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-compbio.metadata</FONT>\r
-<BR>\r
-Class RunnerConfig<T></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.metadata.RunnerConfig<T></B>\r
-</PRE>\r
-<DL>\r
-<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of an Executable</DL>\r
-<HR>\r
-<DL>\r
-<DT><PRE><FONT SIZE="-1">@NotThreadSafe\r
-</FONT>public class <B>RunnerConfig<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></DL>\r
-</PRE>\r
-\r
-<P>\r
-The list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>s and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A>s supported by executable.
- The lists is defined in and loaded from <ExecutableName>Parameters.xml file.\r
-<P>\r
-\r
-<P>\r
-<DL>\r
-<DT><B>Version:</B></DT>\r
- <DD>1.0 October 2009</DD>\r
-<DT><B>Author:</B></DT>\r
- <DD>pvtroshin</DD>\r
-</DL>\r
-<HR>\r
-\r
-<P>\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/metadata/RunnerConfig.html#RunnerConfig()">RunnerConfig</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
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-<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> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)">addOption</A></B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</CODE>\r
-\r
-<BR>\r
- Adds Option to the internal list of options</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)">addParameter</A></B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</CODE>\r
-\r
-<BR>\r
- Adds parameter to the internal parameter list</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/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)">copyAndValidateRConfig</A></B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.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> <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</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> name)</CODE>\r
-\r
-<BR>\r
- Returns the argument by its name if found, NULL otherwise.</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/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</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> optionName)</CODE>\r
-\r
-<BR>\r
- Returns the argument by option name, NULL if the argument is not found</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="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
- runner</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="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns the list of the Options supported by the executable of type T</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="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>></CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#getParameters()">getParameters</A></B>()</CODE>\r
-\r
-<BR>\r
- Returns the list of parameters supported executable of type T.</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/metadata/RunnerConfig.html#getPrmSeparator()">getPrmSeparator</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/metadata/RunnerConfig.html#getRunnerClassName()">getRunnerClassName</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> boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#removeArgument(java.lang.String)">removeArgument</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> name)</CODE>\r
-\r
-<BR>\r
- Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found.</TD>\r
-</TR>\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/metadata/RunnerConfig.html#removeArgumentByOptionName(java.lang.String)">removeArgumentByOptionName</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> optionName)</CODE>\r
-\r
-<BR>\r
- Removes the argument which can be a Parameter or an Option instance by
- the value in <optionNames> element of the runner configuration
- descriptor.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</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><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
-\r
-<BR>\r
- Adds the list of options or parameters to the internal list of options</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setParameters(java.util.List)">setParameters</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><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</CODE>\r
-\r
-<BR>\r
- Sets the list of parameters as internal list</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setPrmSeparator(java.lang.String)">setPrmSeparator</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> prmSeparator)</CODE>\r
-\r
-<BR>\r
- Sets name value separator character</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#setRunnerClassName(java.lang.String)">setRunnerClassName</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> runnerClassName)</CODE>\r
-\r
-<BR>\r
- Set the name of a runner class</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/metadata/RunnerConfig.html#toString()">toString</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> void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/RunnerConfig.html#validate()">validate</A></B>()</CODE>\r
-\r
-<BR>\r
- Validate the value of the argument.</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#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#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
-<!-- ========= 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="RunnerConfig()"><!-- --></A><H3>\r
-RunnerConfig</H3>\r
-<PRE>\r
-public <B>RunnerConfig</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="copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><!-- --></A><H3>\r
-copyAndValidateRConfig</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>copyAndValidateRConfig</B>(<A HREF="../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A><?> runnerConf)</PRE>\r
-<DL>\r
-<DD><DL>\r
-</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getOptions()"><!-- --></A><H3>\r
-getOptions</H3>\r
-<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><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getOptions</B>()</PRE>\r
-<DL>\r
-<DD>Returns the list of the Options supported by the executable of type T\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by type T<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addParameter(compbio.metadata.Parameter)"><!-- --></A><H3>\r
-addParameter</H3>\r
-<PRE>\r
-public void <B>addParameter</B>(<A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> param)</PRE>\r
-<DL>\r
-<DD>Adds parameter to the internal parameter list\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>param</CODE> - the <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> to add<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="addOption(compbio.metadata.Option)"><!-- --></A><H3>\r
-addOption</H3>\r
-<PRE>\r
-public void <B>addOption</B>(<A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> option)</PRE>\r
-<DL>\r
-<DD>Adds Option to the internal list of options\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>option</CODE> - the <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> to add</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArguments()"><!-- --></A><H3>\r
-getArguments</H3>\r
-<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><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getArguments</B>()</PRE>\r
-<DL>\r
-<DD>Returns list of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> and <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> supported by current
- runner\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>list of <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getPrmSeparator()"><!-- --></A><H3>\r
-getPrmSeparator</H3>\r
-<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>getPrmSeparator</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>name value separator character</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setPrmSeparator(java.lang.String)"><!-- --></A><H3>\r
-setPrmSeparator</H3>\r
-<PRE>\r
-public void <B>setPrmSeparator</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> prmSeparator)</PRE>\r
-<DL>\r
-<DD>Sets name value separator character\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>prmSeparator</CODE> - the separator char</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setOptions(java.util.List)"><!-- --></A><H3>\r
