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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
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<!-- Generated by javadoc (version 1.7.0_65) on Tue Sep 02 20:47:15 CDT 2014 -->
<meta http-equiv="Content-Type" content="text/html" charset="UTF-8">
<title>DP (biojava-legacy 1.9.1 API)</title>
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<div class="subTitle">org.biojava.bio.dp</div>
<h2 title="Class DP" class="title">Class DP</h2>
</div>
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<ul class="inheritance">
<li><a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</a></li>
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<li>org.biojava.bio.dp.DP</li>
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<dl>
<dt>Direct Known Subclasses:</dt>
<dd><a href="../../../../org/biojava/bio/dp/twohead/PairwiseDP.html" title="class in org.biojava.bio.dp.twohead">PairwiseDP</a>, <a href="../../../../org/biojava/bio/dp/onehead/SingleDP.html" title="class in org.biojava.bio.dp.onehead">SingleDP</a></dd>
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<pre>public abstract class <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.84">DP</a>
extends <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</a></pre>
<div class="block"><p>
Objects that can perform dymamic programming operations upon sequences with
HMMs.
</p>
<p>
The three main DP operations are Forwards, Backwards and Viterbi. Forwards
and Backwards calculate the probability of the sequences having been made in
any way by the model. Viterbi finds the most supported way that the sequence
could have been made.
</p>
<p>
Each of the functions can return the dynamic-programming matrix containing
the intermediate results. This may be useful for model training, or for
visualisation.
</p>
<p>
Each of the funcitons can be calculated using the model probabilities, the
null-model probabilities or the odds (ratio between the two). For Forwards
and Backwards, the odds calculations produce numbers with questionable basis
in reality. For Viterbi with odds, you will recieve the path through the
model that is most different from the null model, and supported by the
probabilities.
</p></div>
<dl><dt><span class="strong">Author:</span></dt>
<dd>Matthew Pocock, Thomas Down</dd></dl>
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<td class="colFirst"><code>static class </code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.ReverseIterator.html" title="class in org.biojava.bio.dp">DP.ReverseIterator</a></strong></code> </td>
</tr>
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<caption><span>Constructors</span><span class="tabEnd"> </span></caption>
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<th class="colOne" scope="col">Constructor and Description</th>
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<td class="colOne"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#DP()">DP</a></strong>()</code>
<div class="block">This method will result in a DP with no model.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colOne"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#DP(org.biojava.bio.dp.MarkovModel)">DP</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model)</code> </td>
</tr>
</table>
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<caption><span>Methods</span><span class="tabEnd"> </span></caption>
<tr>
<th class="colFirst" scope="col">Modifier and Type</th>
<th class="colLast" scope="col">Method and Description</th>
</tr>
<tr class="altColor">
<td class="colFirst"><code>abstract double</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#backward(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.ScoreType)">backward</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.DPMatrix,%20org.biojava.bio.dp.ScoreType)">backwardMatrix</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> matrix,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#backwardMatrix(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.ScoreType)">backwardMatrix</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>static int[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#backwardTransitions(org.biojava.bio.dp.MarkovModel,%20org.biojava.bio.dp.State[])">backwardTransitions</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states)</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>static double[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#backwardTransitionScores(org.biojava.bio.dp.MarkovModel,%20org.biojava.bio.dp.State[],%20int[][],%20org.biojava.bio.dp.ScoreType)">backwardTransitionScores</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states,
int[][] transitions,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>static <a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#flatView(org.biojava.bio.dp.MarkovModel)">flatView</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model)</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>abstract double</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#forward(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.ScoreType)">forward</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.DPMatrix,%20org.biojava.bio.dp.ScoreType)">forwardMatrix</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> matrix,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#forwardMatrix(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.ScoreType)">forwardMatrix</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code><a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#forwardsBackwards(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.ScoreType)">forwardsBackwards</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>static int[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#forwardTransitions(org.biojava.bio.dp.MarkovModel,%20org.biojava.bio.dp.State[])">forwardTransitions</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states)</code>
<div class="block">Returns a matrix for the specified States describing all
valid Transitions between those States.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>static double[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#forwardTransitionScores(org.biojava.bio.dp.MarkovModel,%20org.biojava.bio.dp.State[],%20int[][],%20org.biojava.bio.dp.ScoreType)">forwardTransitionScores</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states,
int[][] transitions,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code>
<div class="block">Compute the log(score) of all transitions
