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+Option\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
+ <A HREF="../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata"><B>PREV CLASS</B></A> \r
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+<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
+ SUMMARY: NESTED | FIELD | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\r
+<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
+</TR>\r
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+<!-- ========= END OF TOP NAVBAR ========= -->\r
+\r
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+<!-- ======== START OF CLASS DATA ======== -->\r
+<H2>\r
+<FONT SIZE="-1">\r
+compbio.metadata</FONT>\r
+<BR>\r
+Class Option<T></H2>\r
+<PRE>\r
+java.lang.Object\r
+ <IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Option<T></B>\r
+</PRE>\r
+<DL>\r
+<DT><DT><B>Type Parameters:</B><DD><CODE>T</CODE> - type of executable</DL>\r
+<DL>\r
+<DT><B>All Implemented Interfaces:</B> <DD><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DD>\r
+</DL>\r
+<DL>\r
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A></DD>\r
+</DL>\r
+<HR>\r
+<DL>\r
+<DT><PRE>public class <B>Option<T></B><DT>extends java.lang.Object<DT>implements <A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><T></DL>\r
+</PRE>\r
+\r
+<P>\r
+Command line option/flag or multiple exclusive options with no value. Example
+ -protein, -dna, -auto\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/Option.html#Option(java.lang.String, java.lang.String)">Option</A></B>(java.lang.String name,\r
+ java.lang.String description)</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> java.util.Set<java.lang.String></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</A></B>(java.lang.String... value)</CODE>\r
+\r
+<BR>\r
+ Adds an option to the optionName list</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/Option.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> java.lang.String</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getDefaultValue()">getDefaultValue</A></B>()</CODE>\r
+\r
+<BR>\r
+ A default value of the option.</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/Option.html#getDescription()">getDescription</A></B>()</CODE>\r
+\r
+<BR>\r
+ A long description of the Option</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> java.net.URL</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getFurtherDetails()">getFurtherDetails</A></B>()</CODE>\r
+\r
+<BR>\r
+ The URL where further details about the option can be found</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/Option.html#getName()">getName</A></B>()</CODE>\r
+\r
+<BR>\r
+ Human readable name of the option</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/metadata/Option.html#getOptionNames()">getOptionNames</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.util.List<java.lang.String></CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
+\r
+<BR>\r
+ List of possible optionNames</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE> int</CODE></FONT></TD>\r
+<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#hashCode()">hashCode</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/Option.html#isRequired()">isRequired</A></B>()</CODE>\r
+\r
+<BR>\r
+ Flag that indicated that this option must be specified in the command
+ line for an executable to run</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/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(java.lang.String defaultVal)</CODE>\r
+\r
+<BR>\r
+ Sets one of the values defined in optionList as default.</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/Option.html#setDescription(java.lang.String)">setDescription</A></B>(java.lang.String description)</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/Option.html#setFurtherDetails(java.net.URL)">setFurtherDetails</A></B>(java.net.URL furtherDetails)</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/Option.html#setName(java.lang.String)">setName</A></B>(java.lang.String name)</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/Option.html#setOptionNames(java.util.Set)">setOptionNames</A></B>(java.util.Set<java.lang.String> optionNames)</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/Option.html#setRequired(boolean)">setRequired</A></B>(boolean isRequired)</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/Option.html#setValue(java.lang.String)">setValue</A></B>(java.lang.String dValue)</CODE>\r
+\r
+<BR>\r
+ Set default values for the parameter or an option</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/Option.html#toCommand(java.lang.String)">toCommand</A></B>(java.lang.String nameValueSeparator)</CODE>\r
+\r
+<BR>\r
+ Convert the option to the command string.</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/Option.html#toString()">toString</A></B>()</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.Object</B></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><CODE>getClass, 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="Option(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
+Option</H3>\r
+<PRE>\r
+public <B>Option</B>(java.lang.String name,\r
+ java.lang.String description)</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="getName()"><!-- --></A><H3>\r
+getName</H3>\r
+<PRE>\r
+public java.lang.String <B>getName</B>()</PRE>\r
+<DL>\r
+<DD>Human readable name of the option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getName()">getName</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setName(java.lang.String)"><!-- --></A><H3>\r
+setName</H3>\r
+<PRE>\r
+public void <B>setName</B>(java.lang.String name)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDescription()"><!-- --></A><H3>\r
+getDescription</H3>\r
+<PRE>\r
+public java.lang.String <B>getDescription</B>()</PRE>\r
+<DL>\r
+<DD>A long description of the Option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDescription()">getDescription</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setDescription(java.lang.String)"><!-- --></A><H3>\r
