website/docs/dm_javadoc/compbio/data/sequence/ScoreManager.html

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  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Class ScoreManager" class="title">Class ScoreManager</h2>
  97 </div>
  98 <div class="contentContainer">
  99 <ul class="inheritance">
 100 <li>java.lang.Object</li>
 101 <li>
 102 <ul class="inheritance">
 103 <li>compbio.data.sequence.ScoreManager</li>
 104 </ul>
 105 </li>
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 110 <dl>
 111 <dt>Direct Known Subclasses:</dt>
 112 <dd><a href="../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></dd>
 113 </dl>
 114 <hr>
 115 <br>
 116 <pre>public class <span class="typeNameLabel">ScoreManager</span>
 117 extends java.lang.Object</pre>
 118 </li>
 119 </ul>
 120 </div>
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 132 <tr>
 133 <th class="colFirst" scope="col">Modifier and Type</th>
 134 <th class="colLast" scope="col">Class and Description</th>
 135 </tr>
 136 <tr class="altColor">
 137 <td class="colFirst"><code>static class&nbsp;</code></td>
 138 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></span></code>&nbsp;</td>
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 150 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 151 <tr>
 152 <th class="colFirst" scope="col">Modifier and Type</th>
 153 <th class="colLast" scope="col">Field and Description</th>
 154 </tr>
 155 <tr class="altColor">
 156 <td class="colFirst"><code>protected java.util.List&lt;<a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a>&gt;</code></td>
 157 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#seqScores">seqScores</a></span></code>&nbsp;</td>
 158 </tr>
 159 <tr class="rowColor">
 160 <td class="colFirst"><code>static java.lang.String</code></td>
 161 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</a></span></code>&nbsp;</td>
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 174 <tr>
 175 <th class="colFirst" scope="col">Modifier</th>
 176 <th class="colLast" scope="col">Constructor and Description</th>
 177 </tr>
 178 <tr class="altColor">
 179 <td class="colFirst"><code>protected </code></td>
 180 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#ScoreManager--">ScoreManager</a></span>()</code>&nbsp;</td>
 181 </tr>
 182 <tr class="rowColor">
 183 <td class="colFirst"><code>private </code></td>
 184 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#ScoreManager-java.util.Map-">ScoreManager</a></span>(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</code>&nbsp;</td>
 185 </tr>
 186 <tr class="altColor">
 187 <td class="colFirst"><code>private </code></td>
 188 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#ScoreManager-java.lang.String-java.util.Set-">ScoreManager</a></span>(java.lang.String&nbsp;id,
 189             java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;data)</code>&nbsp;</td>
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 201 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t1" class="tableTab"><span><a href="javascript:show(1);">Static Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 202 <tr>
 203 <th class="colFirst" scope="col">Modifier and Type</th>
 204 <th class="colLast" scope="col">Method and Description</th>
 205 </tr>
 206 <tr id="i0" class="altColor">
 207 <td class="colFirst"><code>java.util.Map&lt;java.lang.String,java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;</code></td>
 208 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#asMap--">asMap</a></span>()</code>&nbsp;</td>
 209 </tr>
 210 <tr id="i1" class="rowColor">
 211 <td class="colFirst"><code>java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 212 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#asSet--">asSet</a></span>()</code>&nbsp;</td>
 213 </tr>
 214 <tr id="i2" class="altColor">
 215 <td class="colFirst"><code>boolean</code></td>
 216 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#equals-java.lang.Object-">equals</a></span>(java.lang.Object&nbsp;obj)</code>&nbsp;</td>
 217 </tr>
 218 <tr id="i3" class="rowColor">
 219 <td class="colFirst"><code><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></code></td>
 220 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#getAnnotationForSequence-java.lang.String-">getAnnotationForSequence</a></span>(java.lang.String&nbsp;seqId)</code>&nbsp;</td>
 221 </tr>
 222 <tr id="i4" class="altColor">
 223 <td class="colFirst"><code>int</code></td>
 224 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#getNumberOfSeq--">getNumberOfSeq</a></span>()</code>&nbsp;</td>
 225 </tr>
 226 <tr id="i5" class="rowColor">
 227 <td class="colFirst"><code>int</code></td>
 228 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#hashCode--">hashCode</a></span>()</code>&nbsp;</td>
 229 </tr>
 230 <tr id="i6" class="altColor">
 231 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 232 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#newInstance-java.util.Map-">newInstance</a></span>(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</code>&nbsp;</td>
 233 </tr>
 234 <tr id="i7" class="rowColor">
 235 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 236 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleScore-java.util.Map-">newInstanceSingleScore</a></span>(java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;seqScoresMap)</code>&nbsp;</td>
 237 </tr>
 238 <tr id="i8" class="altColor">
 239 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 240 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#newInstanceSingleSequence-java.util.Set-">newInstanceSingleSequence</a></span>(java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;data)</code>&nbsp;</td>
 241 </tr>
 242 <tr id="i9" class="rowColor">
 243 <td class="colFirst"><code>void</code></td>
 244 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/ScoreManager.html#writeOut-java.io.Writer-">writeOut</a></span>(java.io.Writer&nbsp;outStream)</code>&nbsp;</td>
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 249 <!--   -->
 250 </a>
 251 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 252 <code>clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait</code></li>
 253 </ul>
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 265 <!--   -->
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 273 <h4>SINGLE_ENTRY_KEY</h4>
 274 <pre>public static final&nbsp;java.lang.String SINGLE_ENTRY_KEY</pre>
 275 <dl>
 276 <dt><span class="seeLabel">See Also:</span></dt>
 277 <dd><a href="../../../constant-values.html#compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY">Constant Field Values</a></dd>
 278 </dl>
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 282 <!--   -->
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 284 <ul class="blockListLast">
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 286 <h4>seqScores</h4>
 287 <pre>protected&nbsp;java.util.List&lt;<a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a>&gt; seqScores</pre>
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 295 <!--   -->
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 303 <h4>ScoreManager</h4>
 304 <pre>protected&nbsp;ScoreManager()</pre>
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 312 <h4>ScoreManager</h4>
 313 <pre>private&nbsp;ScoreManager(java.lang.String&nbsp;id,
 314                      java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;data)</pre>
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 322 <h4>ScoreManager</h4>
 323 <pre>private&nbsp;ScoreManager(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</pre>
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 339 <h4>newInstance</h4>
 340 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a>&nbsp;newInstance(java.util.Map&lt;java.lang.String,java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;data)</pre>
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 348 <h4>newInstanceSingleScore</h4>
 349 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a>&nbsp;newInstanceSingleScore(java.util.Map&lt;java.lang.String,<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;seqScoresMap)</pre>
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 358 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a>&nbsp;newInstanceSingleSequence(java.util.Set&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;data)</pre>
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 367 <pre>public&nbsp;java.util.Map&lt;java.lang.String,java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&gt;&nbsp;asMap()</pre>
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 384 <h4>getNumberOfSeq</h4>
 385 <pre>public&nbsp;int&nbsp;getNumberOfSeq()</pre>
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 394 <pre>public&nbsp;<a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a>&nbsp;getAnnotationForSequence(java.lang.String&nbsp;seqId)</pre>
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 404               throws java.io.IOException</pre>
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 406 <dt><span class="throwsLabel">Throws:</span></dt>
 407 <dd><code>java.io.IOException</code></dd>
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 420 <dd><code>hashCode</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
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