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7 Uses of Interface compbio.engine.client.ConfiguredExecutable\r
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82 <CENTER>\r
83 <H2>\r
84 <B>Uses of Interface<br>compbio.engine.client.ConfiguredExecutable</B></H2>\r
85 </CENTER>\r
86 \r
87 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
88 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
89 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
90 Packages that use <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
91 </TR>\r
92 <TR BGCOLOR="white" CLASS="TableRowColor">\r
93 <TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
94 <TD>&nbsp;&nbsp;</TD>\r
95 </TR>\r
96 <TR BGCOLOR="white" CLASS="TableRowColor">\r
97 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
98 <TD>&nbsp;&nbsp;</TD>\r
99 </TR>\r
100 <TR BGCOLOR="white" CLASS="TableRowColor">\r
101 <TD><A HREF="#compbio.engine.cluster.drmaa"><B>compbio.engine.cluster.drmaa</B></A></TD>\r
102 <TD>&nbsp;&nbsp;</TD>\r
103 </TR>\r
104 <TR BGCOLOR="white" CLASS="TableRowColor">\r
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107 </TR>\r
108 <TR BGCOLOR="white" CLASS="TableRowColor">\r
109 <TD><A HREF="#compbio.runner"><B>compbio.runner</B></A></TD>\r
110 <TD>Utilities commonly used by all runners.&nbsp;</TD>\r
111 </TR>\r
112 <TR BGCOLOR="white" CLASS="TableRowColor">\r
113 <TD><A HREF="#compbio.ws.server"><B>compbio.ws.server</B></A></TD>\r
114 <TD>&nbsp;&nbsp;</TD>\r
115 </TR>\r
116 </TABLE>\r
117 &nbsp;\r
118 <P>\r
119 <A NAME="compbio.engine"><!-- --></A>\r
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122 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
123 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A></FONT></TH>\r
124 </TR>\r
125 </TABLE>\r
126 &nbsp;\r
127 <P>\r
128 \r
129 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
130 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
131 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
132 </TR>\r
133 <TR BGCOLOR="white" CLASS="TableRowColor">\r
134 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
135 <CODE>static\r
136 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
137 <TR ALIGN="right" VALIGN="">\r
138 <TD NOWRAP><FONT SIZE="-1">\r
139 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
140 </TR>\r
141 </TABLE>\r
142 </CODE></FONT></TD>\r
143 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable)</CODE>\r
144 \r
145 <BR>\r
146 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
147 </TR>\r
148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
149 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
150 <CODE>static\r
151 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
152 <TR ALIGN="right" VALIGN="">\r
153 <TD NOWRAP><FONT SIZE="-1">\r
154 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
155 </TR>\r
156 </TABLE>\r
157 </CODE></FONT></TD>\r
158 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, compbio.engine.client.Executable.ExecProvider)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
159                     <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
160 \r
161 <BR>\r
162 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
163 </TR>\r
164 <TR BGCOLOR="white" CLASS="TableRowColor">\r
165 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
166 <CODE>static\r
167 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
168 <TR ALIGN="right" VALIGN="">\r
169 <TD NOWRAP><FONT SIZE="-1">\r
170 <CODE>&lt;T&gt; <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;</CODE></FONT></TD>\r
171 </TR>\r
172 </TABLE>\r
173 </CODE></FONT></TD>\r
174 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#configureExecutable(compbio.engine.client.Executable, java.util.List)">configureExecutable</A></B>(<A HREF="../../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;T&gt;&nbsp;executable,\r
175                     <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;dataSet)</CODE>\r
176 \r
177 <BR>\r
178 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
179 </TR>\r
180 <TR BGCOLOR="white" CLASS="TableRowColor">\r
181 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
182 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
183 <TD><CODE><B>Job.</B><B><A HREF="../../../../compbio/engine/Job.html#getConfExecutable()">getConfExecutable</A></B>()</CODE>\r
184 \r
185 <BR>\r
186 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
187 </TR>\r
188 <TR BGCOLOR="white" CLASS="TableRowColor">\r
189 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
190 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
191 <TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../../compbio/engine/AsyncExecutor.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
192 \r
193 <BR>\r
194 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Retrieve the results of the job.</TD>\r
195 </TR>\r
196 <TR BGCOLOR="white" CLASS="TableRowColor">\r
197 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
198 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
199 <TD><CODE><B>SyncExecutor.</B><B><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></B>()</CODE>\r
200 \r
201 <BR>\r
202 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
203 </TR>\r
204 </TABLE>\r
205 &nbsp;\r
206 <P>\r
207 \r
208 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
209 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
