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

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