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<a href="Bio-module.html">Package Bio</a> ::
Module MarkovModel
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<!-- ==================== MODULE DESCRIPTION ==================== -->
<h1 class="epydoc">Module MarkovModel</h1><p class="nomargin-top"><span class="codelink"><a href="Bio.MarkovModel-pysrc.html">source code</a></span></p>
<p>This is an implementation of a state-emitting MarkovModel. I am using
terminology similar to Manning and Schutze.</p>
<p>Functions: train_bw Train a markov model using the Baum-Welch
algorithm. train_visible Train a visible markov model using MLE.
find_states Find the a state sequence that explains some
observations.</p>
<p>load Load a MarkovModel. save Save a
MarkovModel.</p>
<p>Classes: MarkovModel Holds the description of a markov model</p>
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<span class="summary-type"> </span>
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<a href="Bio.MarkovModel.MarkovModel-class.html" class="summary-name">MarkovModel</a>
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<td><span class="summary-sig"><a name="_readline_and_check_start"></a><span class="summary-sig-name">_readline_and_check_start</span>(<span class="summary-sig-arg">handle</span>,
<span class="summary-sig-arg">start</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_readline_and_check_start">source code</a></span>
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<span class="summary-type">MarkovModel()</span>
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<td><span class="summary-sig"><a name="load"></a><span class="summary-sig-name">load</span>(<span class="summary-sig-arg">handle</span>)</span></td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#load">source code</a></span>
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<td><span class="summary-sig"><a name="save"></a><span class="summary-sig-name">save</span>(<span class="summary-sig-arg">mm</span>,
<span class="summary-sig-arg">handle</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#save">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.MarkovModel-module.html#train_bw" class="summary-sig-name">train_bw</a>(<span class="summary-sig-arg">states</span>,
<span class="summary-sig-arg">alphabet</span>,
<span class="summary-sig-arg">training_data</span>,
<span class="summary-sig-arg">pseudo_initial</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">pseudo_transition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">pseudo_emission</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">update_fn</span>=<span class="summary-sig-default">None</span>)</span><br />
train_bw(states, alphabet, training_data[, pseudo_initial] [,
pseudo_transition][, pseudo_emission][, update_fn]) -> MarkovModel</td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#train_bw">source code</a></span>
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<td><span class="summary-sig"><a name="_baum_welch"></a><span class="summary-sig-name">_baum_welch</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">M</span>,
<span class="summary-sig-arg">training_outputs</span>,
<span class="summary-sig-arg">p_initial</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">p_transition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">p_emission</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">pseudo_initial</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">pseudo_transition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">pseudo_emission</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">update_fn</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_baum_welch">source code</a></span>
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<td><span class="summary-sig"><a name="_baum_welch_one"></a><span class="summary-sig-name">_baum_welch_one</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">M</span>,
<span class="summary-sig-arg">outputs</span>,
<span class="summary-sig-arg">lp_initial</span>,
<span class="summary-sig-arg">lp_transition</span>,
<span class="summary-sig-arg">lp_emission</span>,
<span class="summary-sig-arg">lpseudo_initial</span>,
<span class="summary-sig-arg">lpseudo_transition</span>,
<span class="summary-sig-arg">lpseudo_emission</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_baum_welch_one">source code</a></span>
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<td><span class="summary-sig"><a name="_forward"></a><span class="summary-sig-name">_forward</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">T</span>,
<span class="summary-sig-arg">lp_initial</span>,
<span class="summary-sig-arg">lp_transition</span>,
<span class="summary-sig-arg">lp_emission</span>,
<span class="summary-sig-arg">outputs</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_forward">source code</a></span>
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<td><span class="summary-sig"><a name="_backward"></a><span class="summary-sig-name">_backward</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">T</span>,
<span class="summary-sig-arg">lp_transition</span>,
<span class="summary-sig-arg">lp_emission</span>,
<span class="summary-sig-arg">outputs</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_backward">source code</a></span>
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<td><span class="summary-sig"><a href="Bio.MarkovModel-module.html#train_visible" class="summary-sig-name">train_visible</a>(<span class="summary-sig-arg">states</span>,
<span class="summary-sig-arg">alphabet</span>,
<span class="summary-sig-arg">training_data</span>,
<span class="summary-sig-arg">pseudo_initial</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">pseudo_transition</span>=<span class="summary-sig-default">None</span>,
