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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.Nexus-module.html">Package Nexus</a> ::
<a href="Bio.Nexus.Nexus-module.html">Module Nexus</a> ::
Class Nexus
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class Nexus</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus">source code</a></span></p>
<pre class="base-tree">
object --+
|
<strong class="uidshort">Nexus</strong>
</pre>
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<!-- ==================== INSTANCE METHODS ==================== -->
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<td><span class="summary-sig"><a href="Bio.Nexus.Nexus.Nexus-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">input</span>=<span class="summary-sig-default">None</span>)</span><br />
x.__init__(...) initializes x; see x.__class__.__doc__ for signature</td>
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<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.__init__">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="get_original_taxon_order"></a><span class="summary-sig-name">get_original_taxon_order</span>(<span class="summary-sig-arg">self</span>)</span><br />
Included for backwards compatibility.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.get_original_taxon_order">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="set_original_taxon_order"></a><span class="summary-sig-name">set_original_taxon_order</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span><br />
Included for backwards compatibility.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.set_original_taxon_order">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="read"></a><span class="summary-sig-name">read</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">input</span>)</span><br />
Read and parse NEXUS imput (filename, file-handle, string.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.read">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_get_nexus_block"></a><span class="summary-sig-name">_get_nexus_block</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">file_contents</span>)</span><br />
Generator for looping through Nexus blocks.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._get_nexus_block">source code</a></span>
</td>
</tr>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="_unknown_nexus_block"></a><span class="summary-sig-name">_unknown_nexus_block</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">title</span>,
<span class="summary-sig-arg">contents</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._unknown_nexus_block">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"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="_parse_nexus_block"></a><span class="summary-sig-name">_parse_nexus_block</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">title</span>,
<span class="summary-sig-arg">contents</span>)</span><br />
Parse a known Nexus Block</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._parse_nexus_block">source code</a></span>
</td>
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</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="_title"></a><span class="summary-sig-name">_title</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._title">source code</a></span>
</td>
</tr>
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</td>
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<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="_dimensions"></a><span class="summary-sig-name">_dimensions</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._dimensions">source code</a></span>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_format"></a><span class="summary-sig-name">_format</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._format">source code</a></span>
</td>
</tr>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="_set"></a><span class="summary-sig-name">_set</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._set">source code</a></span>
</td>
</tr>
</table>
</td>
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<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="_options"></a><span class="summary-sig-name">_options</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._options">source code</a></span>
</td>
</tr>
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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"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="_eliminate"></a><span class="summary-sig-name">_eliminate</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._eliminate">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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.Nexus.Nexus.Nexus-class.html#_taxlabels" class="summary-sig-name" onclick="show_private();">_taxlabels</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span><br />
Get taxon labels.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._taxlabels">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_check_taxlabels"></a><span class="summary-sig-name">_check_taxlabels</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">taxon</span>)</span><br />
Check for presence of taxon in self.taxlabels.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._check_taxlabels">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_charlabels"></a><span class="summary-sig-name">_charlabels</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._charlabels">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_charstatelabels"></a><span class="summary-sig-name">_charstatelabels</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._charstatelabels">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_statelabels"></a><span class="summary-sig-name">_statelabels</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._statelabels">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="_matrix"></a><span class="summary-sig-name">_matrix</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._matrix">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_translate"></a><span class="summary-sig-name">_translate</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._translate">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<td><span class="summary-sig"><a name="_utree"></a><span class="summary-sig-name">_utree</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span><br />
Some software (clustalx) uses 'utree' to denote an unrooted tree.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._utree">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_tree"></a><span class="summary-sig-name">_tree</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._tree">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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">
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<td><span class="summary-sig"><a name="_apply_block_structure"></a><span class="summary-sig-name">_apply_block_structure</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">title</span>,
<span class="summary-sig-arg">lines</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._apply_block_structure">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_taxset"></a><span class="summary-sig-name">_taxset</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._taxset">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_charset"></a><span class="summary-sig-name">_charset</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._charset">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
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<tr>
