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  95 <div class="subTitle">compbio.runner</div>
  96 <h2 title="Class RunnerUtil" class="title">Class RunnerUtil</h2>
  97 </div>
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  99 <ul class="inheritance">
 100 <li>java.lang.Object</li>
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 111 <br>
 112 <pre>public final class <span class="typeNameLabel">RunnerUtil</span>
 113 extends java.lang.Object</pre>
 114 </li>
 115 </ul>
 116 </div>
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 126 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 127 <caption><span>Fields</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">Field and Description</th>
 131 </tr>
 132 <tr class="altColor">
 133 <td class="colFirst"><code>static org.apache.log4j.Logger</code></td>
 134 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#log">log</a></span></code>&nbsp;</td>
 135 </tr>
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 147 <tr>
 148 <th class="colOne" scope="col">Constructor and Description</th>
 149 </tr>
 150 <tr class="altColor">
 151 <td class="colOne"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#RunnerUtil--">RunnerUtil</a></span>()</code>&nbsp;</td>
 152 </tr>
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 162 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 163 <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="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 164 <tr>
 165 <th class="colFirst" scope="col">Modifier and Type</th>
 166 <th class="colLast" scope="col">Method and Description</th>
 167 </tr>
 168 <tr id="i0" class="altColor">
 169 <td class="colFirst"><code>static &lt;T&gt;&nbsp;<a href="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;T&gt;</code></td>
 170 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#getPresets-java.lang.Class-">getPresets</a></span>(java.lang.Class&lt;? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;T&gt;&gt;&nbsp;clazz)</code>&nbsp;</td>
 171 </tr>
 172 <tr id="i1" class="rowColor">
 173 <td class="colFirst"><code>static &lt;T&gt;&nbsp;<a href="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;T&gt;</code></td>
 174 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#getSupportedOptions-java.lang.Class-">getSupportedOptions</a></span>(java.lang.Class&lt;? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;T&gt;&gt;&nbsp;clazz)</code>&nbsp;</td>
 175 </tr>
 176 <tr id="i2" class="altColor">
 177 <td class="colFirst"><code>static <a href="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 178 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#readClustalFile-java.lang.String-java.lang.String-">readClustalFile</a></span>(java.lang.String&nbsp;workDirectory,
 179                java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 180 </tr>
 181 <tr id="i3" class="rowColor">
 182 <td class="colFirst"><code>static java.util.Map&lt;java.lang.String,<a href="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;</code></td>
 183 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#readJronnFile-java.lang.String-java.lang.String-">readJronnFile</a></span>(java.lang.String&nbsp;workDirectory,
 184              java.lang.String&nbsp;clustFile)</code>&nbsp;</td>
 185 </tr>
 186 <tr id="i4" class="altColor">
 187 <td class="colFirst"><code>static <a href="../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></code></td>
 188 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#readRNAStruct-java.lang.String-java.lang.String-">readRNAStruct</a></span>(java.lang.String&nbsp;workDirectory,
 189              java.lang.String&nbsp;structFile)</code>&nbsp;</td>
 190 </tr>
 191 <tr id="i5" class="rowColor">
 192 <td class="colFirst"><code>static void</code></td>
 193 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#writeClustalInput-java.util.List-compbio.engine.client.ConfiguredExecutable-char-">writeClustalInput</a></span>(java.util.List&lt;<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 194                  <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;exec,
 195                  char&nbsp;gapChar)</code>&nbsp;</td>
 196 </tr>
 197 <tr id="i6" class="altColor">
 198 <td class="colFirst"><code>static void</code></td>
 199 <td class="colLast"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#writeInput-java.util.List-compbio.engine.client.ConfiguredExecutable-">writeInput</a></span>(java.util.List&lt;<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 200           <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;exec)</code>&nbsp;</td>
 201 </tr>
 202 </table>
 203 <ul class="blockList">
 204 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 205 <!--   -->
 206 </a>
 207 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 208 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 209 </ul>
 210 </li>
 211 </ul>
 212 </li>
 213 </ul>
 214 </div>
 215 <div class="details">
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 218 <!-- ============ FIELD DETAIL =========== -->
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 221 <!--   -->
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 223 <h3>Field Detail</h3>
 224 <a name="log">
 225 <!--   -->
 226 </a>
 227 <ul class="blockListLast">
 228 <li class="blockList">
 229 <h4>log</h4>
 230 <pre>public static&nbsp;org.apache.log4j.Logger log</pre>
 231 </li>
 232 </ul>
 233 </li>
 234 </ul>
 235 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 236 <ul class="blockList">
 237 <li class="blockList"><a name="constructor.detail">
 238 <!--   -->
 239 </a>
 240 <h3>Constructor Detail</h3>
 241 <a name="RunnerUtil--">
 242 <!--   -->
 243 </a>
 244 <ul class="blockListLast">
 245 <li class="blockList">
 246 <h4>RunnerUtil</h4>
 247 <pre>public&nbsp;RunnerUtil()</pre>
 248 </li>