<span class="summary-sig-arg">pseudo_emission</span>=<span class="summary-sig-default">None</span>)</span><br />
train_visible(states, alphabet, training_data[, pseudo_initial] [,
pseudo_transition][, pseudo_emission]) -> MarkovModel</td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#train_visible">source code</a></span>
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<td><span class="summary-sig"><a name="_mle"></a><span class="summary-sig-name">_mle</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">M</span>,
<span class="summary-sig-arg">training_outputs</span>,
<span class="summary-sig-arg">training_states</span>,
<span class="summary-sig-arg">pseudo_initial</span>,
<span class="summary-sig-arg">pseudo_transition</span>,
<span class="summary-sig-arg">pseudo_emission</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_mle">source code</a></span>
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<td><span class="summary-sig"><a name="_argmaxes"></a><span class="summary-sig-name">_argmaxes</span>(<span class="summary-sig-arg">vector</span>,
<span class="summary-sig-arg">allowance</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_argmaxes">source code</a></span>
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<span class="summary-type">list of (states, score)</span>
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<td><span class="summary-sig"><a name="find_states"></a><span class="summary-sig-name">find_states</span>(<span class="summary-sig-arg">markov_model</span>,
<span class="summary-sig-arg">output</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#find_states">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_viterbi"></a><span class="summary-sig-name">_viterbi</span>(<span class="summary-sig-arg">N</span>,
<span class="summary-sig-arg">lp_initial</span>,
<span class="summary-sig-arg">lp_transition</span>,
<span class="summary-sig-arg">lp_emission</span>,
<span class="summary-sig-arg">output</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_viterbi">source code</a></span>
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<td><span class="summary-sig"><a name="_normalize"></a><span class="summary-sig-name">_normalize</span>(<span class="summary-sig-arg">matrix</span>)</span></td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_normalize">source code</a></span>
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<td><span class="summary-sig"><a name="_uniform_norm"></a><span class="summary-sig-name">_uniform_norm</span>(<span class="summary-sig-arg">shape</span>)</span></td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_uniform_norm">source code</a></span>
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<td><span class="summary-sig"><a name="_random_norm"></a><span class="summary-sig-name">_random_norm</span>(<span class="summary-sig-arg">shape</span>)</span></td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_random_norm">source code</a></span>
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<td><span class="summary-sig"><a name="_copy_and_check"></a><span class="summary-sig-name">_copy_and_check</span>(<span class="summary-sig-arg">matrix</span>,
<span class="summary-sig-arg">desired_shape</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_copy_and_check">source code</a></span>
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<td><span class="summary-sig"><a name="_safe_copy_and_check"></a><span class="summary-sig-name">_safe_copy_and_check</span>(<span class="summary-sig-arg">matrix</span>,
<span class="summary-sig-arg">desired_shape</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_safe_copy_and_check">source code</a></span>
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<td><span class="summary-sig"><a name="_safe_log"></a><span class="summary-sig-name">_safe_log</span>(<span class="summary-sig-arg">n</span>)</span></td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_safe_log">source code</a></span>
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<td><span class="summary-sig"><a name="_safe_asarray"></a><span class="summary-sig-name">_safe_asarray</span>(<span class="summary-sig-arg">a</span>,
<span class="summary-sig-arg">typecode</span>=<span class="summary-sig-default">None</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_safe_asarray">source code</a></span>
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<td><span class="summary-sig"><a name="_logadd"></a><span class="summary-sig-name">_logadd</span>(<span class="summary-sig-arg">logx</span>,
<span class="summary-sig-arg">logy</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_logadd">source code</a></span>
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<td><span class="summary-sig"><a name="_logsum"></a><span class="summary-sig-name">_logsum</span>(<span class="summary-sig-arg">matrix</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_logsum">source code</a></span>
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<td><span class="summary-sig"><a name="_logvecadd"></a><span class="summary-sig-name">_logvecadd</span>(<span class="summary-sig-arg">logvec1</span>,
<span class="summary-sig-arg">logvec2</span>)</span></td>
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<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_logvecadd">source code</a></span>
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<span class="summary-type"> </span>
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<td><span class="summary-sig"><a name="_exp_logsum"></a><span class="summary-sig-name">_exp_logsum</span>(<span class="summary-sig-arg">numbers</span>)</span></td>
<td align="right" valign="top">
<span class="codelink"><a href="Bio.MarkovModel-pysrc.html#_exp_logsum">source code</a></span>