between the specified States.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><code><a href="../../../../org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#generate(int)">generate</a></strong>(int length)</code>
<div class="block">
Generates an alignment from a model.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>int[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#getBackwardTransitions()">getBackwardTransitions</a></strong>()</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>double[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#getBackwardTransitionScores(org.biojava.bio.dp.ScoreType)">getBackwardTransitionScores</a></strong>(<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>int</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#getDotStatesIndex()">getDotStatesIndex</a></strong>()</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>int[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#getForwardTransitions()">getForwardTransitions</a></strong>()</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>double[][]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#getForwardTransitionScores(org.biojava.bio.dp.ScoreType)">getForwardTransitionScores</a></strong>(<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code><a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#getModel()">getModel</a></strong>()</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code><a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#getStates()">getStates</a></strong>()</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#lockModel()">lockModel</a></strong>()</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>static double</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#scoreWeightMatrix(org.biojava.bio.dp.WeightMatrix,%20org.biojava.bio.symbol.SymbolList,%20int)">scoreWeightMatrix</a></strong>(<a href="../../../../org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp">WeightMatrix</a> matrix,
<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a> symList,
int start)</code>
<div class="block">Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix.</div>
</td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>static double</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#scoreWeightMatrix(org.biojava.bio.dp.WeightMatrix,%20org.biojava.bio.symbol.SymbolList,%20org.biojava.bio.dp.ScoreType,%20int)">scoreWeightMatrix</a></strong>(<a href="../../../../org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp">WeightMatrix</a> matrix,
<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a> symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType,
int start)</code>
<div class="block">Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix using a particular ScoreType.</div>
</td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#setModel(org.biojava.bio.dp.MarkovModel)">setModel</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model)</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code><a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[]</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#stateList(org.biojava.bio.dp.MarkovModel)">stateList</a></strong>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> mm)</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#unlockModel()">unlockModel</a></strong>()</code> </td>
</tr>
<tr class="altColor">
<td class="colFirst"><code>void</code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#update()">update</a></strong>()</code> </td>
</tr>
<tr class="rowColor">
<td class="colFirst"><code>abstract <a href="../../../../org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a></code></td>
<td class="colLast"><code><strong><a href="../../../../org/biojava/bio/dp/DP.html#viterbi(org.biojava.bio.symbol.SymbolList[],%20org.biojava.bio.dp.ScoreType)">viterbi</a></strong>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</code> </td>
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<h3>Methods inherited from class java.lang.<a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</a></h3>
<code><a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</a>, <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/Object.html?is-external=true#wait(long,%20int)" title="class or interface in java.lang">wait</a></code></li>
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<h3>Constructor Detail</h3>
<a name="DP(org.biojava.bio.dp.MarkovModel)">
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<h4>DP</h4>
<pre>public <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.499">DP</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model)</pre>
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<h4>DP</h4>
<pre>public <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.507">DP</a>()</pre>
<div class="block">This method will result in a DP with no model. Use the setModel() method
to set the model before use.</div>
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<pre>public static double <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.113">scoreWeightMatrix</a>(<a href="../../../../org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp">WeightMatrix</a> matrix,
<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a> symList,
int start)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></pre>
<div class="block">Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix.</div>
<dl><dt><span class="strong">Parameters:</span></dt><dd><code>matrix</code> - the weight matrix used to evaluate the sequences</dd><dd><code>symList</code> - the SymbolList to assess</dd><dd><code>start</code> - the index of the first symbol in the window to evaluate</dd>
<dt><span class="strong">Returns:</span></dt><dd>the log probability or likelyhood of this weight matrix
having generated symbols start to (start + columns) of symList</dd>
<dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd></dl>
</li>
</ul>
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<pre>public static double <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.145">scoreWeightMatrix</a>(<a href="../../../../org/biojava/bio/dp/WeightMatrix.html" title="interface in org.biojava.bio.dp">WeightMatrix</a> matrix,
<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a> symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType,
int start)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></pre>
<div class="block">Scores the SymbolList from symbol start to symbol (start+columns) with a
weight matrix using a particular ScoreType.
