website/docs/full_javadoc/compbio/runner/conservation/AACon.html

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  76 <li>Summary:&nbsp;</li>
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  94 <div class="header">
  95 <div class="subTitle">compbio.runner.conservation</div>
  96 <h2 title="Class AACon" class="title">Class AACon</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><a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">compbio.engine.client.SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</li>
 104 <li>
 105 <ul class="inheritance">
 106 <li>compbio.runner.conservation.AACon</li>
 107 </ul>
 108 </li>
 109 </ul>
 110 </li>
 111 </ul>
 112 <div class="description">
 113 <ul class="blockList">
 114 <li class="blockList">
 115 <dl>
 116 <dt>All Implemented Interfaces:</dt>
 117 <dd><a href="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</dd>
 118 </dl>
 119 <hr>
 120 <br>
 121 <pre>public class <span class="typeNameLabel">AACon</span>
 122 extends <a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</pre>
 123 <div class="block">Command line
 124
 125  java -Xmx512 -jar jronn_v3.jar -i=test_seq.txt -n=1 -o=out.txt -s=stat.out</div>
 126 <dl>
 127 <dt><span class="simpleTagLabel">Author:</span></dt>
 128 <dd>pvtroshin</dd>
 129 </dl>
 130 </li>
 131 </ul>
 132 </div>
 133 <div class="summary">
 134 <ul class="blockList">
 135 <li class="blockList">
 136 <!-- ======== NESTED CLASS SUMMARY ======== -->
 137 <ul class="blockList">
 138 <li class="blockList"><a name="nested.class.summary">
 139 <!--   -->
 140 </a>
 141 <h3>Nested Class Summary</h3>
 142 <ul class="blockList">
 143 <li class="blockList"><a name="nested.classes.inherited.from.class.compbio.engine.client.Executable">
 144 <!--   -->
 145 </a>
 146 <h3>Nested classes/interfaces inherited from interface&nbsp;compbio.engine.client.<a href="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></h3>
 147 <code><a href="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</a></code></li>
 148 </ul>
 149 </li>
 150 </ul>
 151 <!-- =========== FIELD SUMMARY =========== -->
 152 <ul class="blockList">
 153 <li class="blockList"><a name="field.summary">
 154 <!--   -->
 155 </a>
 156 <h3>Field Summary</h3>
 157 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 158 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 159 <tr>
 160 <th class="colFirst" scope="col">Modifier and Type</th>
 161 <th class="colLast" scope="col">Field and Description</th>
 162 </tr>
 163 <tr class="altColor">
 164 <td class="colFirst"><code>static java.lang.String</code></td>
 165 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></span></code>&nbsp;</td>
 166 </tr>
 167 <tr class="rowColor">
 168 <td class="colFirst"><code>private static org.apache.log4j.Logger</code></td>
 169 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#log">log</a></span></code>&nbsp;</td>
 170 </tr>
 171 <tr class="altColor">
 172 <td class="colFirst"><code>private int</code></td>
 173 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#ncoreNumber">ncoreNumber</a></span></code>
 174 <div class="block">Number of cores to use, defaults to 1 for local execution or the value of
 175  "jronn.cluster.cpunum" property for cluster execution</div>
 176 </td>
 177 </tr>
 178 <tr class="rowColor">
 179 <td class="colFirst"><code>private java.lang.String</code></td>
 180 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#ncorePrm">ncorePrm</a></span></code>&nbsp;</td>
 181 </tr>
 182 <tr class="altColor">
 183 <td class="colFirst"><code>static java.lang.String</code></td>
 184 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#STAT_FILE">STAT_FILE</a></span></code>&nbsp;</td>
 185 </tr>
 186 </table>
 187 <ul class="blockList">
 188 <li class="blockList"><a name="fields.inherited.from.class.compbio.engine.client.SkeletalExecutable">
 189 <!--   -->
 190 </a>