 249 </ul>
 250 </li>
 251 </ul>
 252 <!-- ============ METHOD DETAIL ========== -->
 253 <ul class="blockList">
 254 <li class="blockList"><a name="method.detail">
 255 <!--   -->
 256 </a>
 257 <h3>Method Detail</h3>
 258 <a name="getSupportedOptions-java.lang.Class-">
 259 <!--   -->
 260 </a>
 261 <ul class="blockList">
 262 <li class="blockList">
 263 <h4>getSupportedOptions</h4>
 264 <pre>public static&nbsp;&lt;T&gt;&nbsp;<a href="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;T&gt;&nbsp;getSupportedOptions(java.lang.Class&lt;? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;T&gt;&gt;&nbsp;clazz)</pre>
 265 </li>
 266 </ul>
 267 <a name="getPresets-java.lang.Class-">
 268 <!--   -->
 269 </a>
 270 <ul class="blockList">
 271 <li class="blockList">
 272 <h4>getPresets</h4>
 273 <pre>public static&nbsp;&lt;T&gt;&nbsp;<a href="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;T&gt;&nbsp;getPresets(java.lang.Class&lt;? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a>&lt;T&gt;&gt;&nbsp;clazz)</pre>
 274 </li>
 275 </ul>
 276 <a name="readClustalFile-java.lang.String-java.lang.String-">
 277 <!--   -->
 278 </a>
 279 <ul class="blockList">
 280 <li class="blockList">
 281 <h4>readClustalFile</h4>
 282 <pre>public static final&nbsp;<a href="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;readClustalFile(java.lang.String&nbsp;workDirectory,
 283                                               java.lang.String&nbsp;clustFile)
 284                                        throws <a href="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a>,
 285                                               java.io.IOException,
 286                                               java.io.FileNotFoundException,
 287                                               java.lang.NullPointerException</pre>
 288 <dl>
 289 <dt><span class="throwsLabel">Throws:</span></dt>
 290 <dd><code><a href="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 291 <dd><code>java.io.IOException</code></dd>
 292 <dd><code>java.io.FileNotFoundException</code></dd>
 293 <dd><code>java.lang.NullPointerException</code></dd>
 294 </dl>
 295 </li>
 296 </ul>
 297 <a name="readJronnFile-java.lang.String-java.lang.String-">
 298 <!--   -->
 299 </a>
 300 <ul class="blockList">
 301 <li class="blockList">
 302 <h4>readJronnFile</h4>
 303 <pre>public static final&nbsp;java.util.Map&lt;java.lang.String,<a href="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>&gt;&nbsp;readJronnFile(java.lang.String&nbsp;workDirectory,
 304                                                                         java.lang.String&nbsp;clustFile)
 305                                                                  throws <a href="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a>,
 306                                                                         java.io.IOException,
 307                                                                         java.io.FileNotFoundException,
 308                                                                         java.lang.NullPointerException</pre>
 309 <dl>
 310 <dt><span class="throwsLabel">Throws:</span></dt>
 311 <dd><code><a href="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></code></dd>
 312 <dd><code>java.io.IOException</code></dd>
 313 <dd><code>java.io.FileNotFoundException</code></dd>
 314 <dd><code>java.lang.NullPointerException</code></dd>
 315 </dl>
 316 </li>
 317 </ul>
 318 <a name="writeInput-java.util.List-compbio.engine.client.ConfiguredExecutable-">
 319 <!--   -->
 320 </a>
 321 <ul class="blockList">
 322 <li class="blockList">
 323 <h4>writeInput</h4>
 324 <pre>public static&nbsp;void&nbsp;writeInput(java.util.List&lt;<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 325                               <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;exec)
 326                        throws <a href="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 327 <dl>
 328 <dt><span class="throwsLabel">Throws:</span></dt>
 329 <dd><code><a href="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 330 </dl>
 331 </li>
 332 </ul>
 333 <a name="writeClustalInput-java.util.List-compbio.engine.client.ConfiguredExecutable-char-">
 334 <!--   -->
 335 </a>
 336 <ul class="blockList">
 337 <li class="blockList">
 338 <h4>writeClustalInput</h4>
 339 <pre>public static&nbsp;void&nbsp;writeClustalInput(java.util.List&lt;<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 340                                      <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;?&gt;&nbsp;exec,
 341                                      char&nbsp;gapChar)
 342                               throws <a href="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 343 <dl>
 344 <dt><span class="throwsLabel">Throws:</span></dt>
 345 <dd><code><a href="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 346 </dl>
 347 </li>
 348 </ul>
 349 <a name="readRNAStruct-java.lang.String-java.lang.String-">
 350 <!--   -->
 351 </a>
 352 <ul class="blockListLast">
 353 <li class="blockList">
 354 <h4>readRNAStruct</h4>
 355 <pre>public static&nbsp;<a href="../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a>&nbsp;readRNAStruct(java.lang.String&nbsp;workDirectory,
 356                                                   java.lang.String&nbsp;structFile)
 357                                            throws java.io.IOException,
 358                                                   java.io.FileNotFoundException</pre>
 359 <dl>
 360 <dt><span class="throwsLabel">Throws:</span></dt>
 361 <dd><code>java.io.IOException</code></dd>
 362 <dd><code>java.io.FileNotFoundException</code></dd>
 363 </dl>
 364 </li>
 365 </ul>
 366 </li>
 367 </ul>
 368 </li>
 369 </ul>
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 435 </body>
 436 </html>