero.__init__
Bio.DBXRef.DBXRef.__init__
Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
Bio.Decode.DecodeScanner.__init__
Bio.Decode.Float.__init__
Bio.Decode.Function.__init__
Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
Bio.Decode.FunctionName.__init__
Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
Bio.DocSQL.IterationCursor.__init__
Bio.DocSQL.Query.__init__
Bio.DocSQL.QueryAll.__init__
Bio.DocSQL.QueryGeneric.__init__
Bio.DocSQL.QueryRow.__init__
Bio.DocSQL.QuerySingle.__init__
Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
Bio.ECell.RecordParser.__init__
Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
Bio.EUtils.DBIdsClient.DBIdsClient.__init__
Bio.EUtils.DBIdsClient.DBIdsLookup.__init__
Bio.EUtils.Datatypes.BinaryOp.__init__
Bio.EUtils.Datatypes.CheckLinkSet.__init__
Bio.EUtils.Datatypes.DBIds.__init__
Bio.EUtils.Datatypes.Date.__init__
Bio.EUtils.Datatypes.DateRange.__init__
Bio.EUtils.Datatypes.EUtilsSearchError.__init__
Bio.EUtils.Datatypes.IdCheck.__init__
Bio.EUtils.Datatypes.IdUrlSet.__init__
Bio.EUtils.Datatypes.Link.__init__
Bio.EUtils.Datatypes.LinkSetDb.__init__
Bio.EUtils.Datatypes.LinksLinkSet.__init__
Bio.EUtils.Datatypes.NeighborLinkSet.__init__
Bio.EUtils.Datatypes.ObjUrl.__init__
Bio.EUtils.Datatypes.PostResult.__init__
Bio.EUtils.Datatypes.Problem.__init__
Bio.EUtils.Datatypes.Provider.__init__
Bio.EUtils.Datatypes.Range.__init__
Bio.EUtils.Datatypes.SearchResult.__init__
Bio.EUtils.Datatypes.Summary.__init__
Bio.EUtils.Datatypes.Term.__init__
Bio.EUtils.Datatypes.WithinNDays.__init__
Bio.EUtils.HistoryClient.BaseHistoryRecordSet.__init__
Bio.EUtils.HistoryClient.HistoryClient.__init__
Bio.EUtils.HistoryClient.HistoryCookie.__init__
Bio.EUtils.HistoryClient.HistoryLookup.__init__
Bio.EUtils.HistoryClient.HistoryRecord.__init__
Bio.EUtils.MultiDict.OrderedMultiDict.__init__
Bio.EUtils.MultiDict.UnorderedMultiDict.__init__
Bio.EUtils.POM.Comment.__init__
Bio.EUtils.POM.ContentModel.__init__
Bio.EUtils.POM.DTDConsumerForSourceGeneration.__init__
Bio.EUtils.POM.ElementNode.__init__
Bio.EUtils.POM.IndentedText.__init__
Bio.EUtils.POM.ObjectParserHandler.__init__
Bio.EUtils.POM.POMDocument.__init__
Bio.EUtils.POM.XMLAttribute.__init__
Bio.EUtils.POM._ContentModelGenerator.__init__
Bio.EUtils.ReseekFile.ReseekFile.__init__
Bio.EUtils.ThinClient.ThinClient.__init__
Bio.EUtils.parse.UsePOMParser.__init__
Bio.EUtils.sourcegen.ClassHolder.__init__
Bio.EUtils.sourcegen.FunctionHolder.__init__
Bio.EUtils.sourcegen.MethodHolder.__init__
Bio.EUtils.sourcegen.SourceFile.__init__
Bio.EUtils.sourcegen.SourceGen.__init__
Bio.Emboss.Applications.EConsenseCommandline.__init__
Bio.Emboss.Applications.EInvertedCommandline.__init__
Bio.Emboss.Applications.ENeighborCommandline.__init__
Bio.Emboss.Applications.EProtDistCommandline.__init__
Bio.Emboss.Applications.EProtParsCommandline.__init__
Bio.Emboss.Applications.ESeqBootCommandline.__init__
Bio.Emboss.Applications.ETandemCommandline.__init__
Bio.Emboss.Applications.Est2GenomeCommandline.__init__
Bio.Emboss.Applications.FuzznucCommandline.__init__
Bio.Emboss.Applications.PalindromeCommandline.__init__
Bio.Emboss.Applications.Primer3Commandline.__init__
Bio.Emboss.Applications.PrimerSearchCommandline.__init__
Bio.Emboss.Applications.TranalignCommandline.__init__
Bio.Emboss.Applications.WaterCommandline.__init__
Bio.Emboss.Primer.Primer3Parser.__init__
Bio.Emboss.Primer.Primer3Primers.__init__
Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
Bio.Emboss.Primer.PrimerSearchInputRecord.__init__
Bio.Emboss.Primer.PrimerSearchOutputRecord.__init__
Bio.Emboss.Primer.PrimerSearchParser.__init__
Bio.Emboss.Primer._Primer3RecordConsumer.__init__
Bio.Emboss.Primer._Primer3Scanner.__init__
Bio.Emboss.Primer._PrimerSearchRecordConsumer.__init__
Bio.Emboss.Primer._PrimerSearchScanner.__init__
Bio.Entrez.Parser.DataHandler.__init__
Bio.Entrez.Parser.StructureElement.__init__
Bio.Enzyme.DataRecord.__init__
Bio.Enzyme.EnzymeRecord.__init__
Bio.Enzyme.Iterator.__init__
Bio.Enzyme.RecordParser.__init__
Bio.Enzyme._RecordConsumer.__init__
Bio.FSSP.FSSPAlignDict.__init__
Bio.FSSP.FSSPAlignRec.__init__
Bio.FSSP.FSSPHeader.__init__
Bio.FSSP.FSSPSumRec.__init__
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Bio.FSSP.fssp_rec.fff_rec.__init__
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Bio.Fasta.Record.__init__
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Bio.Fasta.SequenceParser.__init__
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Bio.File.SGMLStripper.MyParser.__init__
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Bio.File.UndoHandle.__init__
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Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
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Bio.GA.Crossover.Uniform.UniformCrossover.__init__
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Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
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Bio.GA.Selection.Diversity.DiversitySelection.__init__
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Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
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Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
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Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
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Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
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Bio.GenBank.LocationParser.Range.__init__
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Bio.GenBank.LocationParser.Token.__init__
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Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
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Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
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Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
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Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
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Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