 191 <h3>Fields inherited from class&nbsp;compbio.engine.client.<a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></h3>
 192 <code><a href="../../../compbio/engine/client/SkeletalExecutable.html#cbuilder">cbuilder</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#errorFile">errorFile</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#inputFile">inputFile</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#outputFile">outputFile</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#ph">ph</a></code></li>
 193 </ul>
 194 </li>
 195 </ul>
 196 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 197 <ul class="blockList">
 198 <li class="blockList"><a name="constructor.summary">
 199 <!--   -->
 200 </a>
 201 <h3>Constructor Summary</h3>
 202 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 203 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 204 <tr>
 205 <th class="colOne" scope="col">Constructor and Description</th>
 206 </tr>
 207 <tr class="altColor">
 208 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#AACon--">AACon</a></span>()</code>&nbsp;</td>
 209 </tr>
 210 </table>
 211 </li>
 212 </ul>
 213 <!-- ========== METHOD SUMMARY =========== -->
 214 <ul class="blockList">
 215 <li class="blockList"><a name="method.summary">
 216 <!--   -->
 217 </a>
 218 <h3>Method Summary</h3>
 219 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 220 <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>
 221 <tr>
 222 <th class="colFirst" scope="col">Modifier and Type</th>
 223 <th class="colLast" scope="col">Method and Description</th>
 224 </tr>
 225 <tr id="i0" class="altColor">
 226 <td class="colFirst"><code>java.util.List&lt;java.lang.String&gt;</code></td>
 227 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#getCreatedFiles--">getCreatedFiles</a></span>()</code>
 228 <div class="block">This method cannot really tell whether the files has actually been
 229  created or not.</div>
 230 </td>
 231 </tr>
 232 <tr id="i1" class="rowColor">
 233 <td class="colFirst"><code>private static java.lang.String</code></td>
 234 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#getLibPath--">getLibPath</a></span>()</code>&nbsp;</td>
 235 </tr>
 236 <tr id="i2" class="altColor">
 237 <td class="colFirst"><code>(package private) int</code></td>
 238 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#getNCore--">getNCore</a></span>()</code>&nbsp;</td>
 239 </tr>
 240 <tr id="i3" class="rowColor">
 241 <td class="colFirst"><code><a href="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></td>
 242 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters</a></span>(<a href="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</a>&nbsp;provider)</code>&nbsp;</td>
 243 </tr>
 244 <tr id="i4" class="altColor">
 245 <td class="colFirst"><code><a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></code></td>
 246 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 247 </tr>
 248 <tr id="i5" class="rowColor">
 249 <td class="colFirst"><code>static java.lang.String</code></td>
 250 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#getStatFile--">getStatFile</a></span>()</code>&nbsp;</td>
 251 </tr>
 252 <tr id="i6" class="altColor">
 253 <td class="colFirst"><code>java.lang.Class&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></td>
 254 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#getType--">getType</a></span>()</code>&nbsp;</td>
 255 </tr>
 256 <tr id="i7" class="rowColor">
 257 <td class="colFirst"><code><a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></code></td>
 258 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#setInput-java.lang.String-">setInput</a></span>(java.lang.String&nbsp;inFile)</code>&nbsp;</td>
 259 </tr>
 260 <tr id="i8" class="altColor">
 261 <td class="colFirst"><code>void</code></td>
 262 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#setNCore-int-">setNCore</a></span>(int&nbsp;ncoreNumber)</code>&nbsp;</td>
 263 </tr>
 264 <tr id="i9" class="rowColor">
