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  76 <li>Summary:&nbsp;</li>
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  78 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
  79 <li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
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  95 <div class="subTitle">compbio.data.sequence</div>
  96 <h2 title="Class Score" class="title">Class Score</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.Score</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <dl>
 111 <dt>All Implemented Interfaces:</dt>
 112 <dd>java.lang.Comparable&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</dd>
 113 </dl>
 114 <hr>
 115 <br>
 116 <pre>@Immutable
 117 public class <span class="typeNameLabel">Score</span>
 118 extends java.lang.Object
 119 implements java.lang.Comparable&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</pre>
 120 <div class="block">A value class for AACon annotation results storage. The objects of this type
 121  are immutable</div>
 122 <dl>
 123 <dt><span class="simpleTagLabel">Author:</span></dt>
 124 <dd>pvtroshin</dd>
 125 </dl>
 126 </li>
 127 </ul>
 128 </div>
 129 <div class="summary">
 130 <ul class="blockList">
 131 <li class="blockList">
 132 <!-- =========== FIELD SUMMARY =========== -->
 133 <ul class="blockList">
 134 <li class="blockList"><a name="field.summary">
 135 <!--   -->
 136 </a>
 137 <h3>Field Summary</h3>
 138 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 139 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 140 <tr>
 141 <th class="colFirst" scope="col">Modifier and Type</th>
 142 <th class="colLast" scope="col">Field and Description</th>
 143 </tr>
 144 <tr class="altColor">
 145 <td class="colFirst"><code>private java.lang.String</code></td>
 146 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#method">method</a></span></code>&nbsp;</td>
 147 </tr>
 148 <tr class="rowColor">
 149 <td class="colFirst"><code>(package private) static java.text.NumberFormat</code></td>
 150 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#NUMBER_FORMAT">NUMBER_FORMAT</a></span></code>&nbsp;</td>
 151 </tr>
 152 <tr class="altColor">
 153 <td class="colFirst"><code>private java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;</code></td>
 154 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#ranges">ranges</a></span></code>&nbsp;</td>
 155 </tr>
 156 <tr class="rowColor">
 157 <td class="colFirst"><code>private java.util.ArrayList&lt;java.lang.Float&gt;</code></td>
 158 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#scores">scores</a></span></code>&nbsp;</td>
 159 </tr>
 160 </table>
 161 </li>
 162 </ul>
 163 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 164 <ul class="blockList">
 165 <li class="blockList"><a name="constructor.summary">
 166 <!--   -->
 167 </a>
 168 <h3>Constructor Summary</h3>
 169 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 170 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 171 <tr>
 172 <th class="colFirst" scope="col">Modifier</th>
 173 <th class="colLast" scope="col">Constructor and Description</th>
 174 </tr>
 175 <tr class="altColor">
 176 <td class="colFirst"><code>private </code></td>
 177 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#Score--">Score</a></span>()</code>&nbsp;</td>
 178 </tr>
 179 <tr class="rowColor">
 180 <td class="colFirst"><code>&nbsp;</code></td>
 181 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#Score-java.lang.Enum-java.util.ArrayList-">Score</a></span>(java.lang.Enum&lt;?&gt;&nbsp;method,
 182      java.util.ArrayList&lt;java.lang.Float&gt;&nbsp;scores)</code>
 183 <div class="block">Instantiate the Score</div>
 184 </td>
 185 </tr>
 186 <tr class="altColor">
 187 <td class="colFirst"><code>&nbsp;</code></td>
 188 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#Score-java.lang.Enum-java.util.ArrayList-java.util.TreeSet-">Score</a></span>(java.lang.Enum&lt;?&gt;&nbsp;method,
 189      java.util.ArrayList&lt;java.lang.Float&gt;&nbsp;scores,
 190      java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;ranges)</code>&nbsp;</td>
 191 </tr>
 192 <tr class="rowColor">
 193 <td class="colFirst"><code>&nbsp;</code></td>
 194 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#Score-java.lang.Enum-float:A-">Score</a></span>(java.lang.Enum&lt;?&gt;&nbsp;method,