<p>
This method allows you to use score types such as ScoreType.ODDS. The other
scoreWeightMatrix methods gives a result similar or identical to
ScoreType.PROBABILITY.
</p></div>
<dl><dt><span class="strong">Parameters:</span></dt><dd><code>matrix</code> - the weight matrix used to evaluate the sequences</dd><dd><code>symList</code> - the SymbolList to assess</dd><dd><code>scoreType</code> - the score type to apply</dd><dd><code>start</code> - the index of the first symbol in the window to evaluate</dd>
<dt><span class="strong">Returns:</span></dt><dd>the sum of log scores of this weight matrix
having generated symbols start to (start + columns) of symList</dd>
<dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd><dt><span class="strong">Since:</span></dt>
<dd>1.4</dd></dl>
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<pre>public static <a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.161">flatView</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model)
throws <a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd></dl>
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<h4>stateList</h4>
<pre>public <a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.176">stateList</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> mm)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a>,
<a href="../../../../org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></code></dd></dl>
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<h4>forwardTransitions</h4>
<pre>public static int[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.280">forwardTransitions</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></pre>
<div class="block">Returns a matrix for the specified States describing all
valid Transitions between those States.
<p>
The matrix is 2-dimensional. The primary array has an element
corresponding to every State in the states argument. That
element is itself an array the elements of which identify
the States that can reach that State. The source States
are identified by their index within the states [] array.</div>
<dl><dt><span class="strong">Parameters:</span></dt><dd><code>model</code> - MarkovModel to be analysed.</dd><dd><code>states</code> - The States for which the transition matrix is to be determined.</dd>
<dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd></dl>
</li>
</ul>
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<pre>public static double[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.320">forwardTransitionScores</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states,
int[][] transitions,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</pre>
<div class="block">Compute the log(score) of all transitions
between the specified States. The layout
of the array is identical to that of the transitions
array.
<p>
Note that all parameters <b>MUST</b> be
consistent with each other!!!!
<p></div>
<dl><dt><span class="strong">Parameters:</span></dt><dd><code>model</code> - The model for which the data is to be computed.</dd><dd><code>states</code> - The States within that model for which scores are required.</dd><dd><code>transitions</code> - The transition matrix obtained by calling forwardTransitions() with the above argument values.</dd><dd><code>scoreType</code> - The type of score to be evaluated.</dd></dl>
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<pre>public static int[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.359">backwardTransitions</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd></dl>
</li>
</ul>
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<pre>public static double[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.385">backwardTransitionScores</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model,
<a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] states,
int[][] transitions,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</pre>
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<pre>public int <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.420">getDotStatesIndex</a>()</pre>
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<pre>public <a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.424">getModel</a>()</pre>
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<pre>public <a href="../../../../org/biojava/bio/dp/State.html" title="interface in org.biojava.bio.dp">State</a>[] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.428">getStates</a>()</pre>
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<pre>public int[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.432">getForwardTransitions</a>()</pre>
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<pre>public double[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.439">getForwardTransitionScores</a>(<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</pre>
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<pre>public int[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.449">getBackwardTransitions</a>()</pre>
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<pre>public double[][] <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.453">getBackwardTransitionScores</a>(<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)</pre>
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<pre>public void <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.463">lockModel</a>()</pre>
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<pre>public void <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.469">unlockModel</a>()</pre>
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<pre>public void <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.475">update</a>()</pre>
