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+<TITLE>\r
+RunnerConfig\r
+</TITLE>\r
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+ <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
+ <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/RunnerConfig.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </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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+ SUMMARY: NESTED | FIELD | <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
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
+<HR>\r
+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class RunnerConfig<T></H2>\r
+<PRE>\r
+java.lang.Object\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 java.lang.Object</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
+<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> 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>(java.lang.Object 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>(java.lang.String 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>(java.lang.String 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> java.util.List<<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> java.util.List<<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> java.util.List<<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> java.lang.String</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> java.lang.String</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>(java.lang.String 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>(java.lang.String 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>(java.util.List<<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>(java.util.List<<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>(java.lang.String 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>(java.lang.String 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> java.lang.String</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.Object</B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE>getClass, hashCode, notify, notifyAll, wait, wait, wait</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 java.util.List<<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 java.util.List<<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 java.lang.String <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>(java.lang.String 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>(java.util.List<<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 java.lang.String <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>(java.lang.String 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>(java.util.List<<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 java.util.List<<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 java.lang.String <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
+</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>(java.lang.Object 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
+</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>(java.lang.String 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>(java.lang.String 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>(java.lang.String 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>(java.lang.String 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 javax.xml.bind.ValidationException</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>javax.xml.bind.ValidationException</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
+\r
+<!-- ======= 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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+<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
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+ <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/RunnerConfig.html"><FONT CLASS="NavBarFont1"><B>Use</B></FONT></A> </TD>\r
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+</TD>\r
+</TR>\r
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+ <SCRIPT type="text/javascript">\r
+ <!--\r
+ if(window==top) {\r
+ document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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