 195      float[]&nbsp;scores)</code>&nbsp;</td>
 196 </tr>
 197 <tr class="altColor">
 198 <td class="colFirst"><code>&nbsp;</code></td>
 199 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#Score-java.lang.Enum-java.util.TreeSet-">Score</a></span>(java.lang.Enum&lt;?&gt;&nbsp;method,
 200      java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;ranges)</code>&nbsp;</td>
 201 </tr>
 202 </table>
 203 </li>
 204 </ul>
 205 <!-- ========== METHOD SUMMARY =========== -->
 206 <ul class="blockList">
 207 <li class="blockList"><a name="method.summary">
 208 <!--   -->
 209 </a>
 210 <h3>Method Summary</h3>
 211 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 212 <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>
 213 <tr>
 214 <th class="colFirst" scope="col">Modifier and Type</th>
 215 <th class="colLast" scope="col">Method and Description</th>
 216 </tr>
 217 <tr id="i0" class="altColor">
 218 <td class="colFirst"><code>int</code></td>
 219 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#compareTo-compbio.data.sequence.Score-">compareTo</a></span>(<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&nbsp;o)</code>&nbsp;</td>
 220 </tr>
 221 <tr id="i1" class="rowColor">
 222 <td class="colFirst"><code>boolean</code></td>
 223 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#equals-java.lang.Object-">equals</a></span>(java.lang.Object&nbsp;obj)</code>&nbsp;</td>
 224 </tr>
 225 <tr id="i2" class="altColor">
 226 <td class="colFirst"><code>java.lang.String</code></td>
 227 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#getMethod--">getMethod</a></span>()</code>
 228 <div class="block">Returns the ConservationMethod</div>
 229 </td>
 230 </tr>
 231 <tr id="i3" class="rowColor">
 232 <td class="colFirst"><code>java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;</code></td>
 233 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#getRanges--">getRanges</a></span>()</code>
 234 <div class="block">Return Ranges if any Collections.EMPTY_SET otherwise</div>
 235 </td>
 236 </tr>
 237 <tr id="i4" class="altColor">
 238 <td class="colFirst"><code>java.util.ArrayList&lt;java.lang.Float&gt;</code></td>
 239 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#getScores--">getScores</a></span>()</code>
 240 <div class="block">The column scores for the alignment</div>
 241 </td>
 242 </tr>
 243 <tr id="i5" class="rowColor">
 244 <td class="colFirst"><code>int</code></td>
 245 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#hashCode--">hashCode</a></span>()</code>&nbsp;</td>
 246 </tr>
 247 <tr id="i6" class="altColor">
 248 <td class="colFirst"><code>void</code></td>
 249 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#setRanges-java.util.TreeSet-">setRanges</a></span>(java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;ranges)</code>&nbsp;</td>
 250 </tr>
 251 <tr id="i7" class="rowColor">
 252 <td class="colFirst"><code>private java.util.ArrayList&lt;java.lang.Float&gt;</code></td>
 253 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#toList-float:A-">toList</a></span>(float[]&nbsp;values)</code>&nbsp;</td>
 254 </tr>
 255 <tr id="i8" class="altColor">
 256 <td class="colFirst"><code>java.lang.String</code></td>
 257 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#toString--">toString</a></span>()</code>&nbsp;</td>
 258 </tr>
 259 <tr id="i9" class="rowColor">
 260 <td class="colFirst"><code>static void</code></td>
 261 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/data/sequence/Score.html#write-java.util.TreeSet-java.io.Writer-">write</a></span>(java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;scores,
 262      java.io.Writer&nbsp;writer)</code>
 263 <div class="block">Outputs the List of Score objects into the Output stream.</div>
 264 </td>
 265 </tr>
 266 </table>
 267 <ul class="blockList">
 268 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 269 <!--   -->
 270 </a>
 271 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 272 <code>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</code></li>
 273 </ul>
 274 </li>
 275 </ul>
 276 </li>
 277 </ul>
 278 </div>
 279 <div class="details">
 280 <ul class="blockList">
 281 <li class="blockList">
 282 <!-- ============ FIELD DETAIL =========== -->
 283 <ul class="blockList">
 284 <li class="blockList"><a name="field.detail">
 285 <!--   -->