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Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
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Bio.SeqFeature.Reference.__init__
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Bio.Sequencing.Ace.ACEFileRecord.__init__
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Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-121', '__init__', 'link-20');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">infile</tt><tt class="py-op">)</tt> </tt>
<a name="L396"></a><tt class="py-lineno">396</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</tt> <tt class="py-op">=</tt> <tt class="py-name">sizehint</tt> </tt>
<a name="L397"></a><tt class="py-lineno">397</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L398"></a><tt class="py-lineno">398</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-122" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-122', 'count', 'link-119');">count</a></tt> <tt class="py-op">=</tt> <tt id="link-123" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-123', 'count', 'link-119');">count</a></tt> </tt>
<a name="L399"></a><tt class="py-lineno">399</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L400"></a><tt class="py-lineno">400</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-op">[</tt><tt class="py-op">]</tt> </tt>
<a name="L401"></a><tt class="py-lineno">401</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-124" 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-124', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L402"></a><tt class="py-lineno">402</tt> <tt class="py-line"> </tt>
<a name="CountLines.next"></a><div id="CountLines.next-def"><a name="L403"></a><tt class="py-lineno">403</tt> <a class="py-toggle" href="#" id="CountLines.next-toggle" onclick="return toggle('CountLines.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.CountLines-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="CountLines.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountLines.next-expanded"><a name="L404"></a><tt class="py-lineno">404</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-125" 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-125', 'index', 'link-37');">index</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-126" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-126', 'count', 'link-119');">count</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">positions</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
<a name="L405"></a><tt class="py-lineno">405</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-127" 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-127', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <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-37');">index</a></tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-129" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-129', 'count', 'link-119');">count</a></tt> </tt>
<a name="L406"></a><tt class="py-lineno">406</tt> <tt class="py-line"> <tt class="py-name">endpos</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt><tt class="py-op">[</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-37');">index</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L407"></a><tt class="py-lineno">407</tt> <tt class="py-line"> <tt id="link-131" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-131', 's', 'link-39');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt><tt class="py-name">endpos</tt><tt class="py-op">]</tt> </tt>
<a name="L408"></a><tt class="py-lineno">408</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">endpos</tt> </tt>
<a name="L409"></a><tt class="py-lineno">409</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-132" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-132', 's', 'link-39');">s</a></tt> </tt>
<a name="L410"></a><tt class="py-lineno">410</tt> <tt class="py-line"> </tt>
<a name="L411"></a><tt class="py-lineno">411</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</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-keyword">while</tt> <tt class="py-number">1</tt><tt class="py-op">:</tt> </tt>
<a name="L413"></a><tt class="py-lineno">413</tt> <tt class="py-line"> <tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt id="link-133" class="py-name"><a title="Martel.RecordReader._find_end_positions" class="py-name" href="#" onclick="return doclink('link-133', '_find_end_positions', 'link-96');">_find_end_positions</a></tt><tt class="py-op">(</tt><tt class="py-name">lookahead</tt><tt class="py-op">,</tt> <tt id="link-134" class="py-name"><a title="Martel.RecordReader._tag_lines_tagtable" class="py-name" href="#" onclick="return doclink('link-134', '_tag_lines_tagtable', 'link-117');">_tag_lines_tagtable</a></tt><tt class="py-op">)</tt> </tt>
<a name="L414"></a><tt class="py-lineno">414</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt> <tt class="py-op">></tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-135" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-135', 'count', 'link-119');">count</a></tt><tt class="py-op">:</tt> </tt>
<a name="L415"></a><tt class="py-lineno">415</tt> <tt class="py-line"> <tt class="py-comment"># Last line may be incomplete, as with "\r" of "\r\n"</tt> </tt>
<a name="L416"></a><tt class="py-lineno">416</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Hmm, is this *really* needed? Doesn't hurt. XXX</tt> </tt>
<a name="L417"></a><tt class="py-lineno">417</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">del</tt> <tt class="py-name">positions</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="L418"></a><tt class="py-lineno">418</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L419"></a><tt class="py-lineno">419</tt> <tt class="py-line"> <tt id="link-136" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-136', 'data', 'link-44');">data</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-137" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-137', 'read', 'link-35');">read</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">sizehint</tt><tt class="py-op">)</tt> </tt>
