+++ /dev/null
-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
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-Util\r
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-Class Util</H2>\r
-<PRE>\r
-<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
- <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.engine.client.Util</B>\r
-</PRE>\r
-<HR>\r
-<DL>\r
-<DT><PRE>public final class <B>Util</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
-</PRE>\r
-\r
-<P>\r
-<HR>\r
-\r
-<P>\r
-\r
-<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
-\r
-<A NAME="constructor_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>Constructor Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#Util()">Util</A></B>()</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\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>static <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/client/Util.html#convertToAbsolute(java.lang.String)">convertToAbsolute</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> relativePath)</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>static <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/client/Util.html#getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)">getCommand</A></B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</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>static <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/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)">getExecProperty</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> propertySpec,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</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>static <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/client/Util.html#getExecProperty(java.lang.String, compbio.engine.client.Executable)">getExecProperty</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> propertySpec,\r
- <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> exec)</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>static <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/client/Util.html#getFullPath(java.lang.String, java.lang.String)">getFullPath</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> workDirectory,\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> fileName)</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>static <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/client/Util.html#getJava()">getJava</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns the absolute path to the Java executable from JAVA_HOME</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
-<TR ALIGN="right" VALIGN="">\r
-<TD NOWRAP><FONT SIZE="-1">\r
-<CODE><T> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T></CODE></FONT></TD>\r
-</TR>\r
-</TABLE>\r
-</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getLimits(java.lang.Class)">getLimits</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><T> clazz)</CODE>\r
-\r
-<BR>\r
- For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getSupportedRuntimes(java.lang.Class)">getSupportedRuntimes</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</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>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isJavaLibrary(java.lang.Class)">isJavaLibrary</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</CODE>\r
-\r
-<BR>\r
- Returns true of executableName.jar.file property has some value in the
- Executable.properties file, false otherwise.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isMarked(java.lang.String, compbio.metadata.JobStatus)">isMarked</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> workDirectory,\r
- <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> marker)</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>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#isValidJobId(java.lang.String)">isValidJobId</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> key)</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>static <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/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> taskId)</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>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<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/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)">mergeEnvVariables</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<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>> sysEnvTobeModified,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<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>> variables)</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>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)">writeFile</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> workDirectory,\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> fileAndEventName,\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> content,\r
- boolean override)</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>static boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeMarker(java.lang.String, compbio.metadata.JobStatus)">writeMarker</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> workDirectory,\r
- <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> fileType)</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>static void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#writeStatFile(java.lang.String, java.lang.String)">writeStatFile</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> workDirectory,\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> fileAndEventName)</CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
-</TR>\r
-</TABLE>\r
- \r
-<P>\r
-\r
-<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
-\r
-<A NAME="constructor_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Constructor Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="Util()"><!-- --></A><H3>\r
-Util</H3>\r
-<PRE>\r
-public <B>Util</B>()</PRE>\r
-<DL>\r
-</DL>\r
-\r
-<!-- ============ METHOD DETAIL ========== -->\r
-\r
-<A NAME="method_detail"><!-- --></A>\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
-<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
-<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
-<B>Method Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="isValidJobId(java.lang.String)"><!-- --></A><H3>\r
-isValidJobId</H3>\r
-<PRE>\r
-public static boolean <B>isValidJobId</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> key)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeStatFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-writeStatFile</H3>\r
-<PRE>\r
-public static void <B>writeStatFile</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> workDirectory,\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> fileAndEventName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)"><!-- --></A><H3>\r