<td><span class="summary-sig"><a name="_taxpartition"></a><span class="summary-sig-name">_taxpartition</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._taxpartition">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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.Nexus.Nexus.Nexus-class.html#_codonposset" class="summary-sig-name" onclick="show_private();">_codonposset</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span><br />
Read codon positions from a codons block as written from McClade.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._codonposset">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_codeset"></a><span class="summary-sig-name">_codeset</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._codeset">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_charpartition"></a><span class="summary-sig-name">_charpartition</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._charpartition">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_get_indices"></a><span class="summary-sig-name">_get_indices</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>,
<span class="summary-sig-arg">set_type</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">chars</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">separator</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">=</code><code class="variable-quote">'</code></span>)</span><br />
Parse the taxset/charset specification '1 2 3 - 5 dog cat 10 - 20
\ 3' --> [0,1,2,3,4,'dog','cat',9,12,15,18]</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._get_indices">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_name_n_vector"></a><span class="summary-sig-name">_name_n_vector</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">opts</span>,
<span class="summary-sig-arg">separator</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">=</code><code class="variable-quote">'</code></span>)</span><br />
Extract name and check that it's not in vector format.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._name_n_vector">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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.Nexus.Nexus.Nexus-class.html#_parse_list" class="summary-sig-name" onclick="show_private();">_parse_list</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options_buffer</span>,
<span class="summary-sig-arg">set_type</span>)</span><br />
Parse a NEXUS list: [1, 2, 4-8\2, dog, cat] --> [1,2,4,6,8,17,21],
(assuming dog is taxon no.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._parse_list">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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.Nexus.Nexus.Nexus-class.html#_resolve" class="summary-sig-name" onclick="show_private();">_resolve</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">identifier</span>,
<span class="summary-sig-arg">set_type</span>=<span class="summary-sig-default">None</span>)</span><br />
Translate identifier in list into character/taxon index.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._resolve">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_stateset"></a><span class="summary-sig-name">_stateset</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._stateset">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_changeset"></a><span class="summary-sig-name">_changeset</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._changeset">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_treeset"></a><span class="summary-sig-name">_treeset</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._treeset">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_treepartition"></a><span class="summary-sig-name">_treepartition</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">options</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._treepartition">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.Nexus.Nexus.Nexus-class.html#write_nexus_data_partitions" class="summary-sig-name">write_nexus_data_partitions</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">matrix</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">blocksize</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">interleave</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">charpartition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">comment</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">mrbayes</span>=<span class="summary-sig-default">False</span>)</span><br />
Writes a nexus file for each partition in charpartition.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.write_nexus_data_partitions">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.Nexus.Nexus.Nexus-class.html#write_nexus_data" class="summary-sig-name">write_nexus_data</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">matrix</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">blocksize</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">interleave</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">interleave_by_partition</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">comment</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">omit_NEXUS</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">append_sets</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">mrbayes</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">codons_block</span>=<span class="summary-sig-default">True</span>)</span><br />
Writes a nexus file with data and sets block to a file or handle.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.write_nexus_data">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="append_sets"></a><span class="summary-sig-name">append_sets</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">mrbayes</span>=<span class="summary-sig-default">False</span>,
<span class="summary-sig-arg">include_codons</span>=<span class="summary-sig-default">True</span>,
<span class="summary-sig-arg">codons_only</span>=<span class="summary-sig-default">False</span>)</span><br />
Returns a sets block</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.append_sets">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="export_fasta"></a><span class="summary-sig-name">export_fasta</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">width</span>=<span class="summary-sig-default">70</span>)</span><br />
Writes matrix into a fasta file: (self, filename=None, width=70).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.export_fasta">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="export_phylip"></a><span class="summary-sig-name">export_phylip</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">filename</span>=<span class="summary-sig-default">None</span>)</span><br />
Writes matrix into a fasta file: (self, filename=None, width=70).</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.export_phylip">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="constant"></a><span class="summary-sig-name">constant</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">matrix</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>)</span><br />
Return a list with all constant characters.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.constant">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.Nexus.Nexus.Nexus-class.html#cstatus" class="summary-sig-name">cstatus</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">site</span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">narrow</span>=<span class="summary-sig-default">True</span>)</span><br />