<a name="L420"></a><tt class="py-lineno">420</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt id="link-138" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-138', 'data', 'link-44');">data</a></tt><tt class="py-op">:</tt> </tt>
<a name="L421"></a><tt class="py-lineno">421</tt> <tt class="py-line"> <tt class="py-keyword">break</tt> </tt>
<a name="L422"></a><tt class="py-lineno">422</tt> <tt class="py-line"> <tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> <tt class="py-op">+</tt> <tt id="link-139" class="py-name"><a title="BioSQL.BioSeq.DBSeq.data" class="py-name" href="#" onclick="return doclink('link-139', 'data', 'link-44');">data</a></tt> </tt>
<a name="L423"></a><tt class="py-lineno">423</tt> <tt class="py-line"> </tt>
<a name="L424"></a><tt class="py-lineno">424</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> </tt>
<a name="L425"></a><tt class="py-lineno">425</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
<a name="L426"></a><tt class="py-lineno">426</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</tt> <tt class="py-op">=</tt> <tt class="py-name">positions</tt> </tt>
<a name="L427"></a><tt class="py-lineno">427</tt> <tt class="py-line"> </tt>
<a name="L428"></a><tt class="py-lineno">428</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-keyword">not</tt> <tt class="py-name">lookahead</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">return</tt> <tt class="py-name">None</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">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</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.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-140', 'count', 'link-119');">count</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-name">self</tt><tt class="py-op">.</tt><tt id="link-141" 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-141', 'index', 'link-37');">index</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-142" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-142', 'count', 'link-119');">count</a></tt> </tt>
<a name="L433"></a><tt class="py-lineno">433</tt> <tt class="py-line"> <tt class="py-name">endpos</tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">positions</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.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-143', 'count', 'link-119');">count</a></tt><tt class="py-op">-</tt><tt class="py-number">1</tt><tt class="py-op">]</tt> </tt>
<a name="L434"></a><tt class="py-lineno">434</tt> <tt class="py-line"> <tt id="link-144" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-144', 's', 'link-39');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-number">0</tt><tt class="py-op">:</tt><tt class="py-name">endpos</tt><tt class="py-op">]</tt> </tt>
<a name="L435"></a><tt class="py-lineno">435</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt> <tt class="py-op">=</tt> <tt class="py-name">endpos</tt> </tt>
<a name="L436"></a><tt class="py-lineno">436</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-145" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-145', 's', 'link-39');">s</a></tt> </tt>
<a name="L437"></a><tt class="py-lineno">437</tt> <tt class="py-line"> </tt>
<a name="L438"></a><tt class="py-lineno">438</tt> <tt class="py-line"> <tt class="py-comment"># Commented out to require final newline</tt> </tt>
<a name="L439"></a><tt class="py-lineno">439</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># Don't allow that case since it is more frequent that the line</tt> </tt>
<a name="L440"></a><tt class="py-lineno">440</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-comment"># count is wrong. (Could change in future releases.)</tt> </tt>
<a name="L441"></a><tt class="py-lineno">441</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## elif len(positions) == self.count - 1 and not data:</tt> </tt>
<a name="L442"></a><tt class="py-lineno">442</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## # This was the last record, and it has no trailing newline</tt> </tt>
<a name="L443"></a><tt class="py-lineno">443</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## s = self.lookahead</tt> </tt>
<a name="L444"></a><tt class="py-lineno">444</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## self.lookahead = ""</tt> </tt>
<a name="L445"></a><tt class="py-lineno">445</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## self.positions = []</tt> </tt>
<a name="L446"></a><tt class="py-lineno">446</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## self.index = 0</tt> </tt>
<a name="L447"></a><tt class="py-lineno">447</tt> <tt class="py-line"><tt class="py-comment"></tt><tt class="py-comment">## return s</tt> </tt>
<a name="L448"></a><tt class="py-lineno">448</tt> <tt class="py-line"><tt class="py-comment"></tt> <tt class="py-keyword">raise</tt> <tt id="link-146" class="py-name"><a title="Martel.RecordReader.ReaderError" class="py-name" href="#" onclick="return doclink('link-146', 'ReaderError', 'link-11');">ReaderError</a></tt><tt class="py-op">,</tt> \ </tt>
<a name="L449"></a><tt class="py-lineno">449</tt> <tt class="py-line"> <tt class="py-string">"Only found %d lines, expecting %d (starting with %s ...)"</tt> <tt class="py-op">%</tt> \ </tt>
<a name="L450"></a><tt class="py-lineno">450</tt> <tt class="py-line"> <tt class="py-op">(</tt><tt class="py-name">len</tt><tt class="py-op">(</tt><tt class="py-name">positions</tt><tt class="py-op">)</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt id="link-147" class="py-name"><a title="Bio.Crystal.Chain.count
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.count
Bio.Seq.MutableSeq.count
Bio.Seq.Seq.count
Bio.listfns.count" class="py-name" href="#" onclick="return doclink('link-147', 'count', 'link-119');">count</a></tt><tt class="py-op">,</tt> <tt class="py-name">repr</tt><tt class="py-op">(</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-op">:</tt><tt class="py-number">20</tt><tt class="py-op">]</tt><tt class="py-op">)</tt><tt class="py-op">)</tt> </tt>
</div><a name="L451"></a><tt class="py-lineno">451</tt> <tt class="py-line"> </tt>