210 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> that return types with arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
211 </TR>\r
212 <TR BGCOLOR="white" CLASS="TableRowColor">\r
213 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
214 <CODE>static&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
215 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#getTask(java.lang.String)">getTask</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId)</CODE>\r
216 \r
217 <BR>\r
218 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
219 </TR>\r
220 </TABLE>\r
221 &nbsp;\r
222 <P>\r
223 \r
224 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
225 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
226 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
227 </TR>\r
228 <TR BGCOLOR="white" CLASS="TableRowColor">\r
229 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
230 <CODE>static&nbsp;void</CODE></FONT></TD>\r
231 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)">addTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
232         <A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
233 \r
234 <BR>\r
235 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
236 </TR>\r
237 <TR BGCOLOR="white" CLASS="TableRowColor">\r
238 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
239 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
240 <TD><CODE><B>Cleaner.</B><B><A HREF="../../../../compbio/engine/Cleaner.html#deleteFiles(compbio.engine.client.ConfiguredExecutable)">deleteFiles</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
241 \r
242 <BR>\r
243 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<B>Deprecated.</B>&nbsp;This method returns true if all files specified by List files were
244  successfully removed or there was no files to remove (files list was
245  empty)</TD>\r
246 </TR>\r
247 <TR BGCOLOR="white" CLASS="TableRowColor">\r
248 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
249 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
250 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable)">getAsyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
251 \r
252 <BR>\r
253 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
254 </TR>\r
255 <TR BGCOLOR="white" CLASS="TableRowColor">\r
256 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
257 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
258 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getAsyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getAsyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
259                <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
260 \r
261 <BR>\r
262 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
263 </TR>\r
264 <TR BGCOLOR="white" CLASS="TableRowColor">\r
265 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
266 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
267 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable)">getSyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
268 \r
269 <BR>\r
270 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
271 </TR>\r
272 <TR BGCOLOR="white" CLASS="TableRowColor">\r
273 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
274 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></FONT></TD>\r
275 <TD><CODE><B>Configurator.</B><B><A HREF="../../../../compbio/engine/Configurator.html#getSyncEngine(compbio.engine.client.ConfiguredExecutable, compbio.engine.client.Executable.ExecProvider)">getSyncEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
276               <A HREF="../../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A>&nbsp;provider)</CODE>\r
277 \r
278 <BR>\r
279 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
280 </TR>\r
281 <TR BGCOLOR="white" CLASS="TableRowColor">\r
282 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
283 <CODE>static&nbsp;void</CODE></FONT></TD>\r
284 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#removeTask(compbio.engine.client.ConfiguredExecutable)">removeTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
285 \r
286 <BR>\r
287 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
288 </TR>\r
289 <TR BGCOLOR="white" CLASS="TableRowColor">\r
290 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
291 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
292 <TD><CODE><B>AsyncExecutor.</B><B><A HREF="../../../../compbio/engine/AsyncExecutor.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
293 \r
294 <BR>\r
295 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Submits job for the execution
296  Immediate execution is not guaranteed, this method puts the job in the queue.</TD>\r
297 </TR>\r
298 </TABLE>\r
299 &nbsp;\r
300 <P>\r
301 \r
302 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
303 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
304 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with type arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
305 </TR>\r
306 <TR BGCOLOR="white" CLASS="TableRowColor">\r
307 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
308 <CODE>static&nbsp;void</CODE></FONT></TD>\r
309 <TD><CODE><B>SubmissionManager.</B><B><A HREF="../../../../compbio/engine/SubmissionManager.html#addTask(compbio.engine.client.ConfiguredExecutable, java.util.concurrent.Future)">addTask</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
310         <A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