 265 <td class="colFirst"><code><a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a></code></td>
 266 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/conservation/AACon.html#setOutput-java.lang.String-">setOutput</a></span>(java.lang.String&nbsp;outFile)</code>&nbsp;</td>
 267 </tr>
 268 </table>
 269 <ul class="blockList">
 270 <li class="blockList"><a name="methods.inherited.from.class.compbio.engine.client.SkeletalExecutable">
 271 <!--   -->
 272 </a>
 273 <h3>Methods inherited from class&nbsp;compbio.engine.client.<a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a></h3>
 274 <code><a href="../../../compbio/engine/client/SkeletalExecutable.html#addParameters-java.util.List-">addParameters</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#equals-java.lang.Object-">equals</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum-java.lang.Class-">getClusterCpuNum</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings--">getClusterJobSettings</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#getError--">getError</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#getInput--">getInput</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#getLimit-java.lang.String-">getLimit</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#getLimits--">getLimits</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#getOutput--">getOutput</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#hashCode--">hashCode</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#isErrorSet--">isErrorSet</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#isInputSet--">isInputSet</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#isOutputSet--">isOutputSet</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#loadRunConfiguration-compbio.engine.client.RunConfiguration-">loadRunConfiguration</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#setError-java.lang.String-">setError</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#setParameter-java.lang.String-">setParameter</a>, <a href="../../../compbio/engine/client/SkeletalExecutable.html#toString--">toString</a></code></li>
 275 </ul>
 276 <ul class="blockList">
 277 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 278 <!--   -->
 279 </a>
 280 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 281 <code>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</code></li>
 282 </ul>
 283 </li>
 284 </ul>
 285 </li>
 286 </ul>
 287 </div>
 288 <div class="details">
 289 <ul class="blockList">
 290 <li class="blockList">
 291 <!-- ============ FIELD DETAIL =========== -->
 292 <ul class="blockList">
 293 <li class="blockList"><a name="field.detail">
 294 <!--   -->
 295 </a>
 296 <h3>Field Detail</h3>
 297 <a name="log">
 298 <!--   -->
 299 </a>
 300 <ul class="blockList">
 301 <li class="blockList">
 302 <h4>log</h4>
 303 <pre>private static&nbsp;org.apache.log4j.Logger log</pre>
 304 </li>
 305 </ul>
 306 <a name="ncoreNumber">
 307 <!--   -->
 308 </a>
 309 <ul class="blockList">
 310 <li class="blockList">
 311 <h4>ncoreNumber</h4>
 312 <pre>private&nbsp;int ncoreNumber</pre>
 313 <div class="block">Number of cores to use, defaults to 1 for local execution or the value of
 314  "jronn.cluster.cpunum" property for cluster execution</div>
 315 </li>
 316 </ul>
 317 <a name="ncorePrm">
 318 <!--   -->
 319 </a>
 320 <ul class="blockList">
 321 <li class="blockList">
 322 <h4>ncorePrm</h4>
 323 <pre>private final&nbsp;java.lang.String ncorePrm</pre>
 324 <dl>
 325 <dt><span class="seeLabel">See Also:</span></dt>
 326 <dd><a href="../../../constant-values.html#compbio.runner.conservation.AACon.ncorePrm">Constant Field Values</a></dd>
 327 </dl>
 328 </li>
 329 </ul>
 330 <a name="KEY_VALUE_SEPARATOR">
 331 <!--   -->
 332 </a>
 333 <ul class="blockList">
 334 <li class="blockList">
 335 <h4>KEY_VALUE_SEPARATOR</h4>
 336 <pre>public static final&nbsp;java.lang.String KEY_VALUE_SEPARATOR</pre>