<a name="CountLines.remainder"></a><div id="CountLines.remainder-def"><a name="L452"></a><tt class="py-lineno">452</tt> <a class="py-toggle" href="#" id="CountLines.remainder-toggle" onclick="return toggle('CountLines.remainder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.CountLines-class.html#remainder">remainder</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="CountLines.remainder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="CountLines.remainder-expanded"><a name="L453"></a><tt class="py-lineno">453</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">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt><tt class="py-op">[</tt><tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">pos</tt><tt class="py-op">:</tt><tt class="py-op">]</tt> </tt>
</div></div><a name="L454"></a><tt class="py-lineno">454</tt> <tt class="py-line"> </tt>
<a name="Nothing"></a><div id="Nothing-def"><a name="L455"></a><tt class="py-lineno">455</tt> <a class="py-toggle" href="#" id="Nothing-toggle" onclick="return toggle('Nothing');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.RecordReader.Nothing-class.html">Nothing</a><tt class="py-op">(</tt><tt class="py-base-class">RecordReader</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Nothing-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Nothing-expanded"><a name="L456"></a><tt class="py-lineno">456</tt> <tt class="py-line"> <tt class="py-docstring">"""Reads nothing"""</tt> </tt>
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Bio.SCOP.Raf.Parser.__init__
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Bio.SCOP.Residues'.Residues.__init__
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Bio.SGMLExtractor.SGMLExtractor.__init__
Bio.SGMLExtractor.SGMLExtractorHandle.__init__
Bio.SVDSuperimposer.SVDSuperimposer'.SVDSuperimposer.__init__
Bio.Saf.Iterator.__init__
Bio.Saf.Record.Record.__init__
Bio.Saf.RecordParser.__init__
Bio.Saf._RecordConsumer.__init__
Bio.Saf._Scanner.__init__
Bio.Search.Algorithm.__init__
Bio.Search.Database.__init__
Bio.Search.HSP.__init__
Bio.Search.HSPSeq.__init__
Bio.Search.Hit.__init__
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Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
Bio.SeqFeature.ExactPosition.__init__
Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
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Bio.Sequencing.Ace._RecordConsumer.__init__
Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
Bio.Sequencing.Ace.ct.__init__
Bio.Sequencing.Ace.ds.__init__
Bio.Sequencing.Ace.qa.__init__
Bio.Sequencing.Ace.rd.__init__
Bio.Sequencing.Ace.rt.__init__
Bio.Sequencing.Ace.wa.__init__
Bio.Sequencing.Ace.wr.__init__
Bio.Sequencing.Phd.Iterator.__init__
Bio.Sequencing.Phd.Record.__init__
Bio.Sequencing.Phd.RecordParser.__init__
Bio.Sequencing.Phd._RecordConsumer.__init__
Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
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Bio.StdHandler.Handle_dbxref.__init__
Bio.StdHandler.Handle_feature_location.__init__
Bio.StdHandler.Handle_feature_qualifier.__init__
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Bio.SwissProt.KeyWList.ListParser.__init__
Bio.SwissProt.KeyWList.Record.__init__
Bio.SwissProt.KeyWList._ListConsumer.__init__
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Bio.SwissProt.SProt.ExPASyDictionary.__init__
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Bio.SwissProt.SProt.Reference.__init__
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Bio.SwissProt.SProt._SequenceConsumer.__init__
Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
Bio.UniGene.UnigeneSequenceRecord.__init__
Bio.UniGene._RecordConsumer.__init__
Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
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Bio.Writer.Writer.__init__
Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
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Bio.config.DBRegistry.BioCorbaDB.__init__
Bio.config.DBRegistry.BioSQLDB.__init__
Bio.config.DBRegistry.CGIDB.__init__
Bio.config.DBRegistry.DBGroup.__init__
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Bio.config.DBRegistry.EUtilsDB.__init__
Bio.config.DBRegistry.IndexedFileDB.__init__
Bio.config.FormatRegistry.FormatGroup.__init__
Bio.config.FormatRegistry.FormatObject.__init__
Bio.config.FormatRegistry.FormatRegistry.__init__
Bio.config.Registry.RegisterableGroup.__init__
Bio.config.Registry.RegisterableObject.__init__
Bio.config.Registry.Registry.__init__
Bio.config.SeqDBRegistry.SeqDBRegistry.__init__
Bio.config._stanzaformat.Stanza.__init__
Bio.config._stanzaformat.StanzaFormat.__init__
Bio.config._support.make_cached_expression.__init__
Bio.config._support.make_rate_limited_function.__init__
Bio.kNN.kNN.__init__
Bio.pairwise2.affine_penalty.__init__
Bio.pairwise2.dictionary_match.__init__
Bio.pairwise2.identity_match.__init__
Bio.writers.SeqRecord.embl.WriteEmbl.__init__
Bio.writers.SeqRecord.fasta.WriteFasta.__init__
BioSQL.BioSeq.DBSeq.__init__
BioSQL.BioSeq.DBSeqRecord.__init__
BioSQL.BioSeqDatabase.Adaptor.__init__
BioSQL.BioSeqDatabase.BioSeqDatabase.__init__
BioSQL.BioSeqDatabase.DBServer.__init__
BioSQL.DBUtils.Generic_dbutils.__init__
BioSQL.Loader.DatabaseLoader.__init__
BioSQL.Loader.DatabaseRemover.__init__
Martel.Dispatch.Callback.__init__
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Martel.Generate._call_calltag.__init__
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Martel.test.test_delimiter.CatchFields.__init__
Martel.test.test_optimize.GetErrorPos.__init__" class="py-name" href="#" onclick="return doclink('link-150', '__init__', 'link-20');">__init__</a></tt><tt class="py-op">(</tt><tt class="py-name">self</tt><tt class="py-op">,</tt> <tt class="py-name">infile</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">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-name">lookahead</tt> </tt>
</div><a name="L460"></a><tt class="py-lineno">460</tt> <tt class="py-line"> </tt>
