--- /dev/null
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">\r
+<!--NewPage-->\r
+<HTML>\r
+<HEAD>\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:30:40 GMT 2011 -->\r
+<TITLE>\r
+Util\r
+</TITLE>\r
+\r
+<META NAME="date" CONTENT="2011-12-07">\r
+\r
+<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
+\r
+<SCRIPT type="text/javascript">\r
+function windowTitle()\r
+{\r
+ if (location.href.indexOf('is-external=true') == -1) {\r
+ parent.document.title="Util";\r
+ }\r
+}\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+</NOSCRIPT>\r
+\r
+</HEAD>\r
+\r
+<BODY BGCOLOR="white" onload="windowTitle();">\r
+<HR>\r
+\r
+\r
+<!-- ========= START OF TOP NAVBAR ======= -->\r
+<A NAME="navbar_top"><!-- --></A>\r
+<A HREF="#skip-navbar_top" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_top_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>PREV CLASS</B></A> \r
+ NEXT CLASS</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/runner/Util.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Util.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\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: <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
+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.runner</FONT>\r
+<BR>\r
+Class Util</H2>\r
+<PRE>\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.runner.Util</B>\r
+</PRE>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public final class <B>Util</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
+</PRE>\r
+\r
+<P>\r
+<HR>\r
+\r
+<P>\r
+<!-- =========== 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 org.apache.log4j.Logger</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#log">log</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/runner/Util.html#SPACE">SPACE</A></B></CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
+\r
+<A NAME="constructor_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Constructor Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#Util()">Util</A></B>()</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<!-- ========== METHOD SUMMARY =========== -->\r
+\r
+<A NAME="method_summary"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+<B>Method Summary</B></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static\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/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T></CODE></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getPresets(java.lang.Class)">getPresets</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><T>> 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\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/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T></CODE></FONT></TD>\r
+</TR>\r
+</TABLE>\r
+</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#getSupportedOptions(java.lang.Class)">getSupportedOptions</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><T>> clazz)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#readClustalFile(java.lang.String, java.lang.String)">readClustalFile</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> clustFile)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>,<A HREF="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#readJronnFile(java.lang.String, java.lang.String)">readJronnFile</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> clustFile)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>static void</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/runner/Util.html#writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)">writeInput</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="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)</CODE>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ <A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+\r
+<!-- ============ 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="log"><!-- --></A><H3>\r
+log</H3>\r
+<PRE>\r
+public static org.apache.log4j.Logger <B>log</B></PRE>\r
+<DL>\r
+<DL>\r
+</DL>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="SPACE"><!-- --></A><H3>\r
+SPACE</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>SPACE</B></PRE>\r
+<DL>\r
+<DL>\r
+<DT><B>See Also:</B><DD><A HREF="../../constant-values.html#compbio.runner.Util.SPACE">Constant Field Values</A></DL>\r
+</DL>\r
+\r
+<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
+\r
+<A NAME="constructor_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Constructor Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="Util()"><!-- --></A><H3>\r
+Util</H3>\r
+<PRE>\r
+public <B>Util</B>()</PRE>\r
+<DL>\r
+</DL>\r
+\r
+<!-- ============ METHOD DETAIL ========== -->\r
+\r
+<A NAME="method_detail"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="1"><FONT SIZE="+2">\r
+<B>Method Detail</B></FONT></TH>\r
+</TR>\r
+</TABLE>\r
+\r
+<A NAME="getSupportedOptions(java.lang.Class)"><!-- --></A><H3>\r
+getSupportedOptions</H3>\r
+<PRE>\r
+public static <T> <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><T> <B>getSupportedOptions</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><T>> clazz)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPresets(java.lang.Class)"><!-- --></A><H3>\r
+getPresets</H3>\r
+<PRE>\r
+public static <T> <A HREF="../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</A><T> <B>getPresets</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><T>> clazz)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readClustalFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+readClustalFile</H3>\r
+<PRE>\r
+public static final <A HREF="../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A> <B>readClustalFile</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> clustFile)\r
+ throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="readJronnFile(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+readJronnFile</H3>\r
+<PRE>\r
+public static final <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="../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>> <B>readJronnFile</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> clustFile)\r
+ throws <A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A>,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/FileNotFoundException.html?is-external=true" title="class or interface in java.io">FileNotFoundException</A></CODE>\r
+<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/NullPointerException.html?is-external=true" title="class or interface in java.lang">NullPointerException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="writeInput(java.util.List, compbio.engine.client.ConfiguredExecutable)"><!-- --></A><H3>\r
+writeInput</H3>\r
+<PRE>\r
+public static void <B>writeInput</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="../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>> sequences,\r
+ <A HREF="../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</A><?> exec)\r
+ throws <A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></PRE>\r
+<DL>\r
+<DD><DL>\r
+\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</A></CODE></DL>\r
+</DD>\r
+</DL>\r
+<!-- ========= END OF CLASS DATA ========= -->\r
+<HR>\r
+\r
+\r
+<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
+<A NAME="navbar_bottom"><!-- --></A>\r
+<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
+<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
+<TR>\r
+<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
+<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
+ <TR ALIGN="center" VALIGN="top">\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/Util.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-tree.html"><FONT CLASS="NavBarFont1"><B>Tree</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../deprecated-list.html"><FONT CLASS="NavBarFont1"><B>Deprecated</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../index-files/index-1.html"><FONT CLASS="NavBarFont1"><B>Index</B></FONT></A> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../help-doc.html"><FONT CLASS="NavBarFont1"><B>Help</B></FONT></A> </TD>\r
+ </TR>\r
+</TABLE>\r
+</TD>\r
+<TD ALIGN="right" VALIGN="top" ROWSPAN=3><EM>\r
+</EM>\r
+</TD>\r
+</TR>\r
+\r
+<TR>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/runner/OptionCombinator.html" title="class in compbio.runner"><B>PREV CLASS</B></A> \r
+ NEXT CLASS</FONT></TD>\r
+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../index.html?compbio/runner/Util.html" target="_top"><B>FRAMES</B></A> \r
+ <A HREF="Util.html" target="_top"><B>NO FRAMES</B></A> \r
+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
+ }\r
+ //-->\r
+</SCRIPT>\r
+<NOSCRIPT>\r
+ <A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>\r
+</NOSCRIPT>\r
+\r
+\r
+</FONT></TD>\r
+</TR>\r
+<TR>\r
+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\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: <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
+<!-- ======== END OF BOTTOM NAVBAR ======= -->\r
+\r
+<HR>\r
+\r
+</BODY>\r
+</HTML>\r