Code/Projects/PacketLevelSignatureExtractor/javadoc/edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html

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  95 <h2 title="Class SequenceAlignment" class="title">Class SequenceAlignment&lt;ALIGNMENT_UNIT&gt;</h2>
  96 </div>
  97 <div class="contentContainer">
  98 <ul class="inheritance">
  99 <li>java.lang.Object</li>
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 102 <li>edu.uci.iotproject.comparison.seqalignment.SequenceAlignment&lt;ALIGNMENT_UNIT&gt;</li>
 103 </ul>
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 105 </ul>
 106 <div class="description">
 107 <ul class="blockList">
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 109 <dl>
 110 <dt><span class="paramLabel">Type Parameters:</span></dt>
 111 <dd><code>ALIGNMENT_UNIT</code> - The <em>unit of the alignment</em>, or, in other words, the <em>granularity</em> of the
 112                         alignment. For example, for 'classical' string alignment (as in sequence alignment where we
 113                         try to align two strings character by character -- the example most often used in books on
 114                         algorithms) this would be a <code>Character</code>. As a second example, by specifying
 115                         <code>String</code>, one can decrease the granularity so as to align <em>blocks</em> of characters
 116                         (e.g., if one wants to align to two string arrays).</dd>
 117 </dl>
 118 <hr>
 119 <br>
 120 <pre>public class <span class="typeNameLabel">SequenceAlignment&lt;ALIGNMENT_UNIT&gt;</span>
 121 extends java.lang.Object</pre>
 122 <div class="block">A generic implementation of the sequence alignment algorithm given in Kleinberg's and Tardos' "Algorithm Design".
 123  This implementation is the basic version. There is a more complex version which significantly reduces the space
 124  complexity at a slight cost to time complexity.</div>
 125 </li>
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 143 <td class="colOne"><code><span class="memberNameLink"><a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html#SequenceAlignment-edu.uci.iotproject.comparison.seqalignment.AlignmentPricer-">SequenceAlignment</a></span>(<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="class in edu.uci.iotproject.comparison.seqalignment">AlignmentPricer</a>&lt;<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="type parameter in SequenceAlignment">ALIGNMENT_UNIT</a>&gt;&nbsp;alignmentPricer)</code>
 144 <div class="block">Constructs a new <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="class in edu.uci.iotproject.comparison.seqalignment"><code>SequenceAlignment</code></a>.</div>
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 163 <td class="colFirst"><code>int</code></td>
 164 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html#calculateAlignment-ALIGNMENT_UNIT:A-ALIGNMENT_UNIT:A-">calculateAlignment</a></span>(<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="type parameter in SequenceAlignment">ALIGNMENT_UNIT</a>[]&nbsp;sequence1,
 165                   <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="type parameter in SequenceAlignment">ALIGNMENT_UNIT</a>[]&nbsp;sequence2)</code>
 166 <div class="block">Calculates the cost of aligning <code>sequence1</code> with <code>sequence2</code>.</div>
 167 </td>
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 192 <!--   -->
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 195 <li class="blockList">
 196 <h4>SequenceAlignment</h4>
 197 <pre>public&nbsp;SequenceAlignment(<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="class in edu.uci.iotproject.comparison.seqalignment">AlignmentPricer</a>&lt;<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="type parameter in SequenceAlignment">ALIGNMENT_UNIT</a>&gt;&nbsp;alignmentPricer)</pre>
 198 <div class="block">Constructs a new <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="class in edu.uci.iotproject.comparison.seqalignment"><code>SequenceAlignment</code></a>. The new instance relies on the provided <code>alignmentPricer</code> to
 199  provide the cost of aligning two <code>ALIGNMENT_UNIT</code>s as well as the cost of aligning an
 200  <code>ALIGNMENT_UNIT</code> with a gap.</div>
 201 <dl>
 202 <dt><span class="paramLabel">Parameters:</span></dt>
 203 <dd><code>alignmentPricer</code> - An <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="class in edu.uci.iotproject.comparison.seqalignment"><code>AlignmentPricer</code></a> that provides the cost of aligning two <code>ALIGNMENT_UNIT</code>s
 204                         with one another as well as the cost of aligning an <code>ALIGNMENT_UNIT</code> with a gap.</dd>
 205 </dl>
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 216 <a name="calculateAlignment-java.lang.Object:A-java.lang.Object:A-">
 217 <!--   -->
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 219 <!--   -->
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 223 <h4>calculateAlignment</h4>
 224 <pre>public&nbsp;int&nbsp;calculateAlignment(<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="type parameter in SequenceAlignment">ALIGNMENT_UNIT</a>[]&nbsp;sequence1,
 225                               <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SequenceAlignment.html" title="type parameter in SequenceAlignment">ALIGNMENT_UNIT</a>[]&nbsp;sequence2)</pre>
 226 <div class="block">Calculates the cost of aligning <code>sequence1</code> with <code>sequence2</code>.</div>
 227 <dl>
 228 <dt><span class="paramLabel">Parameters:</span></dt>
 229 <dd><code>sequence1</code> - A sequence that is to be aligned with <code>sequence2</code>.</dd>
 230 <dd><code>sequence2</code> - A sequence that is to be aligned with <code>sequence1</code>.</dd>
 231 <dt><span class="returnLabel">Returns:</span></dt>
 232 <dd>The cost of aligning <code>sequence1</code> with <code>sequence2</code>.</dd>
 233 </dl>
 234 </li>
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