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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Restriction-module.html">Package Restriction</a> ::
<a href="Bio.Restriction.Restriction-module.html">Module Restriction</a> ::
Class Analysis
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Analysis</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis">source code</a></span></p>
<pre class="base-tree">
object --+
|
sets.BaseSet --+
|
sets.Set --+
|
<a href="Bio.Restriction.Restriction.RestrictionBatch-class.html">RestrictionBatch</a> --+
|
object --+ |
| |
<a href="Bio.Restriction.PrintFormat.PrintFormat-class.html">PrintFormat.PrintFormat</a> --+
|
<strong class="uidshort">Analysis</strong>
</pre>
<hr />
<!-- ==================== INSTANCE METHODS ==================== -->
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<td align="left"><span class="table-header">Instance Methods</span></td>
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<span class="summary-type">new RestrictionBatch.</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Analysis-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">restrictionbatch</span>=<span class="summary-sig-default">RestrictionBatch()</span>,
<span class="summary-sig-arg">sequence</span>=<span class="summary-sig-default">DNA('')</span>,
<span class="summary-sig-arg">linear</span>=<span class="summary-sig-default">True</span>)</span><br />
Analysis([restrictionbatch [, sequence] linear=True]) -> New
Analysis class.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.__init__">source code</a></span>
</td>
</tr>
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</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Analysis-class.html#__repr__" class="summary-sig-name">__repr__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Return string representation of a set.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.__repr__">source code</a></span>
</td>
</tr>
</table>
</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Analysis-class.html#_sub_set" class="summary-sig-name" onclick="show_private();">_sub_set</a>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">set</span>)</span><br />
Internal use only.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis._sub_set">source code</a></span>
</td>
</tr>
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</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">tuple</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="_boundaries"></a><span class="summary-sig-name">_boundaries</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>)</span><br />
Format the boundaries for use with the methods that limit the search
to only part of the sequence given to analyse.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis._boundaries">source code</a></span>
</td>
</tr>
</table>
</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">bool</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="_test_normal"></a><span class="summary-sig-name">_test_normal</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">site</span>)</span><br />
Internal use only Test if site is in between start and end.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis._test_normal">source code</a></span>
</td>
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</td>
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<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">bool</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="_test_reverse"></a><span class="summary-sig-name">_test_reverse</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">site</span>)</span><br />
Internal use only Test if site is in between end and start (for
circular sequences).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis._test_reverse">source code</a></span>
</td>
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</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">print the results from dct</span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Analysis-class.html#print_that" class="summary-sig-name">print_that</a>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>,
<span class="summary-sig-arg">title</span>=<span class="summary-sig-default">...</span>,
<span class="summary-sig-arg">s1</span>=<span class="summary-sig-default">...=...</span>)</span><br />
If dct is not given the full dictionary is used.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.print_that">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">Change attribute of Analysis</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Analysis-class.html#change" class="summary-sig-name">change</a>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">**attribute_name</span>)</span><br />
It is possible to change the width of the shell by setting
self.ConsoleWidth to what you want.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.change">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="full"></a><span class="summary-sig-name">full</span>(<span class="summary-sig-arg">A</span>)</span><br />
Full Restriction Map of the sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.full">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="blunt"></a><span class="summary-sig-name">blunt</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Only the enzymes which have a 3'overhang restriction site.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.blunt">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="overhang5"></a><span class="summary-sig-name">overhang5</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Only the enzymes which have a 5' overhang restriction site.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.overhang5">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="overhang3"></a><span class="summary-sig-name">overhang3</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Only the enzymes which have a 3'overhang restriction site.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.overhang3">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="defined"></a><span class="summary-sig-name">defined</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Only the enzymes that have a defined restriction site in Rebase.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.defined">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="with_sites"></a><span class="summary-sig-name">with_sites</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes which have at least one site in the sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.with_sites">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="without_site"></a><span class="summary-sig-name">without_site</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes which have no site in the sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.without_site">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="with_N_sites"></a><span class="summary-sig-name">with_N_sites</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes which cut N times the sequence.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.with_N_sites">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="with_number_list"></a><span class="summary-sig-name">with_number_list</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">list</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.with_number_list">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">Limit the search to the enzymes named in list_of_names.</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="with_name"></a><span class="summary-sig-name">with_name</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">list_of_names</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.with_name">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">Limit the search to the enzymes whose site is of size