311 \r
312 <BR>\r
313 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
314 </TR>\r
315 </TABLE>\r
316 &nbsp;\r
317 <P>\r
318 \r
319 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
320 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
321 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/package-summary.html">compbio.engine</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
322 </TR>\r
323 <TR BGCOLOR="white" CLASS="TableRowColor">\r
324 <TD><CODE><B><A HREF="../../../../compbio/engine/Job.html#Job(java.lang.String, java.lang.String, compbio.engine.client.ConfiguredExecutable)">Job</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId,\r
325     <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId,\r
326     <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;cexecutable)</CODE>\r
327 \r
328 <BR>\r
329 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
330 </TR>\r
331 </TABLE>\r
332 &nbsp;\r
333 <P>\r
334 <A NAME="compbio.engine.client"><!-- --></A>\r
335 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
336 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
337 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
338 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A></FONT></TH>\r
339 </TR>\r
340 </TABLE>\r
341 &nbsp;\r
342 <P>\r
343 \r
344 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
345 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
346 <TH ALIGN="left" COLSPAN="2">Classes in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that implement <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
347 </TR>\r
348 <TR BGCOLOR="white" CLASS="TableRowColor">\r
349 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
350 <CODE>&nbsp;class</CODE></FONT></TD>\r
351 <TD><CODE><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable&lt;T&gt;</A></B></CODE>\r
352 \r
353 <BR>\r
354 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
355 </TR>\r
356 </TABLE>\r
357 &nbsp;\r
358 <P>\r
359 \r
360 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
361 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
362 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/client/package-summary.html">compbio.engine.client</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
363 </TR>\r
364 <TR BGCOLOR="white" CLASS="TableRowColor">\r
365 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
366 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
367 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/engine/client/Util.html#loadExecutable(java.lang.String)">loadExecutable</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId)</CODE>\r
368 \r
369 <BR>\r
370 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
371 </TR>\r
372 <TR BGCOLOR="white" CLASS="TableRowColor">\r
373 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
374 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
375 <TD><CODE><B>ConfiguredExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)</CODE>\r
376 \r
377 <BR>\r
378 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
379 </TR>\r
380 <TR BGCOLOR="white" CLASS="TableRowColor">\r
381 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
382 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
383 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(java.io.InputStream)">loadRunConfiguration</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/InputStream.html?is-external=true" title="class or interface in java.io">InputStream</A>&nbsp;input)</CODE>\r
384 \r
385 <BR>\r
386 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
387 </TR>\r
388 <TR BGCOLOR="white" CLASS="TableRowColor">\r
389 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
390 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
391 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#loadRunConfiguration(compbio.engine.client.RunConfiguration)">loadRunConfiguration</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
392 \r
393 <BR>\r
394 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
395 </TR>\r
396 <TR BGCOLOR="white" CLASS="TableRowColor">\r
397 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
398 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
399 <TD><CODE><B>ConfExecutable.</B><B><A HREF="../../../../compbio/engine/client/ConfExecutable.html#newConfExecutable(compbio.engine.client.RunConfiguration)">newConfExecutable</A></B>(<A HREF="../../../../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>&nbsp;rconf)</CODE>\r
400 \r
401 <BR>\r
402 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
403 </TR>\r
404 </TABLE>\r
405 &nbsp;\r
406 <P>\r
407 <A NAME="compbio.engine.cluster.drmaa"><!-- --></A>\r
408 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
409 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
410 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
411 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A></FONT></TH>\r
412 </TR>\r
413 </TABLE>\r
414 &nbsp;\r
415 <P>\r
416 \r
417 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
418 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
419 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
420 </TR>\r
421 <TR BGCOLOR="white" CLASS="TableRowColor">\r
422 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
423 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
