<!--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
SkeletalExecutable\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
</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
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <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
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
</TR>\r
</TABLE>\r
<A NAME="skip-navbar_top"></A>\r
<BR>\r
Class SkeletalExecutable<T></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.SkeletalExecutable<T></B>\r
</PRE>\r
<DL>\r
<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T></DD>\r
</DL>\r
<DL>\r
-<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/psiblast/PsiBlast.html" title="class in compbio.runner.psiblast">PsiBlast</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/runner/conservation/AACon.html" title="class in compbio.runner.conservation">AACon</A>, <A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>, <A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>, <A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>, <A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>, <A HREF="../../../compbio/runner/disorder/IUPred.html" title="class in compbio.runner.disorder">IUPred</A>, <A HREF="../../../compbio/runner/disorder/Jronn.html" title="class in compbio.runner.disorder">Jronn</A>, <A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>, <A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>, <A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>, <A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A></DD>\r
</DL>\r
<HR>\r
<DL>\r
-<DT><PRE>public abstract class <B>SkeletalExecutable<T></B><DT>extends java.lang.Object<DT>implements <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T></DL>\r
+<DT><PRE>public abstract class <B>SkeletalExecutable<T></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><DT>implements <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><T></DL>\r
</PRE>\r
\r
<P>\r
</TR>\r
</TABLE>\r
\r
+<!-- =========== FIELD SUMMARY =========== -->\r
\r
+<A NAME="field_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>Field 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/SkeletalExecutable.html#ERROR">ERROR</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>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/SkeletalExecutable.html#INPUT">INPUT</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>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/SkeletalExecutable.html#OUTPUT">OUTPUT</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
\r
<A NAME="constructor_summary"><!-- --></A>\r
</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)">SkeletalExecutable</A></B>(java.lang.String parameterKeyValueDelimiter)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#SkeletalExecutable(java.lang.String)">SkeletalExecutable</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> parameterKeyValueDelimiter)</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> <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></B>(java.util.List<java.lang.String> parameters)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#addParameters(java.util.List)">addParameters</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</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>> parameters)</CODE>\r
\r
<BR>\r
Adds parameter to the list of parameters for a native executable</TD>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object obj)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#equals(java.lang.Object)">equals</A></B>(<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> obj)</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> java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterSettings()">getClusterSettings</A></B>()</CODE>\r
+<CODE>static int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterCpuNum(java.lang.Class)">getClusterCpuNum</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><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> type)</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> java.util.List<java.lang.String></CODE></FONT></TD>\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getClusterJobSettings()">getClusterJobSettings</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</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/SkeletalExecutable.html#getCreatedFiles()">getCreatedFiles</A></B>()</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> java.lang.String</CODE></FONT></TD>\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getError()">getError</A></B>()</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> java.lang.String</CODE></FONT></TD>\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getInput()">getInput</A></B>()</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> java.lang.String</CODE></FONT></TD>\r
+<CODE> <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimit(java.lang.String)">getLimit</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> presetName)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getLimits()">getLimits</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> <A HREF="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/SkeletalExecutable.html#getOutput()">getOutput</A></B>()</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>abstract java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>></CODE></FONT></TD>\r
+<CODE>abstract <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><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#getType()">getType</A></B>()</CODE>\r
\r
<BR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
<CODE> <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</A></B>(java.lang.String errFile)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setError(java.lang.String)">setError</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> errFile)</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> <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</A></B>(java.lang.String inFile)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setInput(java.lang.String)">setInput</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> inFile)</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> <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</A></B>(java.lang.String outFile)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setOutput(java.lang.String)">setOutput</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> outFile)</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> <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</A></B>(java.lang.String parameter)</CODE>\r
+<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#setParameter(java.lang.String)">setParameter</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> parameter)</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> java.lang.String</CODE></FONT></TD>\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../../compbio/engine/client/SkeletalExecutable.html#toString()">toString</A></B>()</CODE>\r
\r
<BR>\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>getClass, notify, notifyAll, 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#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#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#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
<A NAME="methods_inherited_from_class_compbio.engine.client.Executable"><!-- --></A>\r
<TH ALIGN="left"><B>Methods inherited from interface compbio.engine.client.<A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A></B></TH>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A>, <A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A>, <A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE></TD>\r
+<TD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getResults(java.lang.String)">getResults</A></CODE></TD>\r
</TR>\r
</TABLE>\r
\r
<P>\r
\r
+<!-- ============ FIELD DETAIL =========== -->\r
+\r
+<A NAME="field_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>Field Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="INPUT"><!-- --></A><H3>\r
+INPUT</H3>\r
+<PRE>\r
+public static final <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>INPUT</B></PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.INPUT">Constant Field Values</A></DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="OUTPUT"><!-- --></A><H3>\r
+OUTPUT</H3>\r
+<PRE>\r