 286 </a>
 287 <h3>Field Detail</h3>
 288 <a name="NUMBER_FORMAT">
 289 <!--   -->
 290 </a>
 291 <ul class="blockList">
 292 <li class="blockList">
 293 <h4>NUMBER_FORMAT</h4>
 294 <pre>static final&nbsp;java.text.NumberFormat NUMBER_FORMAT</pre>
 295 </li>
 296 </ul>
 297 <a name="method">
 298 <!--   -->
 299 </a>
 300 <ul class="blockList">
 301 <li class="blockList">
 302 <h4>method</h4>
 303 <pre>private final&nbsp;java.lang.String method</pre>
 304 </li>
 305 </ul>
 306 <a name="ranges">
 307 <!--   -->
 308 </a>
 309 <ul class="blockList">
 310 <li class="blockList">
 311 <h4>ranges</h4>
 312 <pre>private&nbsp;java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt; ranges</pre>
 313 </li>
 314 </ul>
 315 <a name="scores">
 316 <!--   -->
 317 </a>
 318 <ul class="blockListLast">
 319 <li class="blockList">
 320 <h4>scores</h4>
 321 <pre>private&nbsp;java.util.ArrayList&lt;java.lang.Float&gt; scores</pre>
 322 </li>
 323 </ul>
 324 </li>
 325 </ul>
 326 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 327 <ul class="blockList">
 328 <li class="blockList"><a name="constructor.detail">
 329 <!--   -->
 330 </a>
 331 <h3>Constructor Detail</h3>
 332 <a name="Score--">
 333 <!--   -->
 334 </a>
 335 <ul class="blockList">
 336 <li class="blockList">
 337 <h4>Score</h4>
 338 <pre>private&nbsp;Score()</pre>
 339 </li>
 340 </ul>
 341 <a name="Score-java.lang.Enum-java.util.ArrayList-">
 342 <!--   -->
 343 </a>
 344 <ul class="blockList">
 345 <li class="blockList">
 346 <h4>Score</h4>
 347 <pre>public&nbsp;Score(java.lang.Enum&lt;?&gt;&nbsp;method,
 348              java.util.ArrayList&lt;java.lang.Float&gt;&nbsp;scores)</pre>
 349 <div class="block">Instantiate the Score</div>
 350 <dl>
 351 <dt><span class="paramLabel">Parameters:</span></dt>
 352 <dd><code>method</code> - the ConservationMethod with which <code>scores</code> were
 353             calculated</dd>
 354 <dd><code>scores</code> - the actual conservation values for each column of the
 355             alignment</dd>
 356 </dl>
 357 </li>
 358 </ul>
 359 <a name="Score-java.lang.Enum-java.util.ArrayList-java.util.TreeSet-">
 360 <!--   -->
 361 </a>
 362 <ul class="blockList">
 363 <li class="blockList">
 364 <h4>Score</h4>
 365 <pre>public&nbsp;Score(java.lang.Enum&lt;?&gt;&nbsp;method,
 366              java.util.ArrayList&lt;java.lang.Float&gt;&nbsp;scores,
 367              java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;ranges)</pre>
 368 <dl>
 369 <dt><span class="paramLabel">Parameters:</span></dt>
 370 <dd><code>method</code> - the ConservationMethod with which <code>scores</code> were
 371             calculated</dd>
 372 <dd><code>scores</code> - the actual conservation values for each column of the
 373             alignment</dd>
 374 <dd><code>ranges</code> - The set of ranges i.e. parts of the sequence with specific
 375             function, usually can be calculated based on scores</dd>
 376 </dl>
 377 </li>
 378 </ul>
 379 <a name="Score-java.lang.Enum-java.util.TreeSet-">
 380 <!--   -->
 381 </a>
 382 <ul class="blockList">
 383 <li class="blockList">
 384 <h4>Score</h4>
 385 <pre>public&nbsp;Score(java.lang.Enum&lt;?&gt;&nbsp;method,
 386              java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;ranges)</pre>
 387 </li>
 388 </ul>
 389 <a name="Score-java.lang.Enum-float:A-">
 390 <!--   -->
 391 </a>
 392 <ul class="blockListLast">
 393 <li class="blockList">
 394 <h4>Score</h4>
 395 <pre>public&nbsp;Score(java.lang.Enum&lt;?&gt;&nbsp;method,
 396              float[]&nbsp;scores)</pre>
 397 </li>
 398 </ul>
 399 </li>
 400 </ul>
 401 <!-- ============ METHOD DETAIL ========== -->
 402 <ul class="blockList">
 403 <li class="blockList"><a name="method.detail">
 404 <!--   -->
 405 </a>
 406 <h3>Method Detail</h3>
 407 <a name="toList-float:A-">
 408 <!--   -->
 409 </a>
 410 <ul class="blockList">
 411 <li class="blockList">
 412 <h4>toList</h4>
 413 <pre>private&nbsp;java.util.ArrayList&lt;java.lang.Float&gt;&nbsp;toList(float[]&nbsp;values)</pre>
 414 </li>
 415 </ul>
 416 <a name="getMethod--">
 417 <!--   -->
 418 </a>
 419 <ul class="blockList">
 420 <li class="blockList">
 421 <h4>getMethod</h4>
 422 <pre>public&nbsp;java.lang.String&nbsp;getMethod()</pre>
 423 <div class="block">Returns the ConservationMethod</div>
 424 <dl>
 425 <dt><span class="returnLabel">Returns:</span></dt>