424 <TD><CODE><B>ClusterSession.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/ClusterSession.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId)</CODE>\r
425 \r
426 <BR>\r
427 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
428 </TR>\r
429 <TR BGCOLOR="white" CLASS="TableRowColor">\r
430 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
431 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
432 <TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;jobId)</CODE>\r
433 \r
434 <BR>\r
435 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
436 </TR>\r
437 <TR BGCOLOR="white" CLASS="TableRowColor">\r
438 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
439 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
440 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
441 \r
442 <BR>\r
443 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
444 </TR>\r
445 </TABLE>\r
446 &nbsp;\r
447 <P>\r
448 \r
449 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
450 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
451 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
452 </TR>\r
453 <TR BGCOLOR="white" CLASS="TableRowColor">\r
454 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
455 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>\r
456 <TD><CODE><B>JobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getInstance(compbio.engine.client.ConfiguredExecutable)">getInstance</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
457 \r
458 <BR>\r
459 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
460 </TR>\r
461 <TR BGCOLOR="white" CLASS="TableRowColor">\r
462 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
463 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
464 <TD><CODE><B>AsyncJobRunner.</B><B><A HREF="../../../../compbio/engine/cluster/drmaa/AsyncJobRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
465 \r
466 <BR>\r
467 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
468 </TR>\r
469 </TABLE>\r
470 &nbsp;\r
471 <P>\r
472 \r
473 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
474 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
475 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/cluster/drmaa/package-summary.html">compbio.engine.cluster.drmaa</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
476 </TR>\r
477 <TR BGCOLOR="white" CLASS="TableRowColor">\r
478 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#JobRunner(compbio.engine.client.ConfiguredExecutable)">JobRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExec)</CODE>\r
479 \r
480 <BR>\r
481 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
482 </TR>\r
483 </TABLE>\r
484 &nbsp;\r
485 <P>\r
486 <A NAME="compbio.engine.local"><!-- --></A>\r
487 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
488 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
489 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
490 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A></FONT></TH>\r
491 </TR>\r
492 </TABLE>\r
493 &nbsp;\r
494 <P>\r
495 \r
496 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
497 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
498 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> that return <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
499 </TR>\r
500 <TR BGCOLOR="white" CLASS="TableRowColor">\r
501 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
502 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
503 <TD><CODE><B>ExecutableWrapper.</B><B><A HREF="../../../../compbio/engine/local/ExecutableWrapper.html#call()">call</A></B>()</CODE>\r
504 \r
505 <BR>\r
506 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;It is vital that output and error streams are captured immediately for
507  this call() to succeed.</TD>\r
508 </TR>\r
509 <TR BGCOLOR="white" CLASS="TableRowColor">\r
510 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
511 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
512 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
513            <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId)</CODE>\r
514 \r
515 <BR>\r
516 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
517 </TR>\r
518 <TR BGCOLOR="white" CLASS="TableRowColor">\r
519 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
520 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
521 <TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../../compbio/engine/local/AsyncLocalRunner.html#getResults(java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId)</CODE>\r
522 \r
523 <BR>\r
524 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
525 </TR>\r
526 <TR BGCOLOR="white" CLASS="TableRowColor">\r
527 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
528 <CODE>&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
529 <TD><CODE><B>LocalRunner.</B><B><A HREF="../../../../compbio/engine/local/LocalRunner.html#waitForResult()">waitForResult</A></B>()</CODE>\r
530 \r
531 <BR>\r
532 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
533 </TR>\r
534 </TABLE>\r
535 &nbsp;\r
536 <P>\r
537 \r
538 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
539 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
540 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
541 </TR>\r
542 <TR BGCOLOR="white" CLASS="TableRowColor">\r
543 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
544 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
