website/docs/full_javadoc/compbio/runner/msa/GLprobs.html

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   6 <title>GLprobs</title>
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  76 <li>Summary:&nbsp;</li>
  77 <li>Nested&nbsp;|&nbsp;</li>
  78 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
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  84 <li><a href="#field.detail">Field</a>&nbsp;|&nbsp;</li>
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  93 <!-- ======== START OF CLASS DATA ======== -->
  94 <div class="header">
  95 <div class="subTitle">compbio.runner.msa</div>
  96 <h2 title="Class GLprobs" class="title">Class GLprobs</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/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</li>
 104 <li>
 105 <ul class="inheritance">
 106 <li>compbio.runner.msa.GLprobs</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/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;, <a href="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</a>&lt;<a href="../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</dd>
 118 </dl>
 119 <hr>
 120 <br>
 121 <pre>public class <span class="typeNameLabel">GLprobs</span>
 122 extends <a href="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;
 123 implements <a href="../../../compbio/engine/client/PipedExecutable.html" title="interface in compbio.engine.client">PipedExecutable</a>&lt;<a href="../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</pre>
 124 </li>
 125 </ul>
 126 </div>
 127 <div class="summary">
 128 <ul class="blockList">
 129 <li class="blockList">
 130 <!-- ======== NESTED CLASS SUMMARY ======== -->
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 135 <h3>Nested Class Summary</h3>
 136 <ul class="blockList">
 137 <li class="blockList"><a name="nested.classes.inherited.from.class.compbio.engine.client.Executable">
 138 <!--   -->
 139 </a>
 140 <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>
 141 <code><a href="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</a></code></li>
 142 </ul>
 143 </li>
 144 </ul>
 145 <!-- =========== FIELD SUMMARY =========== -->
 146 <ul class="blockList">
 147 <li class="blockList"><a name="field.summary">
 148 <!--   -->
 149 </a>
 150 <h3>Field Summary</h3>
 151 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 152 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 153 <tr>
 154 <th class="colFirst" scope="col">Modifier and Type</th>
 155 <th class="colLast" scope="col">Field and Description</th>
 156 </tr>
 157 <tr class="altColor">
 158 <td class="colFirst"><code>private static java.lang.String</code></td>
 159 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#ANNOTATION">ANNOTATION</a></span></code>&nbsp;</td>
 160 </tr>
 161 <tr class="rowColor">
 162 <td class="colFirst"><code>static java.lang.String</code></td>
 163 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></span></code>&nbsp;</td>
 164 </tr>
 165 <tr class="altColor">
 166 <td class="colFirst"><code>private static org.apache.log4j.Logger</code></td>
 167 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#log">log</a></span></code>&nbsp;</td>
 168 </tr>
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 170 <ul class="blockList">
 171 <li class="blockList"><a name="fields.inherited.from.class.compbio.engine.client.SkeletalExecutable">
 172 <!--   -->
 173 </a>
 174 <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>
 175 <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>
 176 </ul>
 177 </li>
 178 </ul>
 179 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 180 <ul class="blockList">
 181 <li class="blockList"><a name="constructor.summary">
 182 <!--   -->
 183 </a>
 184 <h3>Constructor Summary</h3>
 185 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 186 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 187 <tr>
 188 <th class="colOne" scope="col">Constructor and Description</th>
 189 </tr>
 190 <tr class="altColor">
 191 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#GLprobs--">GLprobs</a></span>()</code>&nbsp;</td>
 192 </tr>
 193 </table>
 194 </li>
 195 </ul>
 196 <!-- ========== METHOD SUMMARY =========== -->
 197 <ul class="blockList">
 198 <li class="blockList"><a name="method.summary">
 199 <!--   -->
 200 </a>
 201 <h3>Method Summary</h3>
 202 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 203 <caption><span id="t0" class="activeTableTab"><span>All Methods</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>