 426 <dd>the ConservationMethod</dd>
 427 </dl>
 428 </li>
 429 </ul>
 430 <a name="getScores--">
 431 <!--   -->
 432 </a>
 433 <ul class="blockList">
 434 <li class="blockList">
 435 <h4>getScores</h4>
 436 <pre>public&nbsp;java.util.ArrayList&lt;java.lang.Float&gt;&nbsp;getScores()</pre>
 437 <div class="block">The column scores for the alignment</div>
 438 <dl>
 439 <dt><span class="returnLabel">Returns:</span></dt>
 440 <dd>the column scores for the alignment</dd>
 441 </dl>
 442 </li>
 443 </ul>
 444 <a name="getRanges--">
 445 <!--   -->
 446 </a>
 447 <ul class="blockList">
 448 <li class="blockList">
 449 <h4>getRanges</h4>
 450 <pre>public&nbsp;java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;getRanges()</pre>
 451 <div class="block">Return Ranges if any Collections.EMPTY_SET otherwise</div>
 452 <dl>
 453 <dt><span class="returnLabel">Returns:</span></dt>
 454 <dd>ordered set of Range</dd>
 455 </dl>
 456 </li>
 457 </ul>
 458 <a name="setRanges-java.util.TreeSet-">
 459 <!--   -->
 460 </a>
 461 <ul class="blockList">
 462 <li class="blockList">
 463 <h4>setRanges</h4>
 464 <pre>public&nbsp;void&nbsp;setRanges(java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a>&gt;&nbsp;ranges)</pre>
 465 </li>
 466 </ul>
 467 <a name="toString--">
 468 <!--   -->
 469 </a>
 470 <ul class="blockList">
 471 <li class="blockList">
 472 <h4>toString</h4>
 473 <pre>public&nbsp;java.lang.String&nbsp;toString()</pre>
 474 <dl>
 475 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 476 <dd><code>toString</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 477 </dl>
 478 </li>
 479 </ul>
 480 <a name="hashCode--">
 481 <!--   -->
 482 </a>
 483 <ul class="blockList">
 484 <li class="blockList">
 485 <h4>hashCode</h4>
 486 <pre>public&nbsp;int&nbsp;hashCode()</pre>
 487 <dl>
 488 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 489 <dd><code>hashCode</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 490 </dl>
 491 </li>
 492 </ul>
 493 <a name="equals-java.lang.Object-">
 494 <!--   -->
 495 </a>
 496 <ul class="blockList">
 497 <li class="blockList">
 498 <h4>equals</h4>
 499 <pre>public&nbsp;boolean&nbsp;equals(java.lang.Object&nbsp;obj)</pre>
 500 <dl>
 501 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 502 <dd><code>equals</code>&nbsp;in class&nbsp;<code>java.lang.Object</code></dd>
 503 </dl>
 504 </li>
 505 </ul>
 506 <a name="write-java.util.TreeSet-java.io.Writer-">
 507 <!--   -->
 508 </a>
 509 <ul class="blockList">
 510 <li class="blockList">
 511 <h4>write</h4>
 512 <pre>public static&nbsp;void&nbsp;write(java.util.TreeSet&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;scores,
 513                          java.io.Writer&nbsp;writer)
 514                   throws java.io.IOException</pre>
 515 <div class="block">Outputs the List of Score objects into the Output stream. The output
 516  format is as follows:
 517
 518  <pre>
 519  <code>
 520  #MethodName [comma separated list of ranges] &lt;space separated list of values&gt;
 521
 522  For example:
 523
 524  #KABAT 0.2 0.3 0.2 0 0.645 0.333 1 1 0 0
 525  #SMERFS 0.645 0.333 1 1 0 0 0.2 0.3 0.2 0
 526  #COILS 22-33, 44-56 0.121 3.212
 527  </code>
 528  </pre>
 529
 530  The maximum precision for values is 3 digits, but can be less.</div>
 531 <dl>
 532 <dt><span class="paramLabel">Parameters:</span></dt>
 533 <dd><code>scores</code> - the list of scores to output</dd>
 534 <dd><code>writer</code> - </dd>
 535 <dt><span class="throwsLabel">Throws:</span></dt>
 536 <dd><code>java.io.IOException</code> - if the OutputStream cannot be written into</dd>
 537 <dd><code>java.lang.NullPointerException</code> - if the output stream is null</dd>
 538 </dl>
 539 </li>
 540 </ul>
 541 <a name="compareTo-compbio.data.sequence.Score-">
 542 <!--   -->
 543 </a>
 544 <ul class="blockListLast">
 545 <li class="blockList">
 546 <h4>compareTo</h4>
 547 <pre>public&nbsp;int&nbsp;compareTo(<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&nbsp;o)</pre>
 548 <dl>
 549 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 550 <dd><code>compareTo</code>&nbsp;in interface&nbsp;<code>java.lang.Comparable&lt;<a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></dd>
 551 </dl>
 552 </li>
 553 </ul>
 554 </li>
 555 </ul>
 556 </li>
 557 </ul>
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