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<a href="Bio-module.html">Package Bio</a> ::
<a href="Bio.SubsMat-module.html">Package SubsMat</a> ::
Class SeqMat
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<!-- ==================== CLASS DESCRIPTION ==================== -->
<h1 class="epydoc">Class SeqMat</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat">source code</a></span></p>
<pre class="base-tree">
object --+
|
dict --+
|
<strong class="uidshort">SeqMat</strong>
</pre>
<dl><dt>Known Subclasses:</dt>
<dd>
<ul class="subclass-list">
<li><a href="Bio.SubsMat.AcceptedReplacementsMatrix-class.html">AcceptedReplacementsMatrix</a></li><li>, <a href="Bio.SubsMat.ExpectedFrequencyMatrix-class.html">ExpectedFrequencyMatrix</a></li><li>, <a href="Bio.SubsMat.LogOddsMatrix-class.html">LogOddsMatrix</a></li><li>, <a href="Bio.SubsMat.ObservedFrequencyMatrix-class.html">ObservedFrequencyMatrix</a></li><li>, <a href="Bio.SubsMat.SubstitutionMatrix-class.html">SubstitutionMatrix</a></li> </ul>
</dd></dl>
<hr />
<p>A Generic sequence matrix class The key is a 2-tuple containing the
letter indices of the matrix. Those should be sorted in the tuple (low,
high). Because each matrix is dealt with as a half-matrix.</p>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_alphabet_from_matrix"></a><span class="summary-sig-name">_alphabet_from_matrix</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._alphabet_from_matrix">source code</a></span>
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<span class="summary-type"><pre class="literalblock">
new empty dictionary
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<td><span class="summary-sig"><a href="Bio.SubsMat.SeqMat-class.html#__init__" class="summary-sig-name">__init__</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">data</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">mat_name</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">build_later</span>=<span class="summary-sig-default">0</span>)</span><br />
x.__init__(...) initializes x; see help(type(x)) for signature</td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__init__">source code</a></span>
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<td><span class="summary-sig"><a name="_correct_matrix"></a><span class="summary-sig-name">_correct_matrix</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._correct_matrix">source code</a></span>
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<td><span class="summary-sig"><a name="_full_to_half"></a><span class="summary-sig-name">_full_to_half</span>(<span class="summary-sig-arg">self</span>)</span><br />
Convert a full-matrix to a half-matrix</td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._full_to_half">source code</a></span>
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<td><span class="summary-sig"><a name="_init_zero"></a><span class="summary-sig-name">_init_zero</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat._init_zero">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="make_entropy"></a><span class="summary-sig-name">make_entropy</span>(<span class="summary-sig-arg">self</span>)</span></td>
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<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.make_entropy">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="sum"></a><span class="summary-sig-name">sum</span>(<span class="summary-sig-arg">self</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.sum">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="print_full_mat"></a><span class="summary-sig-name">print_full_mat</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">f</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">format</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4d</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">topformat</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4s</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">factor</span>=<span class="summary-sig-default">1</span>,
<span class="summary-sig-arg">non_sym</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.print_full_mat">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.SubsMat.SeqMat-class.html#print_mat" class="summary-sig-name">print_mat</a>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">f</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">format</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4d</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">bottomformat</span>=<span class="summary-sig-default"><code class="variable-quote">'</code><code class="variable-string">%4s</code><code class="variable-quote">'</code></span>,
<span class="summary-sig-arg">alphabet</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">factor</span>=<span class="summary-sig-default">1</span>)</span><br />
Print a nice half-matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.print_mat">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a href="Bio.SubsMat.SeqMat-class.html#__str__" class="summary-sig-name">__str__</a>(<span class="summary-sig-arg">self</span>)</span><br />
Print a nice half-matrix.</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__str__">source code</a></span>
</td>
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<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="__sub__"></a><span class="summary-sig-name">__sub__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
returns a number which is the subtraction product of the two matrices</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__sub__">source code</a></span>
</td>
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<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="__mul__"></a><span class="summary-sig-name">__mul__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span><br />
returns a matrix for which each entry is the multiplication product
of the two matrices passed</td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__mul__">source code</a></span>
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<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="__add__"></a><span class="summary-sig-name">__add__</span>(<span class="summary-sig-arg">self</span>,
<span class="summary-sig-arg">other</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__add__">source code</a></span>
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<p class="indent-wrapped-lines"><b>Inherited from <code>dict</code></b>:
<code>__cmp__</code>,
<code>__contains__</code>,
<code>__delitem__</code>,
<code>__eq__</code>,
<code>__ge__</code>,
<code>__getattribute__</code>,
<code>__getitem__</code>,
<code>__gt__</code>,
<code>__iter__</code>,
<code>__le__</code>,
<code>__len__</code>,
<code>__lt__</code>,
<code>__ne__</code>,
<code>__new__</code>,
<code>__repr__</code>,
<code>__setitem__</code>,
<code>__sizeof__</code>,
<code>clear</code>,
<code>copy</code>,
<code>fromkeys</code>,
<code>get</code>,
<code>has_key</code>,
<code>items</code>,
<code>iteritems</code>,
<code>iterkeys</code>,
<code>itervalues</code>,
<code>keys</code>,
<code>pop</code>,
<code>popitem</code>,
<code>setdefault</code>,
<code>update</code>,
<code>values</code>,
<code>viewitems</code>,
<code>viewkeys</code>,
<code>viewvalues</code>
</p>
<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__delattr__</code>,
<code>__format__</code>,
<code>__reduce__</code>,
<code>__reduce_ex__</code>,
<code>__setattr__</code>,
<code>__subclasshook__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>dict</code></b>:
<code>__hash__</code>
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<p class="indent-wrapped-lines"><b>Inherited from <code>object</code></b>:
<code>__class__</code>
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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">data</span>=<span class="sig-default">None</span>,
<span class="sig-arg">alphabet</span>=<span class="sig-default">None</span>,
<span class="sig-arg">mat_name</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">build_later</span>=<span class="sig-default">0</span>)</span>
<br /><em class="fname">(Constructor)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__init__">source code</a></span>
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<p>x.__init__(...) initializes x; see help(type(x)) for signature</p>
<dl class="fields">
<dt>Returns: <pre class="literalblock">
new empty dictionary
</pre></dt>
<dt>Overrides:
object.__init__
<dd><em class="note">(inherited documentation)</em></dd>
</dt>
</dl>
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<a name="print_mat"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">print_mat</span>(<span class="sig-arg">self</span>,
<span class="sig-arg">f</span>=<span class="sig-default">None</span>,
<span class="sig-arg">format</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">%4d</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">bottomformat</span>=<span class="sig-default"><code class="variable-quote">'</code><code class="variable-string">%4s</code><code class="variable-quote">'</code></span>,
<span class="sig-arg">alphabet</span>=<span class="sig-default">None</span>,
<span class="sig-arg">factor</span>=<span class="sig-default">1</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.print_mat">source code</a></span>
</td>
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<p>Print a nice half-matrix. f=sys.stdout to see on the screen User may
pass own alphabet, which should contain all letters in the alphabet of
the matrix, but may be in a different order. This order will be the order
of the letters on the axes</p>
<dl class="fields">
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<a name="__str__"></a>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">__str__</span>(<span class="sig-arg">self</span>)</span>
<br /><em class="fname">(Informal representation operator)</em>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.SubsMat-pysrc.html#SeqMat.__str__">source code</a></span>
</td>
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<p>Print a nice half-matrix.</p>
<dl class="fields">
<dt>Overrides:
object.__str__
</dt>
</dl>
</td></tr></table>
</div>
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