 204 <tr>
 205 <th class="colFirst" scope="col">Modifier and Type</th>
 206 <th class="colLast" scope="col">Method and Description</th>
 207 </tr>
 208 <tr id="i0" class="altColor">
 209 <td class="colFirst"><code>java.util.List&lt;java.lang.String&gt;</code></td>
 210 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#getCreatedFiles--">getCreatedFiles</a></span>()</code>
 211 <div class="block">This method cannot really tell whether the files has actually been
 212  created or not.</div>
 213 </td>
 214 </tr>
 215 <tr id="i1" class="rowColor">
 216 <td class="colFirst"><code><a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 217 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#getResults-java.lang.String-">getResults</a></span>(java.lang.String&nbsp;workDirectory)</code>&nbsp;</td>
 218 </tr>
 219 <tr id="i2" class="altColor">
 220 <td class="colFirst"><code>java.lang.Class&lt;<a href="../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</code></td>
 221 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#getType--">getType</a></span>()</code>&nbsp;</td>
 222 </tr>
 223 <tr id="i3" class="rowColor">
 224 <td class="colFirst"><code><a href="../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a></code></td>
 225 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/runner/msa/GLprobs.html#setInput-java.lang.String-">setInput</a></span>(java.lang.String&nbsp;inFile)</code>&nbsp;</td>
 226 </tr>
 227 </table>
 228 <ul class="blockList">
 229 <li class="blockList"><a name="methods.inherited.from.class.compbio.engine.client.SkeletalExecutable">
 230 <!--   -->
 231 </a>
 232 <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>
 233 <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#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters</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#setOutput-java.lang.String-">setOutput</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>
 234 </ul>
 235 <ul class="blockList">
 236 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 237 <!--   -->
 238 </a>
 239 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 240 <code>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</code></li>
 241 </ul>
 242 <ul class="blockList">
 243 <li class="blockList"><a name="methods.inherited.from.class.compbio.engine.client.Executable">
 244 <!--   -->
 245 </a>
 246 <h3>Methods inherited from interface&nbsp;compbio.engine.client.<a href="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a></h3>
 247 <code><a href="../../../compbio/engine/client/Executable.html#addParameters-java.util.List-">addParameters</a>, <a href="../../../compbio/engine/client/Executable.html#getClusterJobSettings--">getClusterJobSettings</a>, <a href="../../../compbio/engine/client/Executable.html#getError--">getError</a>, <a href="../../../compbio/engine/client/Executable.html#getInput--">getInput</a>, <a href="../../../compbio/engine/client/Executable.html#getLimit-java.lang.String-">getLimit</a>, <a href="../../../compbio/engine/client/Executable.html#getLimits--">getLimits</a>, <a href="../../../compbio/engine/client/Executable.html#getOutput--">getOutput</a>, <a href="../../../compbio/engine/client/Executable.html#getParameters-compbio.engine.client.Executable.ExecProvider-">getParameters</a>, <a href="../../../compbio/engine/client/Executable.html#loadRunConfiguration-compbio.engine.client.RunConfiguration-">loadRunConfiguration</a></code></li>
 248 </ul>
 249 </li>
 250 </ul>
 251 </li>
 252 </ul>
 253 </div>
 254 <div class="details">
 255 <ul class="blockList">
 256 <li class="blockList">
 257 <!-- ============ FIELD DETAIL =========== -->
 258 <ul class="blockList">
 259 <li class="blockList"><a name="field.detail">
 260 <!--   -->
 261 </a>
 262 <h3>Field Detail</h3>
 263 <a name="log">
 264 <!--   -->
 265 </a>
 266 <ul class="blockList">
 267 <li class="blockList">
 268 <h4>log</h4>
 269 <pre>private static&nbsp;org.apache.log4j.Logger log</pre>
 270 </li>
 271 </ul>
 272 <a name="ANNOTATION">
 273 <!--   -->
 274 </a>
 275 <ul class="blockList">
 276 <li class="blockList">
 277 <h4>ANNOTATION</h4>
 278 <pre>private static final&nbsp;java.lang.String ANNOTATION</pre>
 279 <dl>
 280 <dt><span class="seeLabel">See Also:</span></dt>
 281 <dd><a href="../../../constant-values.html#compbio.runner.msa.GLprobs.ANNOTATION">Constant Field Values</a></dd>