<site_size>.</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="with_site_size"></a><span class="summary-sig-name">with_site_size</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">site_size</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.with_site_size">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="only_between"></a><span class="summary-sig-name">only_between</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes that cut the sequence only in between start and end.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.only_between">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Analysis-class.html#between" class="summary-sig-name">between</a>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes that cut the sequence at least in between start and end.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.between">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="show_only_between"></a><span class="summary-sig-name">show_only_between</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes that cut the sequence outside of the region in between start
and end but do not cut inside.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.show_only_between">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="only_outside"></a><span class="summary-sig-name">only_outside</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes that cut the sequence outside of the region in between start
and end but do not cut inside.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.only_outside">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a href="Bio.Restriction.Restriction.Analysis-class.html#outside" class="summary-sig-name">outside</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">None</span>)</span><br />
A.outside((start, end [, dct]) -> dict.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.outside">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type">dict</span>
</td><td class="summary">
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr>
<td><span class="summary-sig"><a name="do_not_cut"></a><span class="summary-sig-name">do_not_cut</span>(<span class="summary-sig-arg">A</span>,
<span class="summary-sig-arg">start</span>,
<span class="summary-sig-arg">end</span>,
<span class="summary-sig-arg">dct</span>=<span class="summary-sig-default">...</span>)</span><br />
Enzymes that do not cut the region in between start and end.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.do_not_cut">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html">RestrictionBatch</a></code></b>:
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#__add__">__add__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#__contains__">__contains__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#__div__">__div__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#__iadd__">__iadd__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#__rdiv__">__rdiv__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#__str__">__str__</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#add">add</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#add_nocheck">add_nocheck</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#add_supplier">add_supplier</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#as_string">as_string</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#current_suppliers">current_suppliers</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#elements">elements</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#format">format</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#get">get</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#is_restriction">is_restriction</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#lambdasplit">lambdasplit</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#remove">remove</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#search">search</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#split">split</a></code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>sets.Set</code></b>:
<code>__as_immutable__</code>,
<code>__as_temporarily_immutable__</code>,
<code>__getstate__</code>,
<code>__hash__</code>,
<code>__iand__</code>,
<code>__ior__</code>,
<code>__isub__</code>,
<code>__ixor__</code>,
<code>__setstate__</code>,
<code>clear</code>,
<code>difference_update</code>,
<code>discard</code>,
<code>intersection_update</code>,
<code>pop</code>,
<code>symmetric_difference_update</code>,
<code>union_update</code>,
<code>update</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>sets.BaseSet</code></b>:
<code>__and__</code>,
<code>__cmp__</code>,
<code>__copy__</code>,
<code>__deepcopy__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__gt__</code>,
<code>__iter__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__ne__</code>,
<code>__or__</code>,
<code>__sub__</code>,
<code>__xor__</code>,
<code>copy</code>,
<code>difference</code>,
<code>intersection</code>,
<code>issubset</code>,
<code>issuperset</code>,
<code>symmetric_difference</code>,
<code>union</code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code>sets.BaseSet</code></b> (private):
<code>_binary_sanity_check</code>,
<code>_compute_hash</code>,
<code>_repr</code>,
<code>_update</code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html">PrintFormat.PrintFormat</a></code></b>:
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#make_format">make_format</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#print_as">print_as</a></code>
</p>
<div class="private"> <p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html">PrintFormat.PrintFormat</a></code></b> (private):
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_list" onclick="show_private();">_make_list</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_list_only" onclick="show_private();">_make_list_only</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_map" onclick="show_private();">_make_map</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_map_only" onclick="show_private();">_make_map_only</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_nocut" onclick="show_private();">_make_nocut</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_nocut_only" onclick="show_private();">_make_nocut_only</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_number" onclick="show_private();">_make_number</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#_make_number_only" onclick="show_private();">_make_number_only</a></code>