<a name="Nothing.next"></a><div id="Nothing.next-def"><a name="L461"></a><tt class="py-lineno">461</tt> <a class="py-toggle" href="#" id="Nothing.next-toggle" onclick="return toggle('Nothing.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.Nothing-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="Nothing.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Nothing.next-expanded"><a name="L462"></a><tt class="py-lineno">462</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt class="py-name">None</tt> </tt>
</div><a name="L463"></a><tt class="py-lineno">463</tt> <tt class="py-line"> </tt>
<a name="Nothing.remainder"></a><div id="Nothing.remainder-def"><a name="L464"></a><tt class="py-lineno">464</tt> <a class="py-toggle" href="#" id="Nothing.remainder-toggle" onclick="return toggle('Nothing.remainder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.Nothing-class.html#remainder">remainder</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="Nothing.remainder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Nothing.remainder-expanded"><a name="L465"></a><tt class="py-lineno">465</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">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> </tt>
</div></div><a name="L466"></a><tt class="py-lineno">466</tt> <tt class="py-line"> </tt>
<a name="Everything"></a><div id="Everything-def"><a name="L467"></a><tt class="py-lineno">467</tt> <a class="py-toggle" href="#" id="Everything-toggle" onclick="return toggle('Everything');">-</a><tt class="py-line"><tt class="py-keyword">class</tt> <a class="py-def-name" href="Martel.RecordReader.Everything-class.html">Everything</a><tt class="py-op">(</tt><tt class="py-base-class">RecordReader</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Everything-collapsed" style="display:none;" pad="+++" indent="++++"></div><div id="Everything-expanded"><a name="L468"></a><tt class="py-lineno">468</tt> <tt class="py-line"> <tt class="py-docstring">"""Reads everything"""</tt> </tt>
<a name="Everything.__init__"></a><div id="Everything.__init__-def"><a name="L469"></a><tt class="py-lineno">469</tt> <a class="py-toggle" href="#" id="Everything.__init__-toggle" onclick="return toggle('Everything.__init__');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.Everything-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">infile</tt><tt class="py-op">,</tt> <tt class="py-param">sizehint</tt> <tt class="py-op">=</tt> <tt id="link-151" class="py-name"><a title="Martel.RecordReader.SIZEHINT" class="py-name" href="#" onclick="return doclink('link-151', 'SIZEHINT', 'link-0');">SIZEHINT</a></tt><tt class="py-op">,</tt> <tt class="py-param">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt><tt class="py-op">)</tt><tt class="py-op">:</tt> </tt>
</div><div id="Everything.__init__-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Everything.__init__-expanded"><a name="L470"></a><tt class="py-lineno">470</tt> <tt class="py-line"> <tt id="link-152" class="py-name"><a title="Martel.RecordReader
Martel.RecordReader.RecordReader" class="py-name" href="#" onclick="return doclink('link-152', 'RecordReader', 'link-19');">RecordReader</a></tt><tt class="py-op">.</tt><tt id="link-153" class="py-name"><a title="Bio.Affy.CelFile.CelConsumer.__init__
Bio.Affy.CelFile.CelParser.__init__
Bio.Affy.CelFile.CelRecord.__init__
Bio.Ais.Immune.__init__
Bio.Ais.Lymphocyte.__init__
Bio.Align.AlignInfo.PSSM.__init__
Bio.Align.AlignInfo.SummaryInfo.__init__
Bio.Align.FormatConvert.FormatConverter.__init__
Bio.Align.Generic.Alignment.__init__
Bio.AlignAce.Applications.AlignAceCommandline.__init__
Bio.AlignAce.Applications.CompareAceCommandline.__init__
Bio.AlignAce.Motif.Motif.__init__
Bio.AlignAce.Parser.AlignAceConsumer.__init__
Bio.AlignAce.Parser.AlignAceParser.__init__
Bio.AlignAce.Parser.CompareAceConsumer.__init__
Bio.AlignAce.Parser.CompareAceParser.__init__
Bio.AlignIO.Interfaces.AlignmentIterator.__init__
Bio.AlignIO.Interfaces.AlignmentWriter.__init__
Bio.AlignIO.Interfaces.SequentialAlignmentWriter.__init__
Bio.Alphabet.AlphabetEncoder.__init__
Bio.Alphabet.Gapped.__init__
Bio.Alphabet.HasStopCodon.__init__
Bio.Application.AbstractCommandline.__init__
Bio.Application.ApplicationResult.__init__
Bio.Application._AbstractParameter.__init__
Bio.Blast.Applications.BlastallCommandline.__init__
Bio.Blast.Applications.FastacmdCommandline.__init__
Bio.Blast.NCBIStandalone.BlastErrorParser.__init__
Bio.Blast.NCBIStandalone.BlastParser.__init__
Bio.Blast.NCBIStandalone.Iterator.__init__
Bio.Blast.NCBIStandalone.PSIBlastParser.__init__
Bio.Blast.NCBIStandalone._BlastConsumer.__init__
Bio.Blast.NCBIStandalone._BlastErrorConsumer.__init__
Bio.Blast.NCBIStandalone._PSIBlastConsumer.__init__
Bio.Blast.NCBIWWW.BlastParser.__init__
Bio.Blast.NCBIXML.BlastParser.__init__
Bio.Blast.NCBIXML._XMLparser.__init__
Bio.Blast.ParseBlastTable.BlastTableEntry.__init__
Bio.Blast.ParseBlastTable.BlastTableReader.__init__
Bio.Blast.ParseBlastTable.BlastTableRec.__init__
Bio.Blast.Record.Alignment.__init__
Bio.Blast.Record.Blast.__init__
Bio.Blast.Record.DatabaseReport.__init__
Bio.Blast.Record.Description.__init__
Bio.Blast.Record.HSP.__init__
Bio.Blast.Record.Header.__init__
Bio.Blast.Record.MultipleAlignment.__init__
Bio.Blast.Record.PSIBlast.__init__
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Bio.CAPS.DifferentialCutsite.__init__
Bio.CDD.Iterator.__init__
Bio.CDD.Record.Record.__init__
Bio.CDD.RecordParser.__init__
Bio.CDD._RecordConsumer.__init__
Bio.CDD._Scanner.__init__
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Bio.Cluster.DataFile.__init__
Bio.Cluster.Record.__init__
Bio.Compass.Iterator.__init__
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Bio.Crystal.Chain.__init__
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Bio.Data.CodonTable.AmbiguousCodonTable.__init__
Bio.Data.CodonTable.AmbiguousForwardTable.__init__
Bio.Data.CodonTable.CodonTable.__init__
Bio.Data.CodonTable.NCBICodonTable.__init__
Bio.Decode.DecodeParser.__init__
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Bio.Decode.Float.__init__
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Bio.Decode.FunctionCall.__init__
Bio.Decode.FunctionCallChain.__init__
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Bio.Decode.Integer.__init__
Bio.Decode.String.__init__
Bio.Decode.Token.__init__
Bio.Decode.ValueToken.__init__
Bio.DocSQL.Create.__init__
