<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:49 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:41 GMT 2011 -->\r
<TITLE>\r
Util\r
</TITLE>\r
\r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
\r
<BR>\r
Class Util</H2>\r
<PRE>\r
-java.lang.Object\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 java.lang.Object</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
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#convertToAbsolute(java.lang.String)">convertToAbsolute</A></B>(java.lang.String relativePath)</CODE>\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 java.lang.String</CODE></FONT></TD>\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
- java.lang.Class<?> clazz)</CODE>\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 java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getExecProperty(java.lang.String, java.lang.Class)">getExecProperty</A></B>(java.lang.String propertySpec,\r
- java.lang.Class<?> clazz)</CODE>\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 java.lang.String</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>(java.lang.String propertySpec,\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
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#getFullPath(java.lang.String, java.lang.String)">getFullPath</A></B>(java.lang.String workDirectory,\r
- java.lang.String fileName)</CODE>\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>(java.lang.Class<?> clazz)</CODE>\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 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>(java.lang.String workDirectory,\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
<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>(java.lang.String key)</CODE>\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 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>(java.lang.String taskId)</CODE>\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 java.util.Map<java.lang.String,java.lang.String></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#mergeEnvVariables(java.util.Map, java.util.Map)">mergeEnvVariables</A></B>(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,\r
- java.util.Map<java.lang.String,java.lang.String> variables)</CODE>\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 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>(java.lang.String workDirectory,\r
- java.lang.String fileAndEventName,\r
- java.lang.String content,\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
<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>(java.lang.String workDirectory,\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
<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>(java.lang.String workDirectory,\r
- java.lang.String fileAndEventName)</CODE>\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
<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.Object</B></TH>\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>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\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
<A NAME="isValidJobId(java.lang.String)"><!-- --></A><H3>\r
isValidJobId</H3>\r
<PRE>\r
-public static boolean <B>isValidJobId</B>(java.lang.String key)</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
<A NAME="writeStatFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
writeStatFile</H3>\r
<PRE>\r
-public static void <B>writeStatFile</B>(java.lang.String workDirectory,\r
- java.lang.String fileAndEventName)</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
<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>(java.lang.String workDirectory,\r
- java.lang.String fileAndEventName,\r
- java.lang.String content,\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
<A NAME="writeMarker(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>\r
writeMarker</H3>\r
<PRE>\r
-public static final boolean <B>writeMarker</B>(java.lang.String workDirectory,\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
<A NAME="isMarked(java.lang.String, compbio.metadata.JobStatus)"><!-- --></A><H3>\r
isMarked</H3>\r
<PRE>\r
-public static boolean <B>isMarked</B>(java.lang.String workDirectory,\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
<A NAME="mergeEnvVariables(java.util.Map, java.util.Map)"><!-- --></A><H3>\r
mergeEnvVariables</H3>\r
<PRE>\r
-public static java.util.Map<java.lang.String,java.lang.String> <B>mergeEnvVariables</B>(java.util.Map<java.lang.String,java.lang.String> sysEnvTobeModified,\r
- java.util.Map<java.lang.String,java.lang.String> variables)</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
<A NAME="convertToAbsolute(java.lang.String)"><!-- --></A><H3>\r
convertToAbsolute</H3>\r
<PRE>\r
-public static java.lang.String <B>convertToAbsolute</B>(java.lang.String relativePath)</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
<A NAME="getExecProperty(java.lang.String, compbio.engine.client.Executable)"><!-- --></A><H3>\r
getExecProperty</H3>\r
<PRE>\r
-public static java.lang.String <B>getExecProperty</B>(java.lang.String propertySpec,\r
- <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?> exec)</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
<A NAME="getExecProperty(java.lang.String, java.lang.Class)"><!-- --></A><H3>\r
getExecProperty</H3>\r
<PRE>\r
-public static java.lang.String <B>getExecProperty</B>(java.lang.String propertySpec,\r
- java.lang.Class<?> clazz)</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
<A NAME="getFullPath(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
getFullPath</H3>\r
<PRE>\r
-public static java.lang.String <B>getFullPath</B>(java.lang.String workDirectory,\r
- java.lang.String fileName)</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
<A NAME="getCommand(compbio.engine.client.Executable.ExecProvider, java.lang.Class)"><!-- --></A><H3>\r
getCommand</H3>\r
<PRE>\r
-public static java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engine/client/Executable.ExecProvider.html" title="enum in compbio.engine.client">Executable.ExecProvider</A> provider,\r
- java.lang.Class<?> clazz)</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
</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>(java.lang.Class<?> clazz)</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
<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>(java.lang.String taskId)\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
<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