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

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  95 <h2 title="Class AlignmentPricer" class="title">Class AlignmentPricer&lt;T&gt;</h2>
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  98 <ul class="inheritance">
  99 <li>java.lang.Object</li>
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 109 <dl>
 110 <dt><span class="paramLabel">Type Parameters:</span></dt>
 111 <dd><code>T</code> - The type of the elements that are being aligned.</dd>
 112 </dl>
 113 <dl>
 114 <dt>Direct Known Subclasses:</dt>
 115 <dd><a href="../../../../../edu/uci/iotproject/comparison/seqalignment/SampleIntegerAlignmentPricer.html" title="class in edu.uci.iotproject.comparison.seqalignment">SampleIntegerAlignmentPricer</a></dd>
 116 </dl>
 117 <hr>
 118 <br>
 119 <pre>public class <span class="typeNameLabel">AlignmentPricer&lt;T&gt;</span>
 120 extends java.lang.Object</pre>
 121 <div class="block">Provides a generic implementation for the calculation of the cost of aligning two elements of a sequence as part of
 122  the sequence alignment algorithm (the algorithm is implemented in <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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 138 <th class="colOne" scope="col">Constructor and Description</th>
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 140 <tr class="altColor">
 141 <td class="colOne"><code><span class="memberNameLink"><a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html#AlignmentPricer-java.util.function.ToIntBiFunction-java.util.function.ToIntFunction-">AlignmentPricer</a></span>(java.util.function.ToIntBiFunction&lt;<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>,<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&gt;&nbsp;alignmentCostFunction,
 142                java.util.function.ToIntFunction&lt;<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&gt;&nbsp;gapCostFunction)</code>
 143 <div class="block">Constructs a new <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="class in edu.uci.iotproject.comparison.seqalignment"><code>AlignmentPricer</code></a>.</div>
 144 </td>
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 162 <td class="colFirst"><code>int</code></td>
 163 <td class="colLast"><code><span class="memberNameLink"><a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html#alignmentCost-T-T-">alignmentCost</a></span>(<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&nbsp;item1,
 164              <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&nbsp;item2)</code>
 165 <div class="block">Calculate the cost of aligning <code>item1</code> with <code>item2</code>.</div>
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 195 <h4>AlignmentPricer</h4>
 196 <pre>public&nbsp;AlignmentPricer(java.util.function.ToIntBiFunction&lt;<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>,<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&gt;&nbsp;alignmentCostFunction,
 197                        java.util.function.ToIntFunction&lt;<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&gt;&nbsp;gapCostFunction)</pre>
 198 <div class="block">Constructs a new <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="class in edu.uci.iotproject.comparison.seqalignment"><code>AlignmentPricer</code></a>.</div>
 199 <dl>
 200 <dt><span class="paramLabel">Parameters:</span></dt>
 201 <dd><code>alignmentCostFunction</code> - A function that specifies the cost of aligning a <code>T</code> with some other <code>T</code>
 202                               (e.g., based on the values of the properties of the two instances).</dd>
 203 <dd><code>gapCostFunction</code> - A function that specifies the cost of aligning a <code>T</code> with a gap. Note that the
 204                         function is free to specify <em>different</em> gap costs for different <code>T</code>s.</dd>
 205 </dl>
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 218 </a><a name="alignmentCost-T-T-">
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 223 <h4>alignmentCost</h4>
 224 <pre>public&nbsp;int&nbsp;alignmentCost(<a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&nbsp;item1,
 225                          <a href="../../../../../edu/uci/iotproject/comparison/seqalignment/AlignmentPricer.html" title="type parameter in AlignmentPricer">T</a>&nbsp;item2)</pre>
 226 <div class="block">Calculate the cost of aligning <code>item1</code> with <code>item2</code>. If either of the two arguments is set to
 227  <code>null</code>, the cost of aligning the other argument with a gap will be returned. Note that both arguments
 228  cannot be <code>null</code> at the same time as that translates to aligning a gap with a gap, which is pointless.</div>
 229 <dl>
 230 <dt><span class="paramLabel">Parameters:</span></dt>
 231 <dd><code>item1</code> - The first of the two aligned objects. Set to <code>null</code> to calculate the cost of aligning
 232               <code>item2</code> with a gap.</dd>
 233 <dd><code>item2</code> - The second of the two aligned objects. Set to <code>null</code> to calculate the cost of aligning
 234               <code>item2</code> with a gap.</dd>
 235 <dt><span class="returnLabel">Returns:</span></dt>
 236 <dd>The cost of aligning <code>item1</code> with <code>item2</code>.</dd>
 237 </dl>
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