 337 <dl>
 338 <dt><span class="seeLabel">See Also:</span></dt>
 339 <dd><a href="../../../constant-values.html#compbio.runner.conservation.AACon.KEY_VALUE_SEPARATOR">Constant Field Values</a></dd>
 340 </dl>
 341 </li>
 342 </ul>
 343 <a name="STAT_FILE">
 344 <!--   -->
 345 </a>
 346 <ul class="blockListLast">
 347 <li class="blockList">
 348 <h4>STAT_FILE</h4>
 349 <pre>public static final&nbsp;java.lang.String STAT_FILE</pre>
 350 <dl>
 351 <dt><span class="seeLabel">See Also:</span></dt>
 352 <dd><a href="../../../constant-values.html#compbio.runner.conservation.AACon.STAT_FILE">Constant Field Values</a></dd>
 353 </dl>
 354 </li>
 355 </ul>
 356 </li>
 357 </ul>
 358 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 359 <ul class="blockList">
 360 <li class="blockList"><a name="constructor.detail">
 361 <!--   -->
 362 </a>
 363 <h3>Constructor Detail</h3>
 364 <a name="AACon--">
 365 <!--   -->
 366 </a>
 367 <ul class="blockListLast">
 368 <li class="blockList">
 369 <h4>AACon</h4>
 370 <pre>public&nbsp;AACon()</pre>
 371 </li>
 372 </ul>
 373 </li>
 374 </ul>
 375 <!-- ============ METHOD DETAIL ========== -->
 376 <ul class="blockList">
 377 <li class="blockList"><a name="method.detail">
 378 <!--   -->
 379 </a>
 380 <h3>Method Detail</h3>
 381 <a name="getResults-java.lang.String-">
 382 <!--   -->
 383 </a>
 384 <ul class="blockList">
 385 <li class="blockList">
 386 <h4>getResults</h4>
 387 <pre>public&nbsp;<a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a>&nbsp;getResults(java.lang.String&nbsp;workDirectory)
 388                         throws <a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
 389 <dl>
 390 <dt><span class="throwsLabel">Throws:</span></dt>
 391 <dd><code><a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></code></dd>
 392 </dl>
 393 </li>
 394 </ul>
 395 <a name="getLibPath--">
 396 <!--   -->
 397 </a>
 398 <ul class="blockList">
 399 <li class="blockList">
 400 <h4>getLibPath</h4>
 401 <pre>private static&nbsp;java.lang.String&nbsp;getLibPath()</pre>
 402 </li>
 403 </ul>
 404 <a name="getCreatedFiles--">
 405 <!--   -->
 406 </a>
 407 <ul class="blockList">
 408 <li class="blockList">
 409 <h4>getCreatedFiles</h4>
 410 <pre>public&nbsp;java.util.List&lt;java.lang.String&gt;&nbsp;getCreatedFiles()</pre>
 411 <div class="block"><span class="descfrmTypeLabel">Description copied from class:&nbsp;<code><a href="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles--">SkeletalExecutable</a></code></span></div>
 412 <div class="block">This method cannot really tell whether the files has actually been
 413  created or not. It must be overridden as required.</div>
 414 <dl>
 415 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 416 <dd><code><a href="../../../compbio/engine/client/Executable.html#getCreatedFiles--">getCreatedFiles</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></dd>
 417 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 418 <dd><code><a href="../../../compbio/engine/client/SkeletalExecutable.html#getCreatedFiles--">getCreatedFiles</a></code>&nbsp;in class&nbsp;<code><a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></dd>
 419 <dt><span class="seeLabel">See Also:</span></dt>
 420 <dd><a href="../../../compbio/engine/client/Executable.html#getCreatedFiles--"><code>Executable.getCreatedFiles()</code></a></dd>
 421 </dl>
 422 </li>
 423 </ul>
 424 <a name="setInput-java.lang.String-">
 425 <!--   -->
 426 </a>
 427 <ul class="blockList">
 428 <li class="blockList">
 429 <h4>setInput</h4>
 430 <pre>public&nbsp;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&nbsp;setInput(java.lang.String&nbsp;inFile)</pre>
 431 <dl>
 432 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 433 <dd><code><a href="../../../compbio/engine/client/SkeletalExecutable.html#setInput-java.lang.String-">setInput</a></code>&nbsp;in class&nbsp;<code><a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></dd>
