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-compbio.metadata</FONT>\r
-<BR>\r
-Class Option<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.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 <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><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>(<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,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> 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> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</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/metadata/Option.html#addOptionNames(java.lang.String...)">addOptionNames</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>... 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>(<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="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/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> <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/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> <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A></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> <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/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> <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/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> <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/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>(<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> 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>(<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> 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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> 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>(<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
- </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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</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>> 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>(<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> 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> <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/Option.html#toCommand(java.lang.String)">toCommand</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> 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> <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/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.<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#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="Option(java.lang.String, java.lang.String)"><!-- --></A><H3>\r
-Option</H3>\r
-<PRE>\r
-public <B>Option</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,\r
- <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> 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 <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>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>(<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><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 <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>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>(<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> 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 <A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> <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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/net/URL.html?is-external=true" title="class or interface in java.net">URL</A> 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 <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>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>(<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> 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 <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>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>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</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>> 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 <A HREF="http://java.sun.com/javase/6/docs/api/java/util/Set.html?is-external=true" title="class or interface in java.util">Set</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>addOptionNames</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>... 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 <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="toCommand(java.lang.String)"><!-- --></A><H3>\r
-toCommand</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>toCommand</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> 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>(<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="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><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></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="getPossibleValues()"><!-- --></A><H3>\r
-getPossibleValues</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="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>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>(<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> 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
-<A HREF="#skip-navbar_bottom" title="Skip navigation links"></A>\r
-<TABLE BORDER="0" WIDTH="100%" CELLPADDING="1" CELLSPACING="0" SUMMARY="">\r
-<TR>\r
-<TD COLSPAN=2 BGCOLOR="#EEEEFF" CLASS="NavBarCell1">\r
-<A NAME="navbar_bottom_firstrow"><!-- --></A>\r
-<TABLE BORDER="0" CELLPADDING="0" CELLSPACING="3" SUMMARY="">\r
- <TR ALIGN="center" VALIGN="top">\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="../../overview-summary.html"><FONT CLASS="NavBarFont1"><B>Overview</B></FONT></A> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="package-summary.html"><FONT CLASS="NavBarFont1"><B>Package</B></FONT></A> </TD>\r
- <TD BGCOLOR="#FFFFFF" CLASS="NavBarCell1Rev"> <FONT CLASS="NavBarFont1Rev"><B>Class</B></FONT> </TD>\r
- <TD BGCOLOR="#EEEEFF" CLASS="NavBarCell1"> <A HREF="class-use/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
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-</TD>\r
-</TR>\r
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-<TR>\r
-<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 BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
- <A HREF="../../index.html?compbio/metadata/Option.html" target="_top"><B>FRAMES</B></A> \r
- <A HREF="Option.html" target="_top"><B>NO FRAMES</B></A> \r
- <SCRIPT type="text/javascript">\r
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- if(window==top) {\r
- document.writeln('<A HREF="../../allclasses-noframe.html"><B>All Classes</B></A>');\r
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-<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
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