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Re-formatting the file
[jabaws.git] / website / full_javadoc / compbio / engine / client / Util.html
diff --git a/website/full_javadoc/compbio/engine/client/Util.html b/website/full_javadoc/compbio/engine/client/Util.html
index 5574f03..c765a17 100644 (file)
--- a/website/full_javadoc/compbio/engine/client/Util.html
+++ b/website/full_javadoc/compbio/engine/client/Util.html
@@ -2,12 +2,12 @@
 <!--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
@@ -92,12 +92,12 @@ compbio.engine.client</FONT>
 <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
@@ -131,34 +131,34 @@ java.lang.Object
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;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&nbsp;relativePath)</CODE>\r
+<CODE>static&nbsp;<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>&nbsp;relativePath)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.lang.String</CODE></FONT></TD>\r
+<CODE>static&nbsp;<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>&nbsp;provider,\r
-           java.lang.Class&lt;?&gt;&nbsp;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>&lt;?&gt;&nbsp;clazz)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;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&nbsp;propertySpec,\r
-                java.lang.Class&lt;?&gt;&nbsp;clazz)</CODE>\r
+<CODE>static&nbsp;<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>&nbsp;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>&lt;?&gt;&nbsp;clazz)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;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&nbsp;propertySpec,\r
+<CODE>static&nbsp;<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>&nbsp;propertySpec,\r
                 <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</CODE>\r
 \r
 <BR>\r
@@ -166,17 +166,41 @@ java.lang.Object
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;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&nbsp;workDirectory,\r
-            java.lang.String&nbsp;fileName)</CODE>\r
+<CODE>static&nbsp;<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>&nbsp;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>&nbsp;fileName)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static&nbsp;<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
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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>&lt;T&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt;</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>&lt;T&gt;&nbsp;clazz)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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&nbsp;<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&lt;?&gt;&nbsp;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>&lt;?&gt;&nbsp;clazz)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -184,7 +208,16 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;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&nbsp;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>&lt;?&gt;&nbsp;clazz)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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&nbsp;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>&nbsp;workDirectory,\r
          <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;marker)</CODE>\r
 \r
 <BR>\r
@@ -193,7 +226,7 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;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&nbsp;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>&nbsp;key)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -201,16 +234,16 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;<A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt;</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/Util.html#loadExecutable(java.lang.String)">loadExecutable</A></B>(java.lang.String&nbsp;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>&nbsp;taskId)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.Map&lt;java.lang.String,java.lang.String&gt;</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&lt;java.lang.String,java.lang.String&gt;&nbsp;sysEnvTobeModified,\r
-                  java.util.Map&lt;java.lang.String,java.lang.String&gt;&nbsp;variables)</CODE>\r
+<CODE>static&nbsp;<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>&lt;<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>&gt;</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>&lt;<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>&gt;&nbsp;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>&lt;<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>&gt;&nbsp;variables)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -218,9 +251,9 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;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&nbsp;workDirectory,\r
-          java.lang.String&nbsp;fileAndEventName,\r
-          java.lang.String&nbsp;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>&nbsp;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>&nbsp;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>&nbsp;content,\r
           boolean&nbsp;override)</CODE>\r
 \r
 <BR>\r
@@ -229,7 +262,7 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;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&nbsp;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>&nbsp;workDirectory,\r
             <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;fileType)</CODE>\r
 \r
 <BR>\r
@@ -238,8 +271,8 @@ java.lang.Object
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;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&nbsp;workDirectory,\r
-              java.lang.String&nbsp;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>&nbsp;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>&nbsp;fileAndEventName)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -248,10 +281,10 @@ java.lang.Object
 &nbsp;<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
 &nbsp;\r
@@ -287,7 +320,7 @@ public <B>Util</B>()</PRE>
 <A NAME="isValidJobId(java.lang.String)"><!-- --></A><H3>\r
 isValidJobId</H3>\r
 <PRE>\r