</p></div>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__getattribute__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== CLASS METHODS ==================== -->
<a name="section-ClassMethods"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Class Methods</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassMethods"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html">RestrictionBatch</a></code></b>:
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#show_codes">show_codes</a></code>,
<code><a href="Bio.Restriction.Restriction.RestrictionBatch-class.html#suppl_codes">suppl_codes</a></code>
</p>
</td>
</tr>
</table>
<!-- ==================== CLASS VARIABLES ==================== -->
<a name="section-ClassVariables"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Class Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-ClassVariables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html">PrintFormat.PrintFormat</a></code></b>:
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#Cmodulo">Cmodulo</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#ConsoleWidth">ConsoleWidth</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#Indent">Indent</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#MaxSize">MaxSize</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#NameWidth">NameWidth</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#PrefWidth">PrefWidth</a></code>,
<code><a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#linesize">linesize</a></code>
</p>
</td>
</tr>
</table>
<!-- ==================== PROPERTIES ==================== -->
<a name="section-Properties"></a>
<table class="summary" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Properties</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Properties"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
</table>
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
</td>
</tr>
</table>
<!-- ==================== METHOD DETAILS ==================== -->
<a name="section-MethodDetails"></a>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr bgcolor="#70b0f0" class="table-header">
<td colspan="2" class="table-header">
<table border="0" cellpadding="0" cellspacing="0" width="100%">
<tr valign="top">
<td align="left"><span class="table-header">Method Details</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-MethodDetails"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
</tr>
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</td>
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</table>
<a name="__init__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">restrictionbatch</span>=<span class="sig-default">RestrictionBatch()</span>,
<span class="sig-arg">sequence</span>=<span class="sig-default">DNA('')</span>,
<span class="sig-arg">linear</span>=<span class="sig-default">True</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.__init__">source code</a></span>
</td>
</tr></table>
<p>Analysis([restrictionbatch [, sequence] linear=True]) -> New
Analysis class.</p>
<p>For most of the method of this class if a dictionary is given it will
be used as the base to calculate the results. If no dictionary is given a
new analysis using the Restriction Batch which has been given when the
Analysis class has been instantiated.</p>
<dl class="fields">
<dt>Returns: new RestrictionBatch.</dt>
<dt>Overrides:
object.__init__
</dt>
</dl>
</td></tr></table>
</div>
<a name="__repr__"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">__repr__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.__repr__">source code</a></span>
</td>
</tr></table>
<p>Return string representation of a set.</p>
<p>This looks like 'Set([<list of elements>])'.</p>
<dl class="fields">
<dt>Overrides:
object.__repr__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_sub_set"></a>
<div class="private">
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_sub_set</span>(<span class="sig-arg">A</span>,
<span class="sig-arg">set</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis._sub_set">source code</a></span>
</td>
</tr></table>
<p>Internal use only.</p>
<p>screen the results through set. Keep only the results for which the
enzymes is in set.</p>
<dl class="fields">
<dt>Returns: dict</dt>
</dl>
</td></tr></table>
</div>
<a name="print_that"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">print_that</span>(<span class="sig-arg">A</span>,
<span class="sig-arg">dct</span>=<span class="sig-default">...</span>,
<span class="sig-arg">title</span>=<span class="sig-default">...</span>,
<span class="sig-arg">s1</span>=<span class="sig-default">...=...</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.print_that">source code</a></span>
</td>
</tr></table>
<p>If dct is not given the full dictionary is used.</p>
<dl class="fields">
<dt>Returns: print the results from dct</dt>
<dt>Overrides:
<a href="Bio.Restriction.PrintFormat.PrintFormat-class.html#print_that">PrintFormat.PrintFormat.print_that</a>
</dt>
</dl>
</td></tr></table>
</div>
<a name="change"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">change</span>(<span class="sig-arg">A</span>,
<span class="sig-arg">**attribute_name</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.change">source code</a></span>
</td>
</tr></table>
<p>It is possible to change the width of the shell by setting
self.ConsoleWidth to what you want. self.NameWidth refer to the maximal
length of the enzyme name.</p>
<p>Changing one of these parameters here might not give the results you
expect. In which case, you can settle back to a 80 columns shell or try
to change self.Cmodulo and self.PrefWidth in PrintFormat until you get it
right.</p>
<dl class="fields">
<dt>Returns: Change attribute of Analysis</dt>
</dl>
</td></tr></table>
</div>
<a name="between"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">between</span>(<span class="sig-arg">A</span>,
<span class="sig-arg">start</span>,
<span class="sig-arg">end</span>,
<span class="sig-arg">dct</span>=<span class="sig-default">...</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.between">source code</a></span>
</td>
</tr></table>
<p>Enzymes that cut the sequence at least in between start and end. They
may cut outside as well.</p>
<dl class="fields">
<dt>Returns: dict</dt>
</dl>
</td></tr></table>
</div>
<a name="outside"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
<tr><td>
<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">outside</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">start</span>,
<span class="sig-arg">end</span>,
<span class="sig-arg">dct</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Restriction.Restriction-pysrc.html#Analysis.outside">source code</a></span>
</td>
</tr></table>
<p>A.outside((start, end [, dct]) -> dict.</p>
<p>Enzymes that cut outside the region in between start and end. No test
is made to know if they cut or not inside this region.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<br />
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