<!--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 12:30:40 GMT 2011 -->\r
<TITLE>\r
OptionCombinator\r
</TITLE>\r
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-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
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<LINK REL ="stylesheet" TYPE="text/css" HREF="../../stylesheet.css" TITLE="Style">\r
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<BR>\r
Class OptionCombinator</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.runner.OptionCombinator</B>\r
</PRE>\r
<HR>\r
<DL>\r
<DT><PRE><FONT SIZE="-1">@Immutable\r
-</FONT>public final class <B>OptionCombinator</B><DT>extends java.lang.Object</DL>\r
+</FONT>public final class <B>OptionCombinator</B><DT>extends <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></DL>\r
</PRE>\r
\r
<P>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> java.util.List<java.lang.String></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">argumentsToCommandString</A></B>(java.util.List<? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments)</CODE>\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/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">argumentsToCommandString</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><? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments)</CODE>\r
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<BR>\r
</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static java.util.List<java.lang.String></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List<? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments,\r
+<CODE>static <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/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</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><? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments,\r
<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> rconfig)</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.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String></CODE></FONT></TD>\r
+<CODE> <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="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</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/runner/OptionCombinator.html#getAllConstrainedParametersWithBorderValues(boolean)">getAllConstrainedParametersWithBorderValues</A></B>(boolean minValue)</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.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String></CODE></FONT></TD>\r
+<CODE> <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="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</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/runner/OptionCombinator.html#getAllConstrainedParametersWithRandomValues()">getAllConstrainedParametersWithRandomValues</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.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>></CODE></FONT></TD>\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="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllOptions()">getAllOptions</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.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>></CODE></FONT></TD>\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="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#getAllParameters()">getAllParameters</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.util.List<java.lang.String></CODE></FONT></TD>\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/runner/OptionCombinator.html#getOptionsAtRandom()">getOptionsAtRandom</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.util.List<java.lang.String></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)">optionsToCommandString</A></B>(java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> options)</CODE>\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/runner/OptionCombinator.html#optionsToCommandString(java.util.List)">optionsToCommandString</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/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> options)</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
-<TD><CODE><B><A HREF="../../compbio/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)">parametersToCommandString</A></B>(java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> orderedList,\r
- java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> prmValue)</CODE>\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/runner/OptionCombinator.html#parametersToCommandString(java.util.List, java.util.Map)">parametersToCommandString</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/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> orderedList,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</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>> prmValue)</CODE>\r
\r
<BR>\r
</TD>\r
<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
</TR>\r
</TABLE>\r
\r
<A NAME="optionsToCommandString(java.util.List)"><!-- --></A><H3>\r
optionsToCommandString</H3>\r
<PRE>\r
-public java.util.List<java.lang.String> <B>optionsToCommandString</B>(java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> options)</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>optionsToCommandString</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/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> options)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="getOptionsAtRandom()"><!-- --></A><H3>\r
getOptionsAtRandom</H3>\r
<PRE>\r
-public java.util.List<java.lang.String> <B>getOptionsAtRandom</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>getOptionsAtRandom</B>()</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="getAllOptions()"><!-- --></A><H3>\r
getAllOptions</H3>\r
<PRE>\r
-public java.util.List<<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> <B>getAllOptions</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="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> <B>getAllOptions</B>()</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="getAllParameters()"><!-- --></A><H3>\r
getAllParameters</H3>\r
<PRE>\r
-public java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> <B>getAllParameters</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="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> <B>getAllParameters</B>()</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="argumentsToCommandString(java.util.List)"><!-- --></A><H3>\r
argumentsToCommandString</H3>\r
<PRE>\r
-public java.util.List<java.lang.String> <B>argumentsToCommandString</B>(java.util.List<? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments)</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>argumentsToCommandString</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><? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
argumentsToCommandString</H3>\r
<PRE>\r
-public static java.util.List<java.lang.String> <B>argumentsToCommandString</B>(java.util.List<? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments,\r
- <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> rconfig)</PRE>\r
+public static <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>argumentsToCommandString</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><? extends <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><?>> arguments,\r
+ <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><? extends <A HREF="../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A><?>> rconfig)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="parametersToCommandString(java.util.List, java.util.Map)"><!-- --></A><H3>\r
parametersToCommandString</H3>\r
<PRE>\r
-public java.util.List<java.lang.String> <B>parametersToCommandString</B>(java.util.List<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> orderedList,\r
- java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> prmValue)</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>parametersToCommandString</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/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>> orderedList,\r
+ <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Map.html?is-external=true" title="class or interface in java.util">Map</A><<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</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>> prmValue)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="getAllConstrainedParametersWithBorderValues(boolean)"><!-- --></A><H3>\r
getAllConstrainedParametersWithBorderValues</H3>\r
<PRE>\r
-public java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> <B>getAllConstrainedParametersWithBorderValues</B>(boolean minValue)</PRE>\r
+public <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="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</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>getAllConstrainedParametersWithBorderValues</B>(boolean minValue)</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r
<A NAME="getAllConstrainedParametersWithRandomValues()"><!-- --></A><H3>\r
getAllConstrainedParametersWithRandomValues</H3>\r
<PRE>\r
-public java.util.Map<<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><?>,java.lang.String> <B>getAllConstrainedParametersWithRandomValues</B>()</PRE>\r
+public <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="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</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>getAllConstrainedParametersWithRandomValues</B>()</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\r