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<!-- ==================== VARIABLES ==================== -->
<a name="section-Variables"></a>
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<tr bgcolor="#70b0f0" class="table-header">
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<td align="left"><span class="table-header">Variables</span></td>
<td align="right" valign="top"
><span class="options">[<a href="#section-Variables"
class="privatelink" onclick="toggle_private();"
>hide private</a>]</span></td>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="VERY_SMALL_NUMBER"></a><span class="summary-name">VERY_SMALL_NUMBER</span> = <code title="1e-300">1e-300</code>
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<span class="summary-type"> </span>
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<a name="LOG0"></a><span class="summary-name">LOG0</span> = <code title="-690.775527898">-690.775527898</code>
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<span class="summary-type"> </span>
</td><td class="summary">
<a name="MATCODE"></a><span class="summary-name">MATCODE</span> = <code title="'d'"><code class="variable-quote">'</code><code class="variable-string">d</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="MAX_ITERATIONS"></a><span class="summary-name">MAX_ITERATIONS</span> = <code title="1000">1000</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="this_module"></a><span class="summary-name">this_module</span> = <code title="sys.modules [__name__]">sys.modules [__name__]</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Complex0"></a><span class="summary-name">Complex0</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Complex16"></a><span class="summary-name">Complex16</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Complex32"></a><span class="summary-name">Complex32</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Complex64"></a><span class="summary-name">Complex64</span> = <code title="'D'"><code class="variable-quote">'</code><code class="variable-string">D</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Complex8"></a><span class="summary-name">Complex8</span> = <code title="'F'"><code class="variable-quote">'</code><code class="variable-string">F</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Float0"></a><span class="summary-name">Float0</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Float16"></a><span class="summary-name">Float16</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Float32"></a><span class="summary-name">Float32</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Float64"></a><span class="summary-name">Float64</span> = <code title="'d'"><code class="variable-quote">'</code><code class="variable-string">d</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Float8"></a><span class="summary-name">Float8</span> = <code title="'f'"><code class="variable-quote">'</code><code class="variable-string">f</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int0"></a><span class="summary-name">Int0</span> = <code title="'1'"><code class="variable-quote">'</code><code class="variable-string">1</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int16"></a><span class="summary-name">Int16</span> = <code title="'s'"><code class="variable-quote">'</code><code class="variable-string">s</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int32"></a><span class="summary-name">Int32</span> = <code title="'i'"><code class="variable-quote">'</code><code class="variable-string">i</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int64"></a><span class="summary-name">Int64</span> = <code title="'l'"><code class="variable-quote">'</code><code class="variable-string">l</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="Int8"></a><span class="summary-name">Int8</span> = <code title="'1'"><code class="variable-quote">'</code><code class="variable-string">1</code><code class="variable-quote">'</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a href="Bio.MarkovModel-module.html#__warningregistry__" class="summary-name">__warningregistry__</a> = <code title="{('Not importing directory \'/usr/lib64/python2.5/site-packages/Numeri\
c\': missing __init__.py',
<type 'exceptions.ImportWarning'>,
20): 1}"><code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Not importing directory \'/usr/lib64/</code><code class="variable-ellipsis">...</code></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="absolute"></a><span class="summary-name">absolute</span> = <code title="<ufunc 'absolute'>"><ufunc 'absolute'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="add"></a><span class="summary-name">add</span> = <code title="<ufunc 'add'>"><ufunc 'add'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="arccos"></a><span class="summary-name">arccos</span> = <code title="<ufunc 'arccos'>"><ufunc 'arccos'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="arccosh"></a><span class="summary-name">arccosh</span> = <code title="<ufunc 'arccosh'>"><ufunc 'arccosh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="arcsin"></a><span class="summary-name">arcsin</span> = <code title="<ufunc 'arcsin'>"><ufunc 'arcsin'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="arcsinh"></a><span class="summary-name">arcsinh</span> = <code title="<ufunc 'arcsinh'>"><ufunc 'arcsinh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="arctan"></a><span class="summary-name">arctan</span> = <code title="<ufunc 'arctan'>"><ufunc 'arctan'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="arctan2"></a><span class="summary-name">arctan2</span> = <code title="<ufunc 'arctan2'>"><ufunc 'arctan2'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="arctanh"></a><span class="summary-name">arctanh</span> = <code