+setDescription</H3>\r
+<PRE>\r
+public void <B>setDescription</B>(java.lang.String description)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getFurtherDetails()"><!-- --></A><H3>\r
+getFurtherDetails</H3>\r
+<PRE>\r
+public java.net.URL <B>getFurtherDetails</B>()</PRE>\r
+<DL>\r
+<DD>The URL where further details about the option can be found\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getFurtherDetails()">getFurtherDetails</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setFurtherDetails(java.net.URL)"><!-- --></A><H3>\r
+setFurtherDetails</H3>\r
+<PRE>\r
+public void <B>setFurtherDetails</B>(java.net.URL furtherDetails)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getDefaultValue()"><!-- --></A><H3>\r
+getDefaultValue</H3>\r
+<PRE>\r
+public java.lang.String <B>getDefaultValue</B>()</PRE>\r
+<DL>\r
+<DD>A default value of the option. Defaults to command line argument name
+ e.g. -auto\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getDefaultValue()">getDefaultValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
+setDefaultValue</H3>\r
+<PRE>\r
+public void <B>setDefaultValue</B>(java.lang.String defaultVal)\r
+ throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD>Sets one of the values defined in optionList as default. Attempting set
+ the value not listed there will result in WrongParameter exception\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>defaultVal</CODE> - \r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - is thrown if the defaultValue is not found in optionList</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="isRequired()"><!-- --></A><H3>\r
+isRequired</H3>\r
+<PRE>\r
+public boolean <B>isRequired</B>()</PRE>\r
+<DL>\r
+<DD>Flag that indicated that this option must be specified in the command
+ line for an executable to run\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>true is the option is required, false otherwise</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setRequired(boolean)"><!-- --></A><H3>\r
+setRequired</H3>\r
+<PRE>\r
+public void <B>setRequired</B>(boolean isRequired)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getOptionNames()"><!-- --></A><H3>\r
+getOptionNames</H3>\r
+<PRE>\r
+public java.util.List<java.lang.String> <B>getOptionNames</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>List of option names</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setOptionNames(java.util.Set)"><!-- --></A><H3>\r
+setOptionNames</H3>\r
+<PRE>\r
+public void <B>setOptionNames</B>(java.util.Set<java.lang.String> optionNames)</PRE>\r
+<DL>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="addOptionNames(java.lang.String...)"><!-- --></A><H3>\r
+addOptionNames</H3>\r
+<PRE>\r
+public java.util.Set<java.lang.String> <B>addOptionNames</B>(java.lang.String... value)</PRE>\r
+<DL>\r
+<DD>Adds an option to the optionName list\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>value</CODE> - \r
+<DT><B>Returns:</B><DD>modified optionName list</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="toCommand(java.lang.String)"><!-- --></A><H3>\r
+toCommand</H3>\r
+<PRE>\r
+public java.lang.String <B>toCommand</B>(java.lang.String nameValueSeparator)</PRE>\r
+<DL>\r
+<DD>Convert the option to the command string.\r
+<P>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>If only one optionName is defined, than it is returned, if many
+ option names are defined, then the defaultValue is returned.
+ Option must have a default value if there are many optionNames to
+ be valid.</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="hashCode()"><!-- --></A><H3>\r
+hashCode</H3>\r
+<PRE>\r
+public int <B>hashCode</B>()</PRE>\r
+<DL>\r
+<DD><DL>\r
+<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="getPossibleValues()"><!-- --></A><H3>\r
+getPossibleValues</H3>\r
+<PRE>\r
+public java.util.List<java.lang.String> <B>getPossibleValues</B>()</PRE>\r
+<DL>\r
+<DD>List of possible optionNames\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#getPossibleValues()">getPossibleValues</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+\r
+<DT><B>Returns:</B><DD>List of values allowed for an Argument</DL>\r
+</DD>\r
+</DL>\r
+<HR>\r
+\r
+<A NAME="setValue(java.lang.String)"><!-- --></A><H3>\r
+setValue</H3>\r
+<PRE>\r
+public void <B>setValue</B>(java.lang.String dValue)\r
+ throws <A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></PRE>\r
+<DL>\r
+<DD><B>Description copied from interface: <CODE><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">Argument</A></CODE></B></DD>\r
+<DD>Set default values for the parameter or an option\r
+<P>\r
+<DD><DL>\r
+<DT><B>Specified by:</B><DD><CODE><A HREF="../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></CODE> in interface <CODE><A HREF="../../compbio/metadata/Argument.html" title="interface in compbio.metadata">Argument</A><<A HREF="../../compbio/metadata/Option.html" title="type parameter in Option">T</A>></CODE></DL>\r
+</DD>\r
+<DD><DL>\r
+<DT><B>Parameters:</B><DD><CODE>dValue</CODE> - the value to be set\r
+<DT><B>Throws:</B>\r
+<DD><CODE><A HREF="../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></CODE> - - when the value to be set is illegal. Wrong value for
+ numeric parameter is the value defined outside it , for
+ string type parameter, wrong value is the one which is not
+ listed in possible values list<DT><B>See Also:</B><DD><A HREF="../../compbio/metadata/ValueConstrain.html" title="class in compbio.metadata"><CODE>ValueConstrain</CODE></A></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
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+<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/Option.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
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+</TD>\r
+</TR>\r
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+<TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
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