Bio.DocSQL.Insert.__init__
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Bio.DocSQL.QueryRow.__init__
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Bio.ECell.ECellError.__init__
Bio.ECell.Error.__init__
Bio.ECell.Iterator.__init__
Bio.ECell.Record.Record.__init__
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Bio.ECell._RecordConsumer.__init__
Bio.ECell._Scanner.__init__
Bio.EUtils.Config.DatabaseInfo.__init__
Bio.EUtils.DBIdsClient.BaseDBIdsRecordSet.__init__
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Bio.Emboss.Primer.Primer3Parser.__init__
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Bio.Emboss.Primer.Primer3Record.__init__
Bio.Emboss.Primer.PrimerSearchAmplifier.__init__
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Bio.Enzyme.DataRecord.__init__
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Bio.Enzyme.Iterator.__init__
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Bio.FSSP.FSSPAlignRec.__init__
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Bio.FSSP.FSSPSumRec.__init__
Bio.FSSP.FSSPTools.FSSPMultAlign.__init__
Bio.FSSP.PosAlign.__init__
Bio.FSSP.fssp_rec.fff_rec.__init__
Bio.Fasta.FastaAlign.FastaAlignment.__init__
Bio.Fasta.Iterator.__init__
Bio.Fasta.Record.__init__
Bio.Fasta.RecordParser.__init__
Bio.Fasta.SequenceParser.__init__
Bio.File.SGMLHandle.__init__
Bio.File.SGMLStripper.MyParser.__init__
Bio.File.SGMLStripper.__init__
Bio.File.UndoHandle.__init__
Bio.FilteredReader.FilteredReader.__init__
Bio.GA.Crossover.General.SafeFitnessCrossover.__init__
Bio.GA.Crossover.GeneralPoint.GeneralPointCrossover.__init__
Bio.GA.Crossover.GeneralPoint.InterleaveCrossover.__init__
Bio.GA.Crossover.Point.SinglePointCrossover.__init__
Bio.GA.Crossover.TwoPoint.TwoPointCrossover.__init__
Bio.GA.Crossover.Uniform.UniformCrossover.__init__
Bio.GA.Evolver.GenerationEvolver.__init__
Bio.GA.Evolver.SteadyStateEvolver.__init__
Bio.GA.Mutation.General.SafeFitnessMutation.__init__
Bio.GA.Mutation.Simple.ConversionMutation.__init__
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Bio.GA.Organism.Organism.__init__
Bio.GA.Repair.Stabilizing.AmbiguousRepair.__init__
Bio.GA.Selection.Abstract.AbstractSelection.__init__
Bio.GA.Selection.Diversity.DiversitySelection.__init__
Bio.GA.Selection.RouletteWheel.RouletteWheelSelection.__init__
Bio.GA.Selection.Tournament.TournamentSelection.__init__
Bio.GFF.Connection.__init__
Bio.GFF.Feature.__init__
Bio.GFF.FeatureAggregate.__init__
Bio.GFF.FeatureQuery.__init__
Bio.GFF.FeatureQueryRow.__init__
Bio.GFF.GenericTools.ArgsParser.__init__
Bio.GFF.GenericTools.Surrogate.__init__
Bio.GFF.GenericTools.TempFile.__init__
Bio.GFF.RetrieveSeqname.__init__
Bio.GFF.Segment.__init__
Bio.GFF.easy.FeatureDict.__init__
Bio.GFF.easy.Location.__init__
Bio.GFF.easy.LocationFromCoords.__init__
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Bio.GFF.easy.LocationJoin.__init__
Bio.GenBank.FeatureParser.__init__
Bio.GenBank.Iterator.__init__
Bio.GenBank.LocationParser.AbsoluteLocation.__init__
Bio.GenBank.LocationParser.Between.__init__
Bio.GenBank.LocationParser.FeatureName.__init__
Bio.GenBank.LocationParser.Function.__init__
Bio.GenBank.LocationParser.HighBound.__init__
Bio.GenBank.LocationParser.Integer.__init__
Bio.GenBank.LocationParser.LocationParser.__init__
Bio.GenBank.LocationParser.LocationScanner.__init__
Bio.GenBank.LocationParser.LowBound.__init__
Bio.GenBank.LocationParser.Path.__init__
Bio.GenBank.LocationParser.Range.__init__
Bio.GenBank.LocationParser.Symbol.__init__
Bio.GenBank.LocationParser.Token.__init__
Bio.GenBank.LocationParser.TwoBound.__init__
Bio.GenBank.NCBIDictionary.__init__
Bio.GenBank.Record.Feature.__init__
Bio.GenBank.Record.Qualifier.__init__
Bio.GenBank.Record.Record.__init__
Bio.GenBank.Record.Reference.__init__
Bio.GenBank.RecordParser.__init__
Bio.GenBank.Scanner.InsdcScanner.__init__
Bio.GenBank._BaseGenBankConsumer.__init__
Bio.GenBank._FeatureConsumer.__init__
Bio.GenBank._RecordConsumer.__init__
Bio.GenBank.utils.FeatureValueCleaner.__init__
Bio.Geo.Record.Record.__init__
Bio.Gobase.Dictionary.__init__
Bio.Gobase.GeneRecord.__init__
Bio.Gobase.Iterator.__init__
Bio.Gobase.ProteinRecord.__init__
Bio.Gobase.Record.__init__
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Bio.Gobase.SequenceRecord.__init__
Bio.Gobase._RecordConsumer.__init__
Bio.Graphics.BasicChromosome.Chromosome.__init__
Bio.Graphics.BasicChromosome.ChromosomeSegment.__init__
Bio.Graphics.BasicChromosome.Organism.__init__
Bio.Graphics.BasicChromosome.TelomereSegment.__init__
Bio.Graphics.BasicChromosome._ChromosomeComponent.__init__
Bio.Graphics.Comparative.ComparativeScatterPlot.__init__
Bio.Graphics.DisplayRepresentation.ChromosomeCounts.__init__
Bio.Graphics.Distribution.BarChartDistribution.__init__
Bio.Graphics.Distribution.DistributionPage.__init__
Bio.Graphics.Distribution.LineDistribution.__init__
Bio.HMM.DynamicProgramming.AbstractDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.LogDPAlgorithms.__init__
Bio.HMM.DynamicProgramming.ScaledDPAlgorithms.__init__
Bio.HMM.MarkovModel.HiddenMarkovModel.__init__
Bio.HMM.MarkovModel.MarkovModelBuilder.__init__
Bio.HMM.Trainer.AbstractTrainer.__init__
Bio.HMM.Trainer.BaumWelchTrainer.__init__
Bio.HMM.Trainer.KnownStateTrainer.__init__
Bio.HMM.Trainer.TrainingSequence.__init__
Bio.HotRand.HotCache.__init__
Bio.HotRand.HotRandom.__init__
Bio.Index._InMemoryIndex.__init__
Bio.Index._ShelveIndex.__init__
Bio.IntelliGenetics.IntelliGeneticsReader.__init__
Bio.IntelliGenetics.Iterator.__init__
Bio.IntelliGenetics.Record.Record.__init__
Bio.IntelliGenetics.RecordParser.__init__
Bio.IntelliGenetics._RecordConsumer.__init__
Bio.IntelliGenetics._Scanner.__init__
Bio.KDTree.CKDTree.KDTree.__init__
Bio.KDTree.CKDTree.KDTreePtr.__init__
Bio.KDTree.KDTree.KDTree.__init__
Bio.KEGG.Compound.Record.__init__
Bio.KEGG.Enzyme.Record.__init__
Bio.LocusLink.Iterator.__init__
Bio.LocusLink.Record.__init__
Bio.LocusLink.RecordParser.__init__
Bio.LocusLink._RecordConsumer.__init__
Bio.LocusLink._Scanner.__init__
Bio.LocusLink.web_parse.Record.__init__
Bio.LocusLink.web_parse.Token.__init__
Bio.LocusLink.web_parse.Url.__init__