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<pre>public void <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.509">setModel</a>(<a href="../../../../org/biojava/bio/dp/MarkovModel.html" title="interface in org.biojava.bio.dp">MarkovModel</a> model)</pre>
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<h4>forward</h4>
<pre>public abstract double <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.518">forward</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd></dl>
</li>
</ul>
<a name="backward(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">
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</a>
<ul class="blockList">
<li class="blockList">
<h4>backward</h4>
<pre>public abstract double <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.521">backward</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd></dl>
</li>
</ul>
<a name="forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">
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</a>
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<li class="blockList">
<h4>forwardMatrix</h4>
<pre>public abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.524">forwardMatrix</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd></dl>
</li>
</ul>
<a name="backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">
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</a>
<ul class="blockList">
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<h4>backwardMatrix</h4>
<pre>public abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.527">backwardMatrix</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd></dl>
</li>
</ul>
<a name="forwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">
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</a>
<ul class="blockList">
<li class="blockList">
<h4>forwardMatrix</h4>
<pre>public abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.530">forwardMatrix</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> matrix,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd></dl>
</li>
</ul>
<a name="backwardMatrix(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.DPMatrix, org.biojava.bio.dp.ScoreType)">
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<h4>backwardMatrix</h4>
<pre>public abstract <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.534">backwardMatrix</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> matrix,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd></dl>
</li>
</ul>
<a name="viterbi(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">
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<li class="blockList">
<h4>viterbi</h4>
<pre>public abstract <a href="../../../../org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.538">viterbi</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</a>,
<a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a>,
<a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="http://docs.oracle.com/javase/1.5.0/docs/api/java/lang/IllegalArgumentException.html?is-external=true" title="class or interface in java.lang">IllegalArgumentException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalAlphabetException.html" title="class in org.biojava.bio.symbol">IllegalAlphabetException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/dp/IllegalTransitionException.html" title="class in org.biojava.bio.dp">IllegalTransitionException</a></code></dd></dl>
</li>
</ul>
<a name="forwardsBackwards(org.biojava.bio.symbol.SymbolList[], org.biojava.bio.dp.ScoreType)">
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</a>
<ul class="blockList">
<li class="blockList">
<h4>forwardsBackwards</h4>
<pre>public <a href="../../../../org/biojava/bio/dp/DPMatrix.html" title="interface in org.biojava.bio.dp">DPMatrix</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.541">forwardsBackwards</a>(<a href="../../../../org/biojava/bio/symbol/SymbolList.html" title="interface in org.biojava.bio.symbol">SymbolList</a>[] symList,
<a href="../../../../org/biojava/bio/dp/ScoreType.html" title="interface in org.biojava.bio.dp">ScoreType</a> scoreType)
throws <a href="../../../../org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></pre>
<dl><dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></code></dd></dl>
</li>
</ul>
<a name="generate(int)">
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</a>
<ul class="blockListLast">
<li class="blockList">
<h4>generate</h4>
<pre>public <a href="../../../../org/biojava/bio/dp/StatePath.html" title="interface in org.biojava.bio.dp">StatePath</a> <a href="../../../../src-html/org/biojava/bio/dp/DP.html#line.591">generate</a>(int length)
throws <a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a>,
<a href="../../../../org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></pre>
<div class="block"><p>
Generates an alignment from a model.
</p>
<p>
If the length is set to -1 then the model length will be sampled
using the model's transition to the end state. If the length is
fixed using length, then the transitions to the end state are implicitly
invoked.
</p></div>
<dl><dt><span class="strong">Parameters:</span></dt><dd><code>length</code> - the length of the sequence to generate</dd>
<dt><span class="strong">Returns:</span></dt><dd>a StatePath generated at random</dd>
<dt><span class="strong">Throws:</span></dt>
<dd><code><a href="../../../../org/biojava/bio/symbol/IllegalSymbolException.html" title="class in org.biojava.bio.symbol">IllegalSymbolException</a></code></dd>
<dd><code><a href="../../../../org/biojava/bio/BioException.html" title="class in org.biojava.bio">BioException</a></code></dd></dl>
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