+public static final <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>OUTPUT</B></PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.OUTPUT">Constant Field Values</A></DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="ERROR"><!-- --></A><H3>\r
+ERROR</H3>\r
+<PRE>\r
+public static final <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>ERROR</B></PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../../constant-values.html#compbio.engine.client.SkeletalExecutable.ERROR">Constant Field Values</A></DL>\r
+</DL>\r
+\r
<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
\r
<A NAME="constructor_detail"><!-- --></A>\r
<A NAME="SkeletalExecutable(java.lang.String)"><!-- --></A><H3>\r
SkeletalExecutable</H3>\r
<PRE>\r
-public <B>SkeletalExecutable</B>(java.lang.String parameterKeyValueDelimiter)</PRE>\r
+public <B>SkeletalExecutable</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> parameterKeyValueDelimiter)</PRE>\r
<DL>\r
</DL>\r
\r
<A NAME="setInput(java.lang.String)"><!-- --></A><H3>\r
setInput</H3>\r
<PRE>\r
-public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setInput</B>(java.lang.String inFile)</PRE>\r
+public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setInput</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> inFile)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="setOutput(java.lang.String)"><!-- --></A><H3>\r
setOutput</H3>\r
<PRE>\r
-public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setOutput</B>(java.lang.String outFile)</PRE>\r
+public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setOutput</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> outFile)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="setError(java.lang.String)"><!-- --></A><H3>\r
setError</H3>\r
<PRE>\r
-public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setError</B>(java.lang.String errFile)</PRE>\r
+public <A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setError</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> errFile)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="addParameters(java.util.List)"><!-- --></A><H3>\r
addParameters</H3>\r
<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>addParameters</B>(java.util.List<java.lang.String> parameters)</PRE>\r
+public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>addParameters</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</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>> parameters)</PRE>\r
<DL>\r
<DD><B>Description copied from interface: <CODE><A HREF="../../../compbio/engine/client/Executable.html#addParameters(java.util.List)">Executable</A></CODE></B></DD>\r
<DD>Adds parameter to the list of parameters for a native executable\r
<A NAME="setParameter(java.lang.String)"><!-- --></A><H3>\r
setParameter</H3>\r
<PRE>\r
-public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setParameter</B>(java.lang.String parameter)</PRE>\r
+public <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>setParameter</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> parameter)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="getCreatedFiles()"><!-- --></A><H3>\r
getCreatedFiles</H3>\r
<PRE>\r
-public java.util.List<java.lang.String> <B>getCreatedFiles</B>()</PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</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>getCreatedFiles</B>()</PRE>\r
<DL>\r
<DD>This method cannot really tell whether the files has actually been
created or not. It must be overridden as required.\r
<A NAME="getInput()"><!-- --></A><H3>\r
getInput</H3>\r
<PRE>\r
-public java.lang.String <B>getInput</B>()</PRE>\r
+public <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>getInput</B>()</PRE>\r
<DL>\r
<DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getInput()">getInput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>\r
<A NAME="getOutput()"><!-- --></A><H3>\r
getOutput</H3>\r
<PRE>\r
-public java.lang.String <B>getOutput</B>()</PRE>\r
+public <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>getOutput</B>()</PRE>\r
<DL>\r
<DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getOutput()">getOutput</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>\r
<A NAME="getError()"><!-- --></A><H3>\r
getError</H3>\r
<PRE>\r
-public java.lang.String <B>getError</B>()</PRE>\r
+public <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>getError</B>()</PRE>\r
<DL>\r
<DD><DL>\r
<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getError()">getError</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>\r
<A NAME="toString()"><!-- --></A><H3>\r
toString</H3>\r
<PRE>\r
-public java.lang.String <B>toString</B>()</PRE>\r
+public <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>toString</B>()</PRE>\r
<DL>\r
<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
+<DT><B>Overrides:</B><DD><CODE><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></CODE> in class <CODE><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></CODE></DL>\r
</DD>\r
<DD><DL>\r
</DL>\r
<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
equals</H3>\r
<PRE>\r
-public boolean <B>equals</B>(java.lang.Object obj)</PRE>\r
+public boolean <B>equals</B>(<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> obj)</PRE>\r
<DL>\r
<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
+<DT><B>Overrides:</B><DD><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></CODE> in class <CODE><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></CODE></DL>\r
</DD>\r
<DD><DL>\r
</DL>\r
public int <B>hashCode</B>()</PRE>\r
<DL>\r
<DD><DL>\r
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
+<DT><B>Overrides:</B><DD><CODE><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></CODE> in class <CODE><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></CODE></DL>\r
</DD>\r
<DD><DL>\r
</DL>\r
</DL>\r
<HR>\r
\r
-<A NAME="getClusterSettings()"><!-- --></A><H3>\r
-getClusterSettings</H3>\r
+<A NAME="getClusterJobSettings()"><!-- --></A><H3>\r
+getClusterJobSettings</H3>\r
<PRE>\r
-public java.lang.String <B>getClusterSettings</B>()</PRE>\r
+public <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>getClusterJobSettings</B>()</PRE>\r
<DL>\r
<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getClusterJobSettings()">getClusterJobSettings</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
</DL>\r
</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getClusterCpuNum(java.lang.Class)"><!-- --></A><H3>\r
+getClusterCpuNum</H3>\r
+<PRE>\r
+public static int <B>getClusterCpuNum</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><? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> type)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>number of cpus to use on the cluster or 0 if the value is
+ undefined</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimit(java.lang.String)"><!-- --></A><H3>\r
+getLimit</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>getLimit</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> presetName)</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimit(java.lang.String)">getLimit</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getLimits()"><!-- --></A><H3>\r
+getLimits</H3>\r
+<PRE>\r
+public <A HREF="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>getLimits</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../../compbio/engine/client/Executable.html#getLimits()">getLimits</A></CODE> in interface <CODE><A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>></CODE></DL>\r
+</DD>\r
<DD><DL>\r
</DL>\r
</DD>\r
<A NAME="getType()"><!-- --></A><H3>\r
getType</H3>\r
<PRE>\r
-public abstract java.lang.Class<? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> <B>getType</B>()</PRE>\r
+public abstract <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><<A HREF="../../../compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</A>> <B>getType</B>()</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
</DD>\r
<DD><DL>\r
-</DL>\r
+\r
+<DT><B>Returns:</B><DD>subclasses must return their type</DL>\r
</DD>\r
</DL>\r
<!-- ========= END OF CLASS DATA ========= -->\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
+ SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <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
+DETAIL: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
</TR>\r
</TABLE>\r
<A NAME="skip-navbar_bottom"></A>\r