Summarize character.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.cstatus">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.Nexus.Nexus.Nexus-class.html#weighted_stepmatrix" class="summary-sig-name">weighted_stepmatrix</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">your_name_here</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>)</span><br />
Calculates a stepmatrix for weighted parsimony.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.weighted_stepmatrix">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="crop_matrix"></a><span class="summary-sig-name">crop_matrix</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">matrix</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>)</span><br />
Return a matrix without deleted taxa and excluded characters.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.crop_matrix">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="bootstrap"></a><span class="summary-sig-name">bootstrap</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">matrix</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">delete</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>)</span><br />
Return a bootstrapped matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.bootstrap">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="add_sequence"></a><span class="summary-sig-name">add_sequence</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">name</span>,
<span class="summary-sig-arg">sequence</span>)</span><br />
Adds a sequence to the matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.add_sequence">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.Nexus.Nexus.Nexus-class.html#insert_gap" class="summary-sig-name">insert_gap</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">pos</span>,
<span class="summary-sig-arg">n</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">leftgreedy</span>=<span class="summary-sig-default">False</span>)</span><br />
Add a gap into the matrix and adjust charsets and partitions.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.insert_gap">source code</a></span>
</td>
</tr>
</table>
</td>
</tr>
<tr class="private">
<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="_adjust_charlabels"></a><span class="summary-sig-name">_adjust_charlabels</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">exclude</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">insert</span>=<span class="summary-sig-default">None</span>)</span><br />
Return adjusted indices of self.charlabels if characters are excluded
or inserted.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._adjust_charlabels">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="invert"></a><span class="summary-sig-name">invert</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">charlist</span>)</span><br />
Returns all character indices that are not in charlist.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.invert">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="gaponly"></a><span class="summary-sig-name">gaponly</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">include_missing</span>=<span class="summary-sig-default">False</span>)</span><br />
Return gap-only sites.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.gaponly">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.Nexus.Nexus.Nexus-class.html#terminal_gap_to_missing" class="summary-sig-name">terminal_gap_to_missing</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">missing</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">skip_n</span>=<span class="summary-sig-default">True</span>)</span><br />
Replaces all terminal gaps with missing character.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.terminal_gap_to_missing">source code</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>__delattr__</code>,
<code>__getattribute__</code>,
<code>__hash__</code>,
<code>__new__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__repr__</code>,
<code>__setattr__</code>,
<code>__str__</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"
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<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.Nexus.Nexus.Nexus-class.html#original_taxon_order" class="summary-name">original_taxon_order</a><br />
Included for backwards compatibility.
</td>
</tr>
<tr>
<td colspan="2" class="summary">
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
</p>
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<!-- ==================== METHOD DETAILS ==================== -->
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<a name="__init__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__init__</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">input</span>=<span class="sig-default">None</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.__init__">source code</a></span>
</td>
</tr></table>
<p>x.__init__(...) initializes x; see x.__class__.__doc__ for
signature</p>
<dl class="fields">
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
</td></tr></table>
</div>
<a name="_taxlabels"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_taxlabels</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">options</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._taxlabels">source code</a></span>
</td>
</tr></table>
<p>Get taxon labels. As the taxon names are already in the matrix, this
is superfluous except for transpose matrices, which are currently
unsupported anyway. Thus, we ignore the taxlabels command to make
handling of duplicate taxon names easier.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_codonposset"></a>
<div class="private">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_codonposset</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">options</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._codonposset">source code</a></span>
</td>
</tr></table>
<p>Read codon positions from a codons block as written from McClade. Here
codonposset is just a fancy name for a character partition with the name
CodonPositions and the partitions N,1,2,3</p>
<dl class="fields">
</dl>
</td></tr></table>
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<a name="_parse_list"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<h3 class="epydoc"><span class="sig"><span class="sig-name">_parse_list</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">options_buffer</span>,
<span class="sig-arg">set_type</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._parse_list">source code</a></span>
</td>
</tr></table>
<p>Parse a NEXUS list: [1, 2, 4-8\2, dog, cat] --> [1,2,4,6,8,17,21],
(assuming dog is taxon no. 17 and cat is taxon no. 21).</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="_resolve"></a>
<div class="private">
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cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">_resolve</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">identifier</span>,
<span class="sig-arg">set_type</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus._resolve">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Translate identifier in list into character/taxon index.
Characters (which are referred to by their index in Nexus.py):
Plain numbers are returned minus 1 (Nexus indices to python indices)
Text identifiers are translaterd into their indices (if plain character indentifiers),
the first hit in charlabels is returned (charlabels don't need to be unique)
or the range of indices is returned (if names of character sets).
Taxa (which are referred to by their unique name in Nexus.py):
Plain numbers are translated in their taxon name, underscores and spaces are considered equal.