545 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#cleanup(compbio.engine.client.ConfiguredExecutable)">cleanup</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confExecutable)</CODE>\r
546 \r
547 <BR>\r
548 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
549 </TR>\r
550 <TR BGCOLOR="white" CLASS="TableRowColor">\r
551 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
552 <CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
553 <TD><CODE><B>AsyncLocalRunner.</B><B><A HREF="../../../../compbio/engine/local/AsyncLocalRunner.html#submitJob(compbio.engine.client.ConfiguredExecutable)">submitJob</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
554 \r
555 <BR>\r
556 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
557 </TR>\r
558 </TABLE>\r
559 &nbsp;\r
560 <P>\r
561 \r
562 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
563 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
564 <TH ALIGN="left" COLSPAN="2">Method parameters in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with type arguments of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
565 </TR>\r
566 <TR BGCOLOR="white" CLASS="TableRowColor">\r
567 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
568 <CODE>static&nbsp;boolean</CODE></FONT></TD>\r
569 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#cancelJob(java.util.concurrent.Future, java.lang.String)">cancelJob</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
570           <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
571 \r
572 <BR>\r
573 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
574 </TR>\r
575 <TR BGCOLOR="white" CLASS="TableRowColor">\r
576 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
577 <CODE>static&nbsp;<A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
578 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getJobStatus(java.util.concurrent.Future)">getJobStatus</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future)</CODE>\r
579 \r
580 <BR>\r
581 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
582 </TR>\r
583 <TR BGCOLOR="white" CLASS="TableRowColor">\r
584 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
585 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
586 <TD><CODE><B>LocalEngineUtil.</B><B><A HREF="../../../../compbio/engine/local/LocalEngineUtil.html#getResults(java.util.concurrent.Future, java.lang.String)">getResults</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/concurrent/Future.html?is-external=true" title="class or interface in java.util.concurrent">Future</A>&lt;<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&gt;&nbsp;future,\r
587            <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;taskId)</CODE>\r
588 \r
589 <BR>\r
590 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
591 </TR>\r
592 </TABLE>\r
593 &nbsp;\r
594 <P>\r
595 \r
596 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
597 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
598 <TH ALIGN="left" COLSPAN="2">Constructors in <A HREF="../../../../compbio/engine/local/package-summary.html">compbio.engine.local</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
599 </TR>\r
600 <TR BGCOLOR="white" CLASS="TableRowColor">\r
601 <TD><CODE><B><A HREF="../../../../compbio/engine/local/ExecutableWrapper.html#ExecutableWrapper(compbio.engine.client.ConfiguredExecutable, java.lang.String)">ExecutableWrapper</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable,\r
602                   <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;workDirectory)</CODE>\r
603 \r
604 <BR>\r
605 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
606 </TR>\r
607 <TR BGCOLOR="white" CLASS="TableRowColor">\r
608 <TD><CODE><B><A HREF="../../../../compbio/engine/local/LocalRunner.html#LocalRunner(compbio.engine.client.ConfiguredExecutable)">LocalRunner</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;executable)</CODE>\r
609 \r
610 <BR>\r
611 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
612 </TR>\r
613 </TABLE>\r
614 &nbsp;\r
615 <P>\r
616 <A NAME="compbio.runner"><!-- --></A>\r
617 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
618 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
619 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
620 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A></FONT></TH>\r
621 </TR>\r
622 </TABLE>\r
623 &nbsp;\r
624 <P>\r
625 \r
626 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
627 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
628 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/runner/package-summary.html">compbio.runner</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
629 </TR>\r
630 <TR BGCOLOR="white" CLASS="TableRowColor">\r
631 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
632 <CODE>static&nbsp;void</CODE></FONT></TD>\r
633 <TD><CODE><B>Util.</B><B><A HREF="../../../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
634            <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
635 \r
636 <BR>\r
637 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
638 </TR>\r
639 </TABLE>\r
640 &nbsp;\r
641 <P>\r
642 <A NAME="compbio.ws.server"><!-- --></A>\r
643 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
644 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
645 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
646 Uses of <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A> in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A></FONT></TH>\r