 434 </dl>
 435 </li>
 436 </ul>
 437 <a name="setOutput-java.lang.String-">
 438 <!--   -->
 439 </a>
 440 <ul class="blockList">
 441 <li class="blockList">
 442 <h4>setOutput</h4>
 443 <pre>public&nbsp;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&nbsp;setOutput(java.lang.String&nbsp;outFile)</pre>
 444 <dl>
 445 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 446 <dd><code><a href="../../../compbio/engine/client/SkeletalExecutable.html#setOutput-java.lang.String-">setOutput</a></code>&nbsp;in class&nbsp;<code><a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></dd>
 447 </dl>
 448 </li>
 449 </ul>
 450 <a name="getType--">
 451 <!--   -->
 452 </a>
 453 <ul class="blockList">
 454 <li class="blockList">
 455 <h4>getType</h4>
 456 <pre>public&nbsp;java.lang.Class&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;&nbsp;getType()</pre>
 457 <dl>
 458 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 459 <dd><code><a href="../../../compbio/engine/client/SkeletalExecutable.html#getType--">getType</a></code>&nbsp;in class&nbsp;<code><a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></dd>
 460 <dt><span class="returnLabel">Returns:</span></dt>
 461 <dd>subclasses must return their type</dd>
 462 </dl>
 463 </li>
 464 </ul>
 465 <a name="getStatFile--">
 466 <!--   -->
 467 </a>
 468 <ul class="blockList">
 469 <li class="blockList">
 470 <h4>getStatFile</h4>
 471 <pre>public static&nbsp;java.lang.String&nbsp;getStatFile()</pre>
 472 </li>
 473 </ul>
 474 <a name="setNCore-int-">
 475 <!--   -->
 476 </a>
 477 <ul class="blockList">
 478 <li class="blockList">
 479 <h4>setNCore</h4>
 480 <pre>public&nbsp;void&nbsp;setNCore(int&nbsp;ncoreNumber)</pre>
 481 </li>
 482 </ul>
 483 <a name="getNCore--">
 484 <!--   -->
 485 </a>
 486 <ul class="blockList">
 487 <li class="blockList">
 488 <h4>getNCore</h4>
 489 <pre>int&nbsp;getNCore()</pre>
 490 </li>
 491 </ul>
 492 <a name="getParameters-compbio.engine.client.Executable.ExecProvider-">
 493 <!--   -->
 494 </a>
 495 <ul class="blockListLast">
 496 <li class="blockList">
 497 <h4>getParameters</h4>
 498 <pre>public&nbsp;<a href="../../../compbio/engine/client/CommandBuilder.html" title="class in compbio.engine.client">CommandBuilder</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;&nbsp;getParameters(<a href="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</a>&nbsp;provider)</pre>
 499 <dl>
 500 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 501 <dd><code><a href="../../../compbio/engine/client/Executable.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></dd>
 502 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 503 <dd><code><a href="../../../compbio/engine/client/SkeletalExecutable.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters</a></code>&nbsp;in class&nbsp;<code><a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</a>&gt;</code></dd>
 504 </dl>
 505 </li>
 506 </ul>
 507 </li>
 508 </ul>
 509 </li>
 510 </ul>
 511 </div>
 512 </div>
 513 <!-- ========= END OF CLASS DATA ========= -->
 514 <!-- ======= START OF BOTTOM NAVBAR ====== -->
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 516 <!--   -->
 517 </a>
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 519 <a name="navbar.bottom.firstrow">
 520 <!--   -->
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 522 <ul class="navList" title="Navigation">
 523 <li><a href="../../../overview-summary.html">Overview</a></li>
 524 <li><a href="package-summary.html">Package</a></li>
 525 <li class="navBarCell1Rev">Class</li>
 526 <li><a href="class-use/AACon.html">Use</a></li>
 527 <li><a href="package-tree.html">Tree</a></li>
 528 <li><a href="../../../deprecated-list.html">Deprecated</a></li>
 529 <li><a href="../../../index-files/index-1.html">Index</a></li>
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 559 <li>Summary:&nbsp;</li>
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