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91 compbio.engine.cluster.drmaa</FONT>
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93 Class JobRunner</H2>
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96 <IMG SRC="../../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.cluster.drmaa.JobRunner</B>
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99 <DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DD>
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103 <DT><PRE>public class <B>JobRunner</B><DT>extends java.lang.Object<DT>implements <A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></DL>
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107 Single cluster job runner class
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112 <DT><B>Author:</B></DT>
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119 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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121 <A NAME="constructor_summary"><!-- --></A>
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122 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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123 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
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124 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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125 <B>Constructor Summary</B></FONT></TH>
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127 <TR BGCOLOR="white" CLASS="TableRowColor">
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128 <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><?> confExec)</CODE>
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131 </TD>
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135 <!-- ========== METHOD SUMMARY =========== -->
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140 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
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141 <B>Method Summary</B></FONT></TH>
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143 <TR BGCOLOR="white" CLASS="TableRowColor">
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144 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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145 <CODE> boolean</CODE></FONT></TD>
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146 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cancelJob()">cancelJob</A></B>()</CODE>
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149 Stops running job.</TD>
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151 <TR BGCOLOR="white" CLASS="TableRowColor">
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152 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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153 <CODE> boolean</CODE></FONT></TD>
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154 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#cleanup()">cleanup</A></B>()</CODE>
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157 Clean up after the job</TD>
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159 <TR BGCOLOR="white" CLASS="TableRowColor">
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160 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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161 <CODE> boolean</CODE></FONT></TD>
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162 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#deepClean()">deepClean</A></B>()</CODE>
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165 </TD>
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167 <TR BGCOLOR="white" CLASS="TableRowColor">
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168 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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169 <CODE> void</CODE></FONT></TD>
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170 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#executeJob()">executeJob</A></B>()</CODE>
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173 Execute the job</TD>
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175 <TR BGCOLOR="white" CLASS="TableRowColor">
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176 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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177 <CODE>static <A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A></CODE></FONT></TD>
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178 <TD><CODE><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><?> executable)</CODE>
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181 </TD>
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183 <TR BGCOLOR="white" CLASS="TableRowColor">
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184 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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185 <CODE> org.ggf.drmaa.JobInfo</CODE></FONT></TD>
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186 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobInfo()">getJobInfo</A></B>()</CODE>
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189 This method will block before the calculation has completed and then
190 return the object containing a job execution statistics</TD>
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192 <TR BGCOLOR="white" CLASS="TableRowColor">
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193 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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194 <CODE> <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>
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195 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getJobStatus()">getJobStatus</A></B>()</CODE>
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198 Query the status of the job by its id.</TD>
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200 <TR BGCOLOR="white" CLASS="TableRowColor">
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201 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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202 <CODE> java.lang.String</CODE></FONT></TD>
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203 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>
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206 </TD>
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208 <TR BGCOLOR="white" CLASS="TableRowColor">
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209 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
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210 <CODE> <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>
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211 <TD><CODE><B><A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html#waitForResult()">waitForResult</A></B>()</CODE>
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214 Call to this method block for as long as it is required for an executable to finish its job.</TD>
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217 <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
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218 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
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220 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
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222 <TR BGCOLOR="white" CLASS="TableRowColor">
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223 <TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>
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229 <!-- ========= CONSTRUCTOR DETAIL ======== -->
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234 <TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">
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235 <B>Constructor Detail</B></FONT></TH>
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239 <A NAME="JobRunner(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>
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242 public <B>JobRunner</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> confExec)
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243 throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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248 <DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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257 <B>Method Detail</B></FONT></TH>
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261 <A NAME="deepClean()"><!-- --></A><H3>
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264 public boolean <B>deepClean</B>()</PRE>
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275 <A NAME="cleanup()"><!-- --></A><H3>
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278 public boolean <B>cleanup</B>()</PRE>
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280 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cleanup()">SyncExecutor</A></CODE></B></DD>
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281 <DD>Clean up after the job
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284 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cleanup()">cleanup</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>
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288 <DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>
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293 <A NAME="cancelJob()"><!-- --></A><H3>
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296 public boolean <B>cancelJob</B>()</PRE>
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298 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cancelJob()">SyncExecutor</A></CODE></B></DD>
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299 <DD>Stops running job.
300 Clean up is not performed.
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303 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#cancelJob()">cancelJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>
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307 <DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>
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312 <A NAME="getWorkDirectory()"><!-- --></A><H3>
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313 getWorkDirectory</H3>
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315 public java.lang.String <B>getWorkDirectory</B>()</PRE>
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318 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getWorkDirectory()">getWorkDirectory</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>
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322 <DT><B>Returns:</B><DD>working directory if the task</DL>
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327 <A NAME="executeJob()"><!-- --></A><H3>
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330 public void <B>executeJob</B>()
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331 throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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333 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#executeJob()">SyncExecutor</A></CODE></B></DD>
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334 <DD>Execute the job
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337 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>
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342 <DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>
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347 <A NAME="getJobInfo()"><!-- --></A><H3>
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350 public org.ggf.drmaa.JobInfo <B>getJobInfo</B>()
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351 throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>
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353 <DD>This method will block before the calculation has completed and then
354 return the object containing a job execution statistics
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361 <DT><B>Returns:</B><DD>
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363 <DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>
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368 <A NAME="waitForResult()"><!-- --></A><H3>
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371 public <A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>waitForResult</B>()
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372 throws <A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>
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374 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">SyncExecutor</A></CODE></B></DD>
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375 <DD>Call to this method block for as long as it is required for an executable to finish its job.
376 If the calculation has been completed already, the this method returns results immediately.
377 This could return the result directly, but that would be type unsafe
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380 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>
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384 <DT><B>Returns:</B><DD>object from wich the result can be obtained
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386 <DD><CODE><A HREF="../../../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>
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391 <A NAME="getJobStatus()"><!-- --></A><H3>
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394 public <A HREF="../../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>
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396 <DD><B>Description copied from interface: <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getJobStatus()">SyncExecutor</A></CODE></B></DD>
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397 <DD>Query the status of the job by its id.
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400 <DT><B>Specified by:</B><DD><CODE><A HREF="../../../../compbio/engine/SyncExecutor.html#getJobStatus()">getJobStatus</A></CODE> in interface <CODE><A HREF="../../../../compbio/engine/SyncExecutor.html" title="interface in compbio.engine">SyncExecutor</A></CODE></DL>
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404 <DT><B>Returns:</B><DD>- JobStatus</DL>
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409 <A NAME="getInstance(compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>
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412 public static <A HREF="../../../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A> <B>getInstance</B>(<A HREF="../../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> executable)
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413 throws <A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>
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421 <DD><CODE><A HREF="../../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>
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