website/full_javadoc/compbio/engine/client/class-use/ConfiguredExecutable.html

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