Names are returned unchanged (if plain taxon identifiers), or the names in
the corresponding taxon set is returned
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="write_nexus_data_partitions"></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">write_nexus_data_partitions</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">matrix</span>=<span class="sig-default">None</span>,
<span class="sig-arg">filename</span>=<span class="sig-default">None</span>,
<span class="sig-arg">blocksize</span>=<span class="sig-default">None</span>,
<span class="sig-arg">interleave</span>=<span class="sig-default">False</span>,
<span class="sig-arg">exclude</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">delete</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">charpartition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">comment</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string"></code><code class="variable-quote">'</code></span>,
<span class="sig-arg">mrbayes</span>=<span class="sig-default">False</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.write_nexus_data_partitions">source code</a></span>
</td>
</tr></table>
<p>Writes a nexus file for each partition in charpartition. Only
non-excluded characters and non-deleted taxa are included, just the data
block is written.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="write_nexus_data"></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">write_nexus_data</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">filename</span>=<span class="sig-default">None</span>,
<span class="sig-arg">matrix</span>=<span class="sig-default">None</span>,
<span class="sig-arg">exclude</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">delete</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">blocksize</span>=<span class="sig-default">None</span>,
<span class="sig-arg">interleave</span>=<span class="sig-default">False</span>,
<span class="sig-arg">interleave_by_partition</span>=<span class="sig-default">False</span>,
<span class="sig-arg">comment</span>=<span class="sig-default">None</span>,
<span class="sig-arg">omit_NEXUS</span>=<span class="sig-default">False</span>,
<span class="sig-arg">append_sets</span>=<span class="sig-default">True</span>,
<span class="sig-arg">mrbayes</span>=<span class="sig-default">False</span>,
<span class="sig-arg">codons_block</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.write_nexus_data">source code</a></span>
</td>
</tr></table>
<pre class="literalblock">
Writes a nexus file with data and sets block to a file or handle.
Character sets and partitions are appended by default, and are
adjusted according to excluded characters (i.e. character sets
still point to the same sites (not necessarily same positions),
without including the deleted characters.
filename - Either a filename as a string (which will be opened,
written to and closed), or a handle object (which will
be written to but NOT closed).
omit_NEXUS - Boolean. If true, the '#NEXUS' line normally at the
start of the file is ommited.
Returns the filename/handle used to write the data.
</pre>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="cstatus"></a>
<div>
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cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">cstatus</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">site</span>,
<span class="sig-arg">delete</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">narrow</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.cstatus">source code</a></span>
</td>
</tr></table>
<p>Summarize character. narrow=True: paup-mode (a c ? --> ac; ? ? ?
--> ?) narrow=false: (a c ? --> a c g t -; ? ? ? --> a
c g t -)</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="weighted_stepmatrix"></a>
<div>
<table class="details" border="1" cellpadding="3"
cellspacing="0" width="100%" bgcolor="white">
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<table width="100%" cellpadding="0" cellspacing="0" border="0">
<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">weighted_stepmatrix</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">name</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">your_name_here</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">exclude</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>,
<span class="sig-arg">delete</span>=<span class="sig-default"><code class="variable-group">[</code><code class="variable-group">]</code></span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.weighted_stepmatrix">source code</a></span>
</td>
</tr></table>
<p>Calculates a stepmatrix for weighted parsimony. See Wheeler (1990),
Cladistics 6:269-275 and Felsenstein (1981), Biol. J. Linn. Soc.
16:183-196</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="insert_gap"></a>
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cellspacing="0" width="100%" bgcolor="white">
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<tr valign="top"><td>
<h3 class="epydoc"><span class="sig"><span class="sig-name">insert_gap</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">pos</span>,
<span class="sig-arg">n</span>=<span class="sig-default">1</span>,
<span class="sig-arg">leftgreedy</span>=<span class="sig-default">False</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.insert_gap">source code</a></span>
</td>
</tr></table>
<p>Add a gap into the matrix and adjust charsets and partitions.</p>
<p>pos=0: first position pos=nchar: last position</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
<a name="terminal_gap_to_missing"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">terminal_gap_to_missing</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">missing</span>=<span class="sig-default">None</span>,
<span class="sig-arg">skip_n</span>=<span class="sig-default">True</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.Nexus.Nexus-pysrc.html#Nexus.terminal_gap_to_missing">source code</a></span>
</td>
</tr></table>
<p>Replaces all terminal gaps with missing character.</p>
<p>Mixtures like ???------??------- are properly resolved.</p>
<dl class="fields">
</dl>
</td></tr></table>
</div>
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<a name="original_taxon_order"></a>
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<h3 class="epydoc">original_taxon_order</h3>
<p>Included for backwards compatibility.</p>
<dl class="fields">
<dt>Get Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Nexus.Nexus.Nexus-class.html#get_original_taxon_order" class="summary-sig-name">get_original_taxon_order</a>(<span class="summary-sig-arg">self</span>)</span>
- Included for backwards compatibility.
</dd>
<dt>Set Method:</dt>
<dd class="value"><span class="summary-sig"><a href="Bio.Nexus.Nexus.Nexus-class.html#set_original_taxon_order" class="summary-sig-name">set_original_taxon_order</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">value</span>)</span>
- Included for backwards compatibility.
</dd>
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