-public static boolean <B>isValidJobId</B>(java.lang.String&nbsp;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>&nbsp;key)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -298,8 +331,8 @@ public static boolean <B>isValidJobId</B>(java.lang.String&nbsp;key)</PRE>
 <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&nbsp;workDirectory,\r
-                                 java.lang.String&nbsp;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>&nbsp;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>&nbsp;fileAndEventName)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -310,9 +343,9 @@ public static void <B>writeStatFile</B>(java.lang.String&nbsp;workDirectory,
 <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&nbsp;workDirectory,\r
-                             java.lang.String&nbsp;fileAndEventName,\r
-                             java.lang.String&nbsp;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>&nbsp;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>&nbsp;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>&nbsp;content,\r
                              boolean&nbsp;override)</PRE>\r
 <DL>\r
 <DD><DL>\r
@@ -324,7 +357,7 @@ public static void <B>writeFile</B>(java.lang.String&nbsp;workDirectory,
 <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&nbsp;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>&nbsp;workDirectory,\r
                                         <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;fileType)</PRE>\r
 <DL>\r
 <DD><DL>\r
@@ -336,7 +369,7 @@ public static final boolean <B>writeMarker</B>(java.lang.String&nbsp;workDirecto
 <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&nbsp;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>&nbsp;workDirectory,\r
                                <A HREF="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</A>&nbsp;marker)</PRE>\r
 <DL>\r
 <DD><DL>\r
@@ -348,8 +381,8 @@ public static boolean <B>isMarked</B>(java.lang.String&nbsp;workDirectory,
 <A NAME="mergeEnvVariables(java.util.Map, java.util.Map)"><!-- --></A><H3>\r
 mergeEnvVariables</H3>\r
 <PRE>\r
-public static java.util.Map&lt;java.lang.String,java.lang.String&gt; <B>mergeEnvVariables</B>(java.util.Map&lt;java.lang.String,java.lang.String&gt;&nbsp;sysEnvTobeModified,\r
-                                                                                 java.util.Map&lt;java.lang.String,java.lang.String&gt;&nbsp;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>&lt;<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>&gt; <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>&lt;<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>&gt;&nbsp;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>&lt;<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>&gt;&nbsp;variables)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -360,7 +393,7 @@ public static java.util.Map&lt;java.lang.String,java.lang.String&gt; <B>mergeEnv
 <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&nbsp;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>&nbsp;relativePath)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -371,8 +404,8 @@ public static java.lang.String <B>convertToAbsolute</B>(java.lang.String&nbsp;re
 <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&nbsp;propertySpec,\r
-                                               <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;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>&nbsp;propertySpec,\r
+                                     <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&nbsp;exec)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -383,8 +416,8 @@ public static java.lang.String <B>getExecProperty</B>(java.lang.String&nbsp;prop
 <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&nbsp;propertySpec,\r
-                                               java.lang.Class&lt;?&gt;&nbsp;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>&nbsp;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>&lt;?&gt;&nbsp;clazz)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -395,8 +428,8 @@ public static java.lang.String <B>getExecProperty</B>(java.lang.String&nbsp;prop
 <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&nbsp;workDirectory,\r
-                                           java.lang.String&nbsp;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>&nbsp;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>&nbsp;fileName)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -407,8 +440,8 @@ public static java.lang.String <B>getFullPath</B>(java.lang.String&nbsp;workDire
 <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>&nbsp;provider,\r
-                                          java.lang.Class&lt;?&gt;&nbsp;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>&nbsp;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>&lt;?&gt;&nbsp;clazz)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -416,10 +449,39 @@ public static java.lang.String <B>getCommand</B>(<A HREF="../../../compbio/engin
 </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>&lt;?&gt;&nbsp;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&lt;?&gt;&nbsp;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>&lt;?&gt;&nbsp;clazz)</PRE>\r
 <DL>\r
 <DD><DL>\r
 </DL>\r
@@ -430,7 +492,7 @@ public static <A HREF="../../../compbio/engine/client/Executable.ExecProvider.ht
 <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>&lt;?&gt; <B>loadExecutable</B>(java.lang.String&nbsp;taskId)\r
+public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A>&lt;?&gt; <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>&nbsp;taskId)\r
                                               throws <A HREF="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</A></PRE>\r
 <DL>\r
 <DD><DL>\r
@@ -439,6 +501,27 @@ public static <A HREF="../../../compbio/engine/client/ConfiguredExecutable.html"
 <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 &lt;T&gt; <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A>&lt;T&gt; <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>&lt;T&gt;&nbsp;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