 282 </dl>
 283 </li>
 284 </ul>
 285 <a name="KEY_VALUE_SEPARATOR">
 286 <!--   -->
 287 </a>
 288 <ul class="blockListLast">
 289 <li class="blockList">
 290 <h4>KEY_VALUE_SEPARATOR</h4>
 291 <pre>public static final&nbsp;java.lang.String KEY_VALUE_SEPARATOR</pre>
 292 <dl>
 293 <dt><span class="seeLabel">See Also:</span></dt>
 294 <dd><a href="../../../constant-values.html#compbio.runner.msa.GLprobs.KEY_VALUE_SEPARATOR">Constant Field Values</a></dd>
 295 </dl>
 296 </li>
 297 </ul>
 298 </li>
 299 </ul>
 300 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 301 <ul class="blockList">
 302 <li class="blockList"><a name="constructor.detail">
 303 <!--   -->
 304 </a>
 305 <h3>Constructor Detail</h3>
 306 <a name="GLprobs--">
 307 <!--   -->
 308 </a>
 309 <ul class="blockListLast">
 310 <li class="blockList">
 311 <h4>GLprobs</h4>
 312 <pre>public&nbsp;GLprobs()</pre>
 313 </li>
 314 </ul>
 315 </li>
 316 </ul>
 317 <!-- ============ METHOD DETAIL ========== -->
 318 <ul class="blockList">
 319 <li class="blockList"><a name="method.detail">
 320 <!--   -->
 321 </a>
 322 <h3>Method Detail</h3>
 323 <a name="getResults-java.lang.String-">
 324 <!--   -->
 325 </a>
 326 <ul class="blockList">
 327 <li class="blockList">
 328 <h4>getResults</h4>
 329 <pre>public&nbsp;<a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;getResults(java.lang.String&nbsp;workDirectory)
 330                      throws <a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
 331 <dl>
 332 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 333 <dd><code><a href="../../../compbio/engine/client/Executable.html#getResults-java.lang.String-">getResults</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/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</code></dd>
 334 <dt><span class="throwsLabel">Throws:</span></dt>
 335 <dd><code><a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></code></dd>
 336 </dl>
 337 </li>
 338 </ul>
 339 <a name="getCreatedFiles--">
 340 <!--   -->
 341 </a>
 342 <ul class="blockList">
 343 <li class="blockList">
 344 <h4>getCreatedFiles</h4>
 345 <pre>public&nbsp;java.util.List&lt;java.lang.String&gt;&nbsp;getCreatedFiles()</pre>
 346 <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>
 347 <div class="block">This method cannot really tell whether the files has actually been
 348  created or not. It must be overridden as required.</div>
 349 <dl>
 350 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 351 <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/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</code></dd>
 352 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 353 <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/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</code></dd>
 354 <dt><span class="seeLabel">See Also:</span></dt>
 355 <dd><a href="../../../compbio/engine/client/Executable.html#getCreatedFiles--"><code>Executable.getCreatedFiles()</code></a></dd>
 356 </dl>
 357 </li>
 358 </ul>
 359 <a name="setInput-java.lang.String-">
 360 <!--   -->
 361 </a>
 362 <ul class="blockList">
 363 <li class="blockList">
 364 <h4>setInput</h4>
 365 <pre>public&nbsp;<a href="../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&nbsp;setInput(java.lang.String&nbsp;inFile)</pre>
 366 <dl>
 367 <dt><span class="overrideSpecifyLabel">Overrides:</span></dt>
 368 <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/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</code></dd>
 369 </dl>
 370 </li>
 371 </ul>
 372 <a name="getType--">
 373 <!--   -->
 374 </a>
 375 <ul class="blockListLast">
 376 <li class="blockList">
 377 <h4>getType</h4>
 378 <pre>public&nbsp;java.lang.Class&lt;<a href="../../../compbio/runner/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;&nbsp;getType()</pre>
 379 <dl>
 380 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 381 <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/msa/GLprobs.html" title="class in compbio.runner.msa">GLprobs</a>&gt;</code></dd>
 382 <dt><span class="returnLabel">Returns:</span></dt>
 383 <dd>subclasses must return their type</dd>
 384 </dl>
 385 </li>
 386 </ul>
 387 </li>
 388 </ul>
 389 </li>
 390 </ul>
 391 </div>
 392 </div>
 393 <!-- ========= END OF CLASS DATA ========= -->
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 404 <li><a href="package-summary.html">Package</a></li>
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