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

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  76 <li>Summary:&nbsp;</li>
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  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Class RNAStructReader" class="title">Class RNAStructReader</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.RNAStructReader</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
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 110 <hr>
 111 <br>
 112 <pre>public class <span class="typeNameLabel">RNAStructReader</span>
 113 extends java.lang.Object</pre>
 114 </li>
 115 </ul>
 116 </div>
 117 <div class="summary">
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 127 <caption><span>Nested Classes</span><span class="tabEnd">&nbsp;</span></caption>
 128 <tr>
 129 <th class="colFirst" scope="col">Modifier and Type</th>
 130 <th class="colLast" scope="col">Class and Description</th>
 131 </tr>
 132 <tr class="altColor">
 133 <td class="colFirst"><code>(package private) static class&nbsp;</code></td>
 134 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldLine</a></span></code>&nbsp;</td>
 135 </tr>
 136 <tr class="rowColor">
 137 <td class="colFirst"><code>static class&nbsp;</code></td>
 138 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.AlifoldResult.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldResult</a></span></code>&nbsp;</td>
 139 </tr>
 140 <tr class="altColor">
 141 <td class="colFirst"><code>(package private) static class&nbsp;</code></td>
 142 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.RNAOut.html" title="enum in compbio.data.sequence">RNAStructReader.RNAOut</a></span></code>&nbsp;</td>
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 154 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 155 <tr>
 156 <th class="colFirst" scope="col">Modifier and Type</th>
 157 <th class="colLast" scope="col">Field and Description</th>
 158 </tr>
 159 <tr class="altColor">
 160 <td class="colFirst"><code>(package private) static java.lang.String</code></td>
 161 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#alignmentP">alignmentP</a></span></code>&nbsp;</td>
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 168 <td class="colFirst"><code>(package private) static java.lang.String</code></td>
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 180 <td class="colFirst"><code>(package private) static java.lang.String</code></td>
 181 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#floatP">floatP</a></span></code>&nbsp;</td>
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 184 <td class="colFirst"><code>(package private) static java.lang.String</code></td>
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 241 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 242 <tr>
 243 <th class="colOne" scope="col">Constructor and Description</th>
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 245 <tr class="altColor">
 246 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#RNAStructReader--">RNAStructReader</a></span>()</code>&nbsp;</td>
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 259 <tr>
 260 <th class="colFirst" scope="col">Modifier and Type</th>
 261 <th class="colLast" scope="col">Method and Description</th>
 262 </tr>
 263 <tr id="i0" class="altColor">
 264 <td class="colFirst"><code>private static <a href="../../../compbio/data/sequence/RNAStructReader.RNAOut.html" title="enum in compbio.data.sequence">RNAStructReader.RNAOut</a></code></td>
 265 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#identify-java.lang.String-">identify</a></span>(java.lang.String&nbsp;token)</code>&nbsp;</td>
 266 </tr>
 267 <tr id="i1" class="rowColor">
 268 <td class="colFirst"><code>private static <a href="../../../compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldLine</a></code></td>
 269 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#identifyLine-java.lang.String-">identifyLine</a></span>(java.lang.String&nbsp;line)</code>&nbsp;</td>
 270 </tr>
 271 <tr id="i2" class="altColor">
 272 <td class="colFirst"><code>static void</code></td>
 273 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#main-java.lang.String:A-">main</a></span>(java.lang.String[]&nbsp;args)</code>&nbsp;</td>
 274 </tr>
 275 <tr id="i3" class="rowColor">
 276 <td class="colFirst"><code>static java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 277 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#newEmptyScore-java.lang.Enum-">newEmptyScore</a></span>(java.lang.Enum&lt;?&gt;&nbsp;res)</code>&nbsp;</td>
 278 </tr>
 279 <tr id="i4" class="altColor">
 280 <td class="colFirst"><code>private static java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 281 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#newSetScore-java.lang.Enum-java.util.List-">newSetScore</a></span>(java.lang.Enum&lt;?&gt;&nbsp;res,