647 </TR>\r
648 </TABLE>\r
649 &nbsp;\r
650 <P>\r
651 \r
652 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
653 <TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">\r
654 <TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../../compbio/ws/server/package-summary.html">compbio.ws.server</A> with parameters of type <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A></FONT></TH>\r
655 </TR>\r
656 <TR BGCOLOR="white" CLASS="TableRowColor">\r
657 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
658 <CODE>static\r
659 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
660 <TR ALIGN="right" VALIGN="">\r
661 <TD NOWRAP><FONT SIZE="-1">\r
662 <CODE>&lt;T&gt; <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
663 </TR>\r
664 </TABLE>\r
665 </CODE></FONT></TD>\r
666 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#align(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">align</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
667       <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
668       org.apache.log4j.Logger&nbsp;logger,\r
669       <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;callingMethod,\r
670       <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
671 \r
672 <BR>\r
673 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
674 </TR>\r
675 <TR BGCOLOR="white" CLASS="TableRowColor">\r
676 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
677 <CODE>static\r
678 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
679 <TR ALIGN="right" VALIGN="">\r
680 <TD NOWRAP><FONT SIZE="-1">\r
681 <CODE>&lt;T&gt; <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
682 </TR>\r
683 </TABLE>\r
684 </CODE></FONT></TD>\r
685 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#analize(java.util.List, compbio.engine.client.ConfiguredExecutable, org.apache.log4j.Logger, java.lang.String, compbio.metadata.Limit)">analize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
686         <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;T&gt;&nbsp;confExec,\r
687         org.apache.log4j.Logger&nbsp;log,\r
688         <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;method,\r
689         <A HREF="../../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>&lt;T&gt;&nbsp;limit)</CODE>\r
690 \r
691 <BR>\r
692 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
693 </TR>\r
694 <TR BGCOLOR="white" CLASS="TableRowColor">\r
695 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
696 <CODE>static&nbsp;<A HREF="../../../../compbio/engine/AsyncExecutor.html" title="interface in compbio.engine">AsyncExecutor</A></CODE></FONT></TD>\r
697 <TD><CODE><B>WSUtil.</B><B><A HREF="../../../../compbio/ws/server/WSUtil.html#getEngine(compbio.engine.client.ConfiguredExecutable)">getEngine</A></B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;&nbsp;confClustal)</CODE>\r
698 \r
699 <BR>\r
700 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
701 </TR>\r
702 </TABLE>\r
703 &nbsp;\r
704 <P>\r
705 <HR>\r
706 \r
707 \r
708 <!-- ======= START OF BOTTOM NAVBAR ====== -->\r
709 <A NAME="navbar_bottom"><!-- --></A>\r
710 <A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
711 <TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
712 <TR>\r
713 <TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
714 <A NAME="navbar_bottom_firstrow"><!-- --></A>\r
715 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
716   <TR ALIGN="center" VALIGN="top">\r
717   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A>&nbsp;</TD>\r
718   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A>&nbsp;</TD>\r
719   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client"><FONT CLASS="NavBarFont1"><B>Class</B></FONT></A>&nbsp;</TD>\r
720   <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> &nbsp;<FONT CLASS="NavBarFont1Rev"><B>Use</B></FONT>&nbsp;</TD>\r
721   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../overview-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A>&nbsp;</TD>\r
722   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A>&nbsp;</TD>\r
723   <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1">    <A HREF="../../../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A>&nbsp;</TD>\r
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725   </TR>\r
726 </TABLE>\r
727 </TD>\r
728 <TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
729 </EM>\r
730 </TD>\r
731 </TR>\r
732 \r
733 <TR>\r
734 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
735 &nbsp;PREV&nbsp;\r
736 &nbsp;NEXT</FONT></TD>\r
737 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
738   <A HREF="../../../../index.html?compbio/engine/client/\class-useConfiguredExecutable.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
739 &nbsp;<A HREF="ConfiguredExecutable.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
740 &nbsp;<SCRIPT type="text/javascript">\r
741   <!--\r
742   if(window==top) {\r
743     document.writeln('<A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
744   }\r
745   //-->\r
746 </SCRIPT>\r
747 <NOSCRIPT>\r
748   <A HREF="../../../../allclasses-noframe.html"><B>All Classes</B></A>\r
749 </NOSCRIPT>\r
750 \r
751 \r
752 </FONT></TD>\r
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756 <!-- ======== END OF BOTTOM NAVBAR ======= -->\r
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759 \r
760 </BODY>\r
761 </HTML>\r