Bio.LogisticRegression.LogisticRegression.__init__
Bio.MEME.Motif.Instance.__init__
Bio.MEME.Motif.MEMEMotif.__init__
Bio.MEME.Motif.Motif.__init__
Bio.MEME.Parser.MASTParser.__init__
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Bio.MEME.Parser.MEMEParser.__init__
Bio.MEME.Parser.MEMERecord.__init__
Bio.MEME.Parser._MASTConsumer.__init__
Bio.MEME.Parser._MEMEConsumer.__init__
Bio.MarkovModel.MarkovModel.__init__
Bio.MaxEntropy.MaxEntropy.__init__
Bio.Medline.Iterator.__init__
Bio.Medline.Record.__init__
Bio.Medline.RecordParser.__init__
Bio.Medline._RecordConsumer.__init__
Bio.MetaTool.Iterator.__init__
Bio.MetaTool.Record.Metabolite.__init__
Bio.MetaTool.Record.MetaboliteRole.__init__
Bio.MetaTool.Record.PathwayTransform.__init__
Bio.MetaTool.Record.Record.__init__
Bio.MetaTool.RecordParser.__init__
Bio.MetaTool._RecordConsumer.__init__
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Bio.Mindy.BaseDB.OpenDB.__init__
Bio.Mindy.BerkeleyDB.BerkeleyDB.__init__
Bio.Mindy.BerkeleyDB.PrimaryNamespace.__init__
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Bio.Mindy.FlatDB.BaseFlatDB.__init__
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Bio.Mindy.SimpleSeqRecord.BaseSeqRecordIndexer.__init__
Bio.Mindy.SimpleSeqRecord.FixDocumentBuilder.__init__
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Bio.Mindy.XPath.GrabXPathNodes.__init__
Bio.NBRF.Iterator.__init__
Bio.NBRF.Record.Record.__init__
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Bio.NBRF._Scanner.__init__
Bio.NMR.xpktools.Peaklist.__init__
Bio.NMR.xpktools.XpkEntry.__init__
Bio.NaiveBayes.NaiveBayes.__init__
Bio.Ndb.Record.__init__
Bio.NetCatch.ExtractUrls.__init__
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Bio.NetCatch.Url.__init__
Bio.NeuralNetwork.BackPropagation.Layer.AbstractLayer.__init__
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Bio.NeuralNetwork.Gene.Motif.MotifFinder.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternIO.__init__
Bio.NeuralNetwork.Gene.Pattern.PatternRepository.__init__
Bio.NeuralNetwork.Gene.Schema.DifferentialSchemaFitness.__init__
Bio.NeuralNetwork.Gene.Schema.GeneticAlgorithmFinder.__init__
Bio.NeuralNetwork.Gene.Schema.MostCountSchemaFitness.__init__
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Bio.NeuralNetwork.Gene.Schema.SchemaCoder.__init__
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Bio.NeuralNetwork.Gene.Signature.SignatureCoder.__init__
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Bio.NeuralNetwork.StopTraining.ValidationIncreaseStop.__init__
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Bio.Nexus.Nexus.Block.__init__
Bio.Nexus.Nexus.CharBuffer.__init__
Bio.Nexus.Nexus.Commandline.__init__
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Bio.Nexus.Trees.NodeData.__init__
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Bio.PDB.AbstractPropertyMap.AbstractAtomPropertyMap.__init__
Bio.PDB.AbstractPropertyMap.AbstractPropertyMap.__init__
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Bio.PDB.HSExposure.ExposureCN.__init__
Bio.PDB.HSExposure.HSExposureCA.__init__
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Bio.PDB.HSExposure._AbstractHSExposure.__init__
Bio.PDB.MMCIF2Dict.MMCIF2Dict.__init__
Bio.PDB.Model.Model.__init__
Bio.PDB.NACCESS.NACCESS.__init__
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Bio.PDB.Vector'.Vector.__init__
Bio.ParserSupport.EventGenerator.__init__
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Bio.ParserSupport.TaggingConsumer.__init__
Bio.Parsers.spark.GenericASTBuilder.__init__
Bio.Parsers.spark.GenericASTMatcher.__init__
Bio.Parsers.spark.GenericASTTraversal.__init__
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Bio.Pathway.Network.__init__
Bio.Pathway.Reaction.__init__
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Bio.Pathway.Rep.HashSet.HashSet.__init__
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Bio.PopGen.Async.Async.__init__
Bio.PopGen.Async.DirectoryRetriever.__init__
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Bio.PopGen.Async.Local.Local.__init__
Bio.PopGen.FDist.Async.FDistAsync.__init__
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Bio.PopGen.GenePop.Record.__init__
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Bio.PopGen.SimCoal.Async.SimCoalCache.__init__
Bio.PopGen.SimCoal.Cache.SimCoalCache.__init__
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Bio.PropertyManager.PropertyManager.__init__
Bio.Prosite.Dictionary.__init__
Bio.Prosite.ExPASyDictionary.__init__
Bio.Prosite.Iterator.__init__
Bio.Prosite.Pattern.Prosite.__init__
Bio.Prosite.Pattern.PrositeMatch.__init__
Bio.Prosite.Pattern.PrositeTerm.__init__
Bio.Prosite.PatternHit.__init__
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Bio.Prosite.Prodoc.ExPASyDictionary.__init__
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Bio.Prosite.Prodoc.Reference.__init__
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Bio.Restriction.Restriction.Analysis.__init__
Bio.Restriction.Restriction.FormattedSeq.__init__
Bio.Restriction.Restriction.RestrictionBatch.__init__
Bio.Restriction.Restriction.RestrictionType.__init__
Bio.Restriction._Update.RestrictionCompiler.DictionaryBuilder.__init__
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Bio.Restriction._Update.Update.FtpNameError.__init__
Bio.Restriction._Update.Update.FtpPasswordError.__init__
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Bio.SCOP.Cla.Index.__init__
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Bio.SCOP.Cla.Record.__init__
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Bio.SCOP.Dom.Iterator.__init__
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Bio.SCOP.Domain.__init__
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Bio.SGMLExtractor.SGMLExtractor.LocalParser.__init__
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Bio.Search.HSP.__init__
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Bio.Search.Hit.__init__
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Bio.Search.TableInfo.__init__
Bio.Search._SeqLength.__init__
Bio.Seq.MutableSeq.__init__
Bio.Seq.Seq.__init__
Bio.SeqFeature.AbstractPosition.__init__