 282            java.util.List&lt;java.lang.Float&gt;&nbsp;scores)</code>&nbsp;</td>
 283 </tr>
 284 <tr id="i5" class="rowColor">
 285 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></code></td>
 286 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#readRNAStructStream-java.io.InputStream-">readRNAStructStream</a></span>(java.io.InputStream&nbsp;stdout)</code>&nbsp;</td>
 287 </tr>
 288 <tr id="i6" class="altColor">
 289 <td class="colFirst"><code>static <a href="../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></code></td>
 290 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/RNAStructReader.html#readRNAStructStream-java.io.InputStream-java.io.InputStream-">readRNAStructStream</a></span>(java.io.InputStream&nbsp;stdout,
 291                    java.io.InputStream&nbsp;alifold)</code>&nbsp;</td>
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 468 <a name="ensembleFreqP">
 469 <!--   -->
 470 </a>
 471 <ul class="blockListLast">
 472 <li class="blockList">
 473 <h4>ensembleFreqP</h4>
 474 <pre>static&nbsp;java.lang.String ensembleFreqP</pre>
 475 </li>
 476 </ul>
 477 </li>
 478 </ul>
 479 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 480 <ul class="blockList">
 481 <li class="blockList"><a name="constructor.detail">
 482 <!--   -->
 483 </a>
 484 <h3>Constructor Detail</h3>
 485 <a name="RNAStructReader--">
 486 <!--   -->
 487 </a>
 488 <ul class="blockListLast">
 489 <li class="blockList">
 490 <h4>RNAStructReader</h4>
 491 <pre>public&nbsp;RNAStructReader()</pre>
 492 </li>
 493 </ul>
 494 </li>
 495 </ul>
 496 <!-- ============ METHOD DETAIL ========== -->
 497 <ul class="blockList">
 498 <li class="blockList"><a name="method.detail">
 499 <!--   -->
 500 </a>
 501 <h3>Method Detail</h3>
 502 <a name="readRNAStructStream-java.io.InputStream-">
 503 <!--   -->
 504 </a>
 505 <ul class="blockList">
 506 <li class="blockList">
 507 <h4>readRNAStructStream</h4>
 508 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a>&nbsp;readRNAStructStream(java.io.InputStream&nbsp;stdout)
 509                                                  throws java.io.IOException</pre>
 510 <dl>
 511 <dt><span class="throwsLabel">Throws:</span></dt>
 512 <dd><code>java.io.IOException</code></dd>
 513 </dl>
 514 </li>
 515 </ul>
 516 <a name="newSetScore-java.lang.Enum-java.util.List-">
 517 <!--   -->
 518 </a>
 519 <ul class="blockList">
 520 <li class="blockList">
 521 <h4>newSetScore</h4>
 522 <pre>private static&nbsp;java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;newSetScore(java.lang.Enum&lt;?&gt;&nbsp;res,
 523                                                     java.util.List&lt;java.lang.Float&gt;&nbsp;scores)</pre>
 524 </li>
 525 </ul>
 526 <a name="newEmptyScore-java.lang.Enum-">
 527 <!--   -->
 528 </a>
 529 <ul class="blockList">
 530 <li class="blockList">
 531 <h4>newEmptyScore</h4>
 532 <pre>public static&nbsp;java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;newEmptyScore(java.lang.Enum&lt;?&gt;&nbsp;res)</pre>
 533 </li>
 534 </ul>
 535 <a name="readRNAStructStream-java.io.InputStream-java.io.InputStream-">
 536 <!--   -->
 537 </a>
 538 <ul class="blockList">
 539 <li class="blockList">
 540 <h4>readRNAStructStream</h4>
 541 <pre>public static&nbsp;<a href="../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a>&nbsp;readRNAStructStream(java.io.InputStream&nbsp;stdout,
 542                                                         java.io.InputStream&nbsp;alifold)
 543                                                  throws java.io.IOException</pre>
 544 <dl>
 545 <dt><span class="throwsLabel">Throws:</span></dt>
 546 <dd><code>java.io.IOException</code></dd>
 547 </dl>
 548 </li>
 549 </ul>
 550 <a name="identify-java.lang.String-">
 551 <!--   -->
 552 </a>
 553 <ul class="blockList">
 554 <li class="blockList">
 555 <h4>identify</h4>
 556 <pre>private static&nbsp;<a href="../../../compbio/data/sequence/RNAStructReader.RNAOut.html" title="enum in compbio.data.sequence">RNAStructReader.RNAOut</a>&nbsp;identify(java.lang.String&nbsp;token)</pre>
 557 </li>
 558 </ul>
 559 <a name="identifyLine-java.lang.String-">
 560 <!--   -->
 561 </a>
 562 <ul class="blockList">
 563 <li class="blockList">
 564 <h4>identifyLine</h4>
 565 <pre>private static&nbsp;<a href="../../../compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldLine</a>&nbsp;identifyLine(java.lang.String&nbsp;line)</pre>
 566 </li>
 567 </ul>
 568 <a name="main-java.lang.String:A-">
 569 <!--   -->
 570 </a>
 571 <ul class="blockListLast">
 572 <li class="blockList">
 573 <h4>main</h4>
 574 <pre>public static&nbsp;void&nbsp;main(java.lang.String[]&nbsp;args)</pre>
 575 </li>
 576 </ul>
 577 </li>
 578 </ul>
 579 </li>
 580 </ul>
 581 </div>
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