title="<ufunc 'arctanh'>"><ufunc 'arctanh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="bitwise_and"></a><span class="summary-name">bitwise_and</span> = <code title="<ufunc 'bitwise_and'>"><ufunc 'bitwise_and'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="bitwise_or"></a><span class="summary-name">bitwise_or</span> = <code title="<ufunc 'bitwise_or'>"><ufunc 'bitwise_or'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="bitwise_xor"></a><span class="summary-name">bitwise_xor</span> = <code title="<ufunc 'bitwise_xor'>"><ufunc 'bitwise_xor'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="ceil"></a><span class="summary-name">ceil</span> = <code title="<ufunc 'ceil'>"><ufunc 'ceil'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="conjugate"></a><span class="summary-name">conjugate</span> = <code title="<ufunc 'conjugate'>"><ufunc 'conjugate'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="cos"></a><span class="summary-name">cos</span> = <code title="<ufunc 'cos'>"><ufunc 'cos'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="cosh"></a><span class="summary-name">cosh</span> = <code title="<ufunc 'cosh'>"><ufunc 'cosh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="divide"></a><span class="summary-name">divide</span> = <code title="<ufunc 'divide'>"><ufunc 'divide'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="divide_safe"></a><span class="summary-name">divide_safe</span> = <code title="<ufunc 'divide_safe'>"><ufunc 'divide_safe'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="e"></a><span class="summary-name">e</span> = <code title="2.71828182846">2.71828182846</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="equal"></a><span class="summary-name">equal</span> = <code title="<ufunc 'equal'>"><ufunc 'equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="exp"></a><span class="summary-name">exp</span> = <code title="<ufunc 'exp'>"><ufunc 'exp'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="fabs"></a><span class="summary-name">fabs</span> = <code title="<ufunc 'fabs'>"><ufunc 'fabs'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="floor"></a><span class="summary-name">floor</span> = <code title="<ufunc 'floor'>"><ufunc 'floor'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="floor_divide"></a><span class="summary-name">floor_divide</span> = <code title="<ufunc 'floor_divide'>"><ufunc 'floor_divide'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="fmod"></a><span class="summary-name">fmod</span> = <code title="<ufunc 'fmod'>"><ufunc 'fmod'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="greater"></a><span class="summary-name">greater</span> = <code title="<ufunc 'greater'>"><ufunc 'greater'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="greater_equal"></a><span class="summary-name">greater_equal</span> = <code title="<ufunc 'greater_equal'>"><ufunc 'greater_equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="hypot"></a><span class="summary-name">hypot</span> = <code title="<ufunc 'hypot'>"><ufunc 'hypot'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="invert"></a><span class="summary-name">invert</span> = <code title="<ufunc 'invert'>"><ufunc 'invert'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="left_shift"></a><span class="summary-name">left_shift</span> = <code title="<ufunc 'left_shift'>"><ufunc 'left_shift'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="less"></a><span class="summary-name">less</span> = <code title="<ufunc 'less'>"><ufunc 'less'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="less_equal"></a><span class="summary-name">less_equal</span> = <code title="<ufunc 'less_equal'>"><ufunc 'less_equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="log"></a><span class="summary-name">log</span> = <code title="<ufunc 'log'>"><ufunc 'log'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="log10"></a><span class="summary-name">log10</span> = <code title="<ufunc 'log10'>"><ufunc 'log10'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_and"></a><span class="summary-name">logical_and</span> = <code title="<ufunc 'logical_and'>"><ufunc 'logical_and'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_not"></a><span class="summary-name">logical_not</span> = <code title="<ufunc 'logical_not'>"><ufunc 'logical_not'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_or"></a><span class="summary-name">logical_or</span> = <code title="<ufunc 'logical_or'>"><ufunc 'logical_or'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="logical_xor"></a><span class="summary-name">logical_xor</span> = <code title="<ufunc 'logical_xor'>"><ufunc 'logical_xor'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="maximum"></a><span class="summary-name">maximum</span> = <code title="<ufunc 'maximum'>"><ufunc 'maximum'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="minimum"></a><span class="summary-name">minimum</span> = <code title="<ufunc 'minimum'>"><ufunc 'minimum'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="multiply"></a><span class="summary-name">multiply</span> = <code title="<ufunc 'multiply'>"><ufunc 'multiply'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="negative"></a><span class="summary-name">negative</span> = <code title="<ufunc 'negative'>"><ufunc 'negative'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="not_equal"></a><span class="summary-name">not_equal</span> = <code title="<ufunc 'not_equal'>"><ufunc 'not_equal'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="pi"></a><span class="summary-name">pi</span> = <code title="3.14159265359">3.14159265359</code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="power"></a><span class="summary-name">power</span> = <code title="<ufunc 'power'>"><ufunc 