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76 <li>Summary: </li>
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95 <div class="subTitle">compbio.runner</div>
96 <h2 title="Class RunnerUtil" class="title">Class RunnerUtil</h2>
98 <div class="contentContainer">
99 <ul class="inheritance">
100 <li>java.lang.Object</li>
102 <ul class="inheritance">
103 <li>compbio.runner.RunnerUtil</li>
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112 <pre>public final class <span class="typeNameLabel">RunnerUtil</span>
113 extends java.lang.Object</pre>
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129 <th class="colFirst" scope="col">Modifier and Type</th>
130 <th class="colLast" scope="col">Field and Description</th>
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> </td>
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148 <th class="colOne" scope="col">Constructor and Description</th>
150 <tr class="altColor">
151 <td class="colOne"><code><span class="memberNameLink"><a href="../../compbio/runner/RunnerUtil.html#RunnerUtil--">RunnerUtil</a></span>()</code> </td>
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161 <h3>Method Summary</h3>
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165 <th class="colFirst" scope="col">Modifier and Type</th>
166 <th class="colLast" scope="col">Method and Description</th>
168 <tr id="i0" class="altColor">
169 <td class="colFirst"><code>static <T> <a href="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a><T></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<? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a><T>> clazz)</code> </td>
172 <tr id="i1" class="rowColor">
173 <td class="colFirst"><code>static <T> <a href="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><T></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<? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a><T>> clazz)</code> </td>
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 workDirectory,
179 java.lang.String clustFile)</code> </td>
181 <tr id="i3" class="rowColor">
182 <td class="colFirst"><code>static java.util.Map<java.lang.String,<a href="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>></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 workDirectory,
184 java.lang.String clustFile)</code> </td>
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 workDirectory,
189 java.lang.String structFile)</code> </td>
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<<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
194 <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a><?> exec,
195 char gapChar)</code> </td>
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<<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
200 <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a><?> exec)</code> </td>
203 <ul class="blockList">
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207 <h3>Methods inherited from class java.lang.Object</h3>
208 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
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230 <pre>public static org.apache.log4j.Logger log</pre>
235 <!-- ========= CONSTRUCTOR DETAIL ======== -->
236 <ul class="blockList">
237 <li class="blockList"><a name="constructor.detail">
240 <h3>Constructor Detail</h3>
241 <a name="RunnerUtil--">
244 <ul class="blockListLast">
245 <li class="blockList">
247 <pre>public RunnerUtil()</pre>
252 <!-- ============ METHOD DETAIL ========== -->
253 <ul class="blockList">
254 <li class="blockList"><a name="method.detail">
257 <h3>Method Detail</h3>
258 <a name="getSupportedOptions-java.lang.Class-">
261 <ul class="blockList">
262 <li class="blockList">
263 <h4>getSupportedOptions</h4>
264 <pre>public static <T> <a href="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><T> getSupportedOptions(java.lang.Class<? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a><T>> clazz)</pre>
267 <a name="getPresets-java.lang.Class-">
270 <ul class="blockList">
271 <li class="blockList">
273 <pre>public static <T> <a href="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a><T> getPresets(java.lang.Class<? extends <a href="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</a><T>> clazz)</pre>
276 <a name="readClustalFile-java.lang.String-java.lang.String-">
279 <ul class="blockList">
280 <li class="blockList">
281 <h4>readClustalFile</h4>
282 <pre>public static final <a href="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> readClustalFile(java.lang.String workDirectory,
283 java.lang.String clustFile)
284 throws <a href="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a>,
286 java.io.FileNotFoundException,
287 java.lang.NullPointerException</pre>
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>
297 <a name="readJronnFile-java.lang.String-java.lang.String-">
300 <ul class="blockList">
301 <li class="blockList">
302 <h4>readJronnFile</h4>
303 <pre>public static final java.util.Map<java.lang.String,<a href="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a>> readJronnFile(java.lang.String workDirectory,
304 java.lang.String clustFile)
305 throws <a href="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a>,
307 java.io.FileNotFoundException,
308 java.lang.NullPointerException</pre>
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>
318 <a name="writeInput-java.util.List-compbio.engine.client.ConfiguredExecutable-">
321 <ul class="blockList">
322 <li class="blockList">
324 <pre>public static void writeInput(java.util.List<<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
325 <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a><?> exec)
326 throws <a href="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
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>
333 <a name="writeClustalInput-java.util.List-compbio.engine.client.ConfiguredExecutable-char-">
336 <ul class="blockList">
337 <li class="blockList">
338 <h4>writeClustalInput</h4>
339 <pre>public static void writeClustalInput(java.util.List<<a href="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
340 <a href="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a><?> exec,
342 throws <a href="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
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>
349 <a name="readRNAStruct-java.lang.String-java.lang.String-">
352 <ul class="blockListLast">
353 <li class="blockList">
354 <h4>readRNAStruct</h4>
355 <pre>public static <a href="../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a> readRNAStruct(java.lang.String workDirectory,
356 java.lang.String structFile)
357 throws java.io.IOException,
358 java.io.FileNotFoundException</pre>
360 <dt><span class="throwsLabel">Throws:</span></dt>
361 <dd><code>java.io.IOException</code></dd>
362 <dd><code>java.io.FileNotFoundException</code></dd>
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