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+SyncExecutor\r
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+ SUMMARY: NESTED | FIELD | CONSTR | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
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+DETAIL: FIELD | CONSTR | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
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+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.engine</FONT>\r
+<BR>\r
+Interface SyncExecutor</H2>\r
+<DL>\r
+<DT><B>All Known Implementing Classes:</B> <DD><A HREF="../../compbio/engine/cluster/drmaa/JobRunner.html" title="class in compbio.engine.cluster.drmaa">JobRunner</A>, <A HREF="../../compbio/engine/local/LocalRunner.html" title="class in compbio.engine.local">LocalRunner</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public interface <B>SyncExecutor</B></DL>\r
+</PRE>\r
+\r
+<P>\r
+Synchronous executor, is an engine to run the Executable synchronously.\r
+<P>\r
+\r
+<P>\r
+<DL>\r
+<DT><B>Author:</B></DT>\r
+ <DD>pvtroshin
+ Date October 2009</DD>\r
+</DL>\r
+<HR>\r
+\r
+<P>\r
+\r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#cancelJob()">cancelJob</A></B>()</CODE>\r
+\r
+<BR>\r
+ Stops running job.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> boolean</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#cleanup()">cleanup</A></B>()</CODE>\r
+\r
+<BR>\r
+ Clean up after the job</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#executeJob()">executeJob</A></B>()</CODE>\r
+\r
+<BR>\r
+ Execute the job</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#getJobStatus()">getJobStatus</A></B>()</CODE>\r
+\r
+<BR>\r
+ Query the status of the job by its id.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <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
+<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#getWorkDirectory()">getWorkDirectory</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/engine/SyncExecutor.html#waitForResult()">waitForResult</A></B>()</CODE>\r
+\r
+<BR>\r
+ Call to this method block for as long as it is required for an executable to finish its job.</TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
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+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="executeJob()"><!-- --></A><H3>\r
+executeJob</H3>\r
+<PRE>\r
+void <B>executeJob</B>()\r
+ throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DD>Execute the job\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE> - if submission fails</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="cleanup()"><!-- --></A><H3>\r
+cleanup</H3>\r
+<PRE>\r
+boolean <B>cleanup</B>()</PRE>\r
+<DL>\r
+<DD>Clean up after the job\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true if all the files created by this job have been removed successfully, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="waitForResult()"><!-- --></A><H3>\r
+waitForResult</H3>\r
+<PRE>\r
+<A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>waitForResult</B>()\r
+ throws <A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></PRE>\r
+<DL>\r
+<DD>Call to this method block for as long as it is required for an executable to finish its job.
+ If the calculation has been completed already, the this method returns results immediately.
+ This could return the result directly, but that would be type unsafe\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>object from wich the result can be obtained\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/JobExecutionException.html" title="class in compbio.metadata">JobExecutionException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getWorkDirectory()"><!-- --></A><H3>\r
+getWorkDirectory</H3>\r
+<PRE>\r
+<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> <B>getWorkDirectory</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>working directory if the task</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="cancelJob()"><!-- --></A><H3>\r
+cancelJob</H3>\r
+<PRE>\r
+boolean <B>cancelJob</B>()</PRE>\r
+<DL>\r
+<DD>Stops running job.
+ Clean up is not performed.\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true if job was cancelled successfully, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getJobStatus()"><!-- --></A><H3>\r
+getJobStatus</H3>\r
+<PRE>\r
+<A HREF="../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> <B>getJobStatus</B>()</PRE>\r
+<DL>\r
+<DD>Query the status of the job by its id.\r
+<P>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>- JobStatus</DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
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+\r
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