'power'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="remainder"></a><span class="summary-name">remainder</span> = <code title="<ufunc 'remainder'>"><ufunc 'remainder'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="right_shift"></a><span class="summary-name">right_shift</span> = <code title="<ufunc 'right_shift'>"><ufunc 'right_shift'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sin"></a><span class="summary-name">sin</span> = <code title="<ufunc 'sin'>"><ufunc 'sin'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sinh"></a><span class="summary-name">sinh</span> = <code title="<ufunc 'sinh'>"><ufunc 'sinh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="sqrt"></a><span class="summary-name">sqrt</span> = <code title="<ufunc 'sqrt'>"><ufunc 'sqrt'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="subtract"></a><span class="summary-name">subtract</span> = <code title="<ufunc 'subtract'>"><ufunc 'subtract'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="tan"></a><span class="summary-name">tan</span> = <code title="<ufunc 'tan'>"><ufunc 'tan'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="tanh"></a><span class="summary-name">tanh</span> = <code title="<ufunc 'tanh'>"><ufunc 'tanh'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="true_divide"></a><span class="summary-name">true_divide</span> = <code title="<ufunc 'true_divide'>"><ufunc 'true_divide'></code>
</td>
</tr>
<tr>
<td width="15%" align="right" valign="top" class="summary">
<span class="summary-type"> </span>
</td><td class="summary">
<a name="x"></a><span class="summary-name">x</span> = <code title="ImportError('No module named cMarkovModel',)">ImportError('No module named cMarkovModel',)</code>
</td>
</tr>
</table>
<!-- ==================== FUNCTION DETAILS ==================== -->
<a name="section-FunctionDetails"></a>
<table class="details" border="1" cellpadding="3"
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<h3 class="epydoc"><span class="sig"><span class="sig-name">train_bw</span>(<span class="sig-arg">states</span>,
<span class="sig-arg">alphabet</span>,
<span class="sig-arg">training_data</span>,
<span class="sig-arg">pseudo_initial</span>=<span class="sig-default">None</span>,
<span class="sig-arg">pseudo_transition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">pseudo_emission</span>=<span class="sig-default">None</span>,
<span class="sig-arg">update_fn</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MarkovModel-pysrc.html#train_bw">source code</a></span>
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<p>train_bw(states, alphabet, training_data[, pseudo_initial] [,
pseudo_transition][, pseudo_emission][, update_fn]) -> MarkovModel</p>
<p>Train a MarkovModel using the Baum-Welch algorithm. states is a list
of strings that describe the names of each state. alphabet is a list of
objects that indicate the allowed outputs. training_data is a list of
observations. Each observation is a list of objects from the
alphabet.</p>
<p>pseudo_initial, pseudo_transition, and pseudo_emission are optional
parameters that you can use to assign pseudo-counts to different
matrices. They should be matrices of the appropriate size that contain
numbers to add to each parameter matrix, before normalization.</p>
<p>update_fn is an optional callback that takes parameters (iteration,
log_likelihood). It is called once per iteration.</p>
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<h3 class="epydoc"><span class="sig"><span class="sig-name">train_visible</span>(<span class="sig-arg">states</span>,
<span class="sig-arg">alphabet</span>,
<span class="sig-arg">training_data</span>,
<span class="sig-arg">pseudo_initial</span>=<span class="sig-default">None</span>,
<span class="sig-arg">pseudo_transition</span>=<span class="sig-default">None</span>,
<span class="sig-arg">pseudo_emission</span>=<span class="sig-default">None</span>)</span>
</h3>
</td><td align="right" valign="top"
><span class="codelink"><a href="Bio.MarkovModel-pysrc.html#train_visible">source code</a></span>
</td>
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<p>train_visible(states, alphabet, training_data[, pseudo_initial] [,
pseudo_transition][, pseudo_emission]) -> MarkovModel</p>
<p>Train a visible MarkovModel using maximum likelihoood estimates for
each of the parameters. states is a list of strings that describe the
names of each state. alphabet is a list of objects that indicate the
allowed outputs. training_data is a list of (outputs, observed states)
where outputs is a list of the emission from the alphabet, and observed
states is a list of states from states.</p>
<p>pseudo_initial, pseudo_transition, and pseudo_emission are optional
parameters that you can use to assign pseudo-counts to different
matrices. They should be matrices of the appropriate size that contain
numbers to add to each parameter matrix</p>
<dl class="fields">
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<h3 class="epydoc">__warningregistry__</h3>
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</dl>
<dl class="fields">
<dt>Value:</dt>
<dd><table><tr><td><pre class="variable">
<code class="variable-group">{</code><code class="variable-group">(</code><code class="variable-quote">'</code><code class="variable-string">Not importing directory \'/usr/lib64/python2.5/site-packages/Numeri</code><span class="variable-linewrap"><img src="crarr.png" alt="\" /></span>
<code class="variable-string">c\': missing __init__.py</code><code class="variable-quote">'</code><code class="variable-op">,</code>
<type 'exceptions.ImportWarning'><code class="variable-op">,</code>
20<code class="variable-group">)</code><code class="variable-op">: </code>1<code class="variable-group">}</code>
</pre></td></tr></table>
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