-setOptions</H3>\r
-<PRE>\r
-public void <B>setOptions</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><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>\r
-<DL>\r
-<DD>Adds the list of options or parameters to the internal list of options\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters to add</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getRunnerClassName()"><!-- --></A><H3>\r
-getRunnerClassName</H3>\r
-<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>getRunnerClassName</B>()</PRE>\r
-<DL>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>fully qualified class name for type T</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setRunnerClassName(java.lang.String)"><!-- --></A><H3>\r
-setRunnerClassName</H3>\r
-<PRE>\r
-public void <B>setRunnerClassName</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> runnerClassName)</PRE>\r
-<DL>\r
-<DD>Set the name of a runner class\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>runnerClassName</CODE> - the name of the executable wrapping class</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="setParameters(java.util.List)"><!-- --></A><H3>\r
-setParameters</H3>\r
-<PRE>\r
-public void <B>setParameters</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><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> parameters)</PRE>\r
-<DL>\r
-<DD>Sets the list of parameters as internal list\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>parameters</CODE> - the list of parameters</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getParameters()"><!-- --></A><H3>\r
-getParameters</H3>\r
-<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><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>>> <B>getParameters</B>()</PRE>\r
-<DL>\r
-<DD>Returns the list of parameters supported executable of type T. Where
- <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> is an <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> with value.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Returns:</B><DD>List of <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A> supported by type T.</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="toString()"><!-- --></A><H3>\r
-toString</H3>\r
-<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><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
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="equals(java.lang.Object)"><!-- --></A><H3>\r
-equals</H3>\r
-<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><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
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArgument(java.lang.String)"><!-- --></A><H3>\r
-getArgument</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgument</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> name)</PRE>\r
-<DL>\r
-<DD>Returns the argument by its name if found, NULL otherwise. Where the
- Argument is a common interface for <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> and <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>
- therefore this method can return either. If you need to retrieve the
- Option by its optionNames use @link
- <A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>getArgumentByOptionName(String)</CODE></A> method. The
- difference between option name and optionName is explained by the
- following example:
-
- <pre>
- <name>Sequence type</name>
- <description>
- --nuc - Assume the sequences are nucleotide.
- --amino - Assume the sequences are amino acid. </description>
- <optionNames>--amino</optionNames>
- <optionNames>--nuc</optionNames>
- <optionNames>--auto</optionNames>
- </pre>
-
- In the example, the "Sequence type" is a name whereas --amino, --nuc and
- --auto are all optionNames. This dichotomy only manifests in
- <code>Option</code> never in <code>Parameters</code> as the latter can
- only have single <optioNames> element\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - the Parameter of Option name\r
-<DT><B>Returns:</B><DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeArgument(java.lang.String)"><!-- --></A><H3>\r
-removeArgument</H3>\r
-<PRE>\r
-public boolean <B>removeArgument</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> name)</PRE>\r
-<DL>\r
-<DD>Removes the argument <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata"><CODE>Argument</CODE></A> if found. Where Argument is either
- <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata"><CODE>Option</CODE></A> or <A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata"><CODE>Parameter</CODE></A>.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>name</CODE> - of the argument\r
-<DT><B>Returns:</B><DD>true if argument was removed, false otherwise</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="getArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
-getArgumentByOptionName</H3>\r
-<PRE>\r
-public <A HREF="../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A><<A HREF="../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>> <B>getArgumentByOptionName</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> optionName)</PRE>\r
-<DL>\r
-<DD>Returns the argument by option name, NULL if the argument is not found\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - - the optionName. This is not the same as an Option name.
-
- For example:
-
- <pre>
- <name>Output sequences order</name>
- <description>--inputorder - Output order: same as input.
- --reorder - Output order: aligned. Default: same as input</description>
- <optionNames>--inputorder</optionNames>
- <optionNames>--reorder</optionNames>
- </pre>
-
- The name of the option in the example is
- "Output sequences order" whereas optionNames are
- "--inputorder" and "--reorder". If you need to retrieve the
- Option or Parameter by its names use
- <A HREF="../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)"><CODE>getArgument(String)</CODE></A> method\r
-<DT><B>Returns:</B><DD>Option</DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="removeArgumentByOptionName(java.lang.String)"><!-- --></A><H3>\r
-removeArgumentByOptionName</H3>\r
-<PRE>\r
-public boolean <B>removeArgumentByOptionName</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> optionName)</PRE>\r
-<DL>\r
-<DD>Removes the argument which can be a Parameter or an Option instance by
- the value in <optionNames> element of the runner configuration
- descriptor.\r
-<P>\r
-<DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>optionName</CODE> - the optionName of the option, do not confuse with the name!\r
-<DT><B>Returns:</B><DD>true if argument with optionName exists and was removed, false
- otherwise<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)"><CODE>for destinctions
- between optionNames and the name of the Option</CODE></A></DL>\r
-</DD>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="validate()"><!-- --></A><H3>\r
-validate</H3>\r
-<PRE>\r
-public void <B>validate</B>()\r
- throws <A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></PRE>\r
-<DL>\r
-<DD>Validate the value of the argument. Checks whether the argument value is
- in the valid values range.\r
-<P>\r
-<DD><DL>\r
-\r
-<DT><B>Throws:</B>\r
-<DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/javax/xml/bind/ValidationException.html?is-external=true" title="class or interface in javax.xml.bind">ValidationException</A></CODE> - if any of the arguments found invalid which is when
- <dl>
- <li>Parameter value outside <A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A> boundary</li>
- <li>Parameter name is not listed in possible values</li>
- </dl></DL>\r
-</DD>\r
-</DL>\r
-<!-- ========= END OF CLASS DATA ========= -->\r
-<HR>\r
-\r
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-<!-- ======= START OF BOTTOM NAVBAR ====== -->\r
-<A NAME="navbar_bottom"><!-- --></A>\r
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
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- <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
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- <A HREF="../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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- <A HREF="RunnerConfig.html" target="_top"><B>NO FRAMES</B></A> \r
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