Bio.SeqFeature.AfterPosition.__init__
Bio.SeqFeature.BeforePosition.__init__
Bio.SeqFeature.BetweenPosition.__init__
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Bio.SeqFeature.FeatureLocation.__init__
Bio.SeqFeature.OneOfPosition.__init__
Bio.SeqFeature.PositionGap.__init__
Bio.SeqFeature.Reference.__init__
Bio.SeqFeature.SeqFeature.__init__
Bio.SeqFeature.WithinPosition.__init__
Bio.SeqIO.ClustalIO.ClustalWriter.__init__
Bio.SeqIO.FastaIO.FastaWriter.__init__
Bio.SeqIO.Interfaces.InterlacedSequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceIterator.__init__
Bio.SeqIO.Interfaces.SequenceWriter.__init__
Bio.SeqIO.Interfaces.SequentialSequenceWriter.__init__
Bio.SeqIO.PhylipIO.PhylipWriter.__init__
Bio.SeqIO.StockholmIO.StockholmIterator.__init__
Bio.SeqIO.StockholmIO.StockholmWriter.__init__
Bio.SeqRecord.SeqRecord.__init__
Bio.SeqUtils.CodonUsage.CodonAdaptationIndex.__init__
Bio.SeqUtils.IsoelectricPoint.IsoelectricPoint.__init__
Bio.SeqUtils.MissingTable.__init__
Bio.SeqUtils.ProtParam.ProteinAnalysis.__init__
Bio.Sequencing.Ace.ACEFileRecord.__init__
Bio.Sequencing.Ace.ACEParser.__init__
Bio.Sequencing.Ace.Contig.__init__
Bio.Sequencing.Ace.Iterator.__init__
Bio.Sequencing.Ace.Reads.__init__
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Bio.Sequencing.Ace.af.__init__
Bio.Sequencing.Ace.bs.__init__
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Bio.Sequencing.Ace.wr.__init__
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Bio.Std.StdTerm.__init__
Bio.StdHandler.ConvertDispatchHandler.__init__
Bio.StdHandler.ConvertHandler.__init__
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Bio.StdHandler.Handle_dbxref.__init__
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Bio.SubsMat.FreqTable.FreqTable.__init__
Bio.SubsMat.SeqMat.__init__
Bio.SwissProt.KeyWList.ListParser.__init__
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Bio.Transcribe.Transcribe.__init__
Bio.Translate.Translator.__init__
Bio.UniGene.Iterator.__init__
Bio.UniGene.RecordParser.__init__
Bio.UniGene.UnigeneProtsimRecord.__init__
Bio.UniGene.UnigeneRecord.__init__
Bio.UniGene.UnigeneSTSRecord.__init__
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Bio.WWW.RequestLimiter.__init__
Bio.Wise.dnal.Statistics.__init__
Bio.Wise.psw.AlignmentColumn.__init__
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Bio.biblio.Biblio.__init__
Bio.biblio.BiblioCollection.__init__
Bio.builders.Search.search.BuildSearch.__init__
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Bio.config.DBRegistry.BioCorbaDB.__init__
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<a name="L472"></a><tt class="py-lineno">472</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">found</tt> <tt class="py-op">=</tt> <tt class="py-number">0</tt> </tt>
</div><a name="L473"></a><tt class="py-lineno">473</tt> <tt class="py-line"> </tt>
<a name="Everything.next"></a><div id="Everything.next-def"><a name="L474"></a><tt class="py-lineno">474</tt> <a class="py-toggle" href="#" id="Everything.next-toggle" onclick="return toggle('Everything.next');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.Everything-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="Everything.next-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Everything.next-expanded"><a name="L475"></a><tt class="py-lineno">475</tt> <tt class="py-line"> <tt class="py-keyword">if</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">found</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">return</tt> <tt class="py-name">None</tt> </tt>
<a name="L477"></a><tt class="py-lineno">477</tt> <tt class="py-line"> <tt id="link-154" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-154', 's', 'link-39');">s</a></tt> <tt class="py-op">=</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">+</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">infile</tt><tt class="py-op">.</tt><tt id="link-155" class="py-name"><a title="Bio.AlignAce.Motif.Motif.read
Bio.AlignIO.read
Bio.Cluster.read
Bio.EUtils.ReseekFile.ReseekFile.read
Bio.Entrez.read
Bio.File.SGMLHandle.read
Bio.File.UndoHandle.read
Bio.FilteredReader.FilteredReader.read
Bio.NeuralNetwork.Gene.Pattern.PatternIO.read
Bio.Nexus.Nexus.Nexus.read
Bio.Prosite.Prodoc.read
Bio.Prosite.read
Bio.SGMLExtractor.SGMLExtractorHandle.read
Bio.SeqIO.read
Bio.SwissProt.read" class="py-name" href="#" onclick="return doclink('link-155', 'read', 'link-35');">read</a></tt><tt class="py-op">(</tt><tt class="py-op">)</tt> </tt>
<a name="L478"></a><tt class="py-lineno">478</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> <tt class="py-op">=</tt> <tt class="py-string">""</tt> </tt>
<a name="L479"></a><tt class="py-lineno">479</tt> <tt class="py-line"> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">found</tt> <tt class="py-op">=</tt> <tt class="py-number">1</tt> </tt>
<a name="L480"></a><tt class="py-lineno">480</tt> <tt class="py-line"> <tt class="py-keyword">return</tt> <tt id="link-156" class="py-name"><a title="Martel.test.test_swissprot38.s" class="py-name" href="#" onclick="return doclink('link-156', 's', 'link-39');">s</a></tt> </tt>
</div><a name="L481"></a><tt class="py-lineno">481</tt> <tt class="py-line"> </tt>
<a name="Everything.remainder"></a><div id="Everything.remainder-def"><a name="L482"></a><tt class="py-lineno">482</tt> <a class="py-toggle" href="#" id="Everything.remainder-toggle" onclick="return toggle('Everything.remainder');">-</a><tt class="py-line"> <tt class="py-keyword">def</tt> <a class="py-def-name" href="Martel.RecordReader.Everything-class.html#remainder">remainder</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="Everything.remainder-collapsed" style="display:none;" pad="+++" indent="++++++++"></div><div id="Everything.remainder-expanded"><a name="L483"></a><tt class="py-lineno">483</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">infile</tt><tt class="py-op">,</tt> <tt class="py-name">self</tt><tt class="py-op">.</tt><tt class="py-name">lookahead</tt> </tt>
</div></div><a name="L484"></a><tt class="py-lineno">484</tt> <tt class="py-line"> </tt><script type="text/javascript">
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