-writeFile</H3>\r
-<PRE>\r
-public static void <B>writeFile</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> workDirectory,\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> fileAndEventName,\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> content,\r
- boolean override)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="writeMarker(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>\r
-writeMarker</H3>\r
-<PRE>\r
-public static final boolean <B>writeMarker</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> workDirectory,\r
- <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> fileType)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isMarked(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>\r
-isMarked</H3>\r
-<PRE>\r
-public static boolean <B>isMarked</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> workDirectory,\r
- <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A> marker)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="mergeEnvVariables(java.util.Map, java.util.Map)"><!-- --></A><H3>\r
-mergeEnvVariables</H3>\r
-<PRE>\r
-public static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<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>mergeEnvVariables</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<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>> sysEnvTobeModified,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<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>,<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>> variables)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="convertToAbsolute(java.lang.String)"><!-- --></A><H3>\r
-convertToAbsolute</H3>\r
-<PRE>\r
-public static <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>convertToAbsolute</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> relativePath)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getExecProperty(java.lang.String, compbio.engine.client.Executable)"><!-- --></A><H3>\r
-getExecProperty</H3>\r
-<PRE>\r
-public static <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>getExecProperty</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> propertySpec,\r
- <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> exec)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getExecProperty(java.lang.String, java.lang.Class)"><!-- --></A><H3>\r
-getExecProperty</H3>\r
-<PRE>\r
-public static <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>getExecProperty</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> propertySpec,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getFullPath(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-getFullPath</H3>\r
-<PRE>\r
-public static <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>getFullPath</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> workDirectory,\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> fileName)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><!-- --></A><H3>\r
-getCommand</H3>\r
-<PRE>\r
-public static <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>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isJavaLibrary(java.lang.Class)"><!-- --></A><H3>\r
-isJavaLibrary</H3>\r
-<PRE>\r
-public static boolean <B>isJavaLibrary</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</PRE>\r
-<DL>\r
-<DD>Returns true of executableName.jar.file property has some value in the
- Executable.properties file, false otherwise.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>clazz</CODE> - \r
-<DT><B>Returns:</B><DD></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getJava()"><!-- --></A><H3>\r
-getJava</H3>\r
-<PRE>\r
-public static <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>getJava</B>()</PRE>\r
-<DL>\r
-<DD>Returns the absolute path to the Java executable from JAVA_HOME\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>returns the absolute path to the Java executable from JAVA_HOME</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getSupportedRuntimes(java.lang.Class)"><!-- --></A><H3>\r
-getSupportedRuntimes</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> <B>getSupportedRuntimes</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><?> clazz)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="loadExecutable(java.lang.String)"><!-- --></A><H3>\r
-loadExecutable</H3>\r
-<PRE>\r
-public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> <B>loadExecutable</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> taskId)\r
- throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></CODE></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getLimits(java.lang.Class)"><!-- --></A><H3>\r
-getLimits</H3>\r
-<PRE>\r
-public static <T> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><T> <B>getLimits</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Class.html?is-external=true" title="class or interface in java.lang">Class</A><T> clazz)</PRE>\r
-<DL>\r
-<DD>For now just assume that all parameters which came in needs setting it
- will be a client responsibility to prepare RunnerConfig object then\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>rconfig</CODE> - \r
-<DT><B>Returns:</B><DD>public static List<String> toOptionString(RunnerConfig<?>
- rconfig) { String option = ""; List<String> options = new
- ArrayList<String>(); for (Parameter<?> par :
- rconfig.getParameters()) { if (par.getPossibleValues().isEmpty())
- { option = par.getOptionName(); } else { option =
- par.getOptionName() + "=" + par.getPossibleValues().get(0); } //
- separate options options.add(option); } return options; }</DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
-\r
-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
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- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
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- </TR>\r
-</TABLE>\r
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-<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
-</EM>\r
-</TD>\r
-</TR>\r
-\r
-<TR>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client"><B>PREV CLASS</B></A> \r
- NEXT CLASS</FONT></TD>\r
-<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../../index.html?compbio/engine/client/Util.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Util.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
- <!--\r
- if(window==top) {\r
- document.writeln('<A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>');\r
- }\r
- //-->\r
-</SCRIPT>\r
-<NOSCRIPT>\r
- <A HREF="../../../allclasses-noframe.html"><B>All Classes</B></A>\r
-</NOSCRIPT>\r
-\r
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-</FONT></TD>\r
-</TR>\r
-<TR>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
-DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
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