<!--NewPage-->\r
<HTML>\r
<HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Thu Nov 18 15:38:37 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:59 GMT 2010 -->\r
<TITLE>\r
Option\r
</TITLE>\r
\r
-<META NAME="date" CONTENT="2010-11-18">\r
+<META NAME="date" CONTENT="2010-12-21">\r
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<TD VALIGN="top" CLASS="NavBarCell3"><FONT SIZE="-2">\r
- SUMMARY: NESTED | <A HREF="#field_summary">FIELD</A> | <A HREF="#constructor_summary">CONSTR</A> | <A HREF="#method_summary">METHOD</A></FONT></TD>\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: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
</TR>\r
</TABLE>\r
<A NAME="skip-navbar_top"></A>\r
<BR>\r
Class Option<T></H2>\r
<PRE>\r
-java.lang.Object\r
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>\r
<IMG SRC="../../resources/inherit.gif" ALT="extended by "><B>compbio.metadata.Option<T></B>\r
</PRE>\r
<DL>\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
+<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
<HR>\r
\r
<P>\r
-<!-- =========== FIELD SUMMARY =========== -->\r
\r
-<A NAME="field_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>Field 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>protected java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#defaultValue">defaultValue</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>protected java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#description">description</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>protected java.net.URL</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#furtherDetails">furtherDetails</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>protected boolean</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#isRequired">isRequired</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>protected java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#name">name</A></B></CODE>\r
-\r
-<BR>\r
- </TD>\r
-</TR>\r
-</TABLE>\r
- \r
<!-- ======== CONSTRUCTOR SUMMARY ======== -->\r
\r
<A NAME="constructor_summary"><!-- --></A>\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
+<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
<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
+<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 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
+<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> java.lang.String</CODE></FONT></TD>\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
</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
+<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
</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
+<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
</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
+<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
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> java.util.List<java.lang.String></CODE></FONT></TD>\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getOptionNames()">getOptionNames</A></B>()</CODE>\r
\r
<BR>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE> java.util.List<java.lang.String></CODE></FONT></TD>\r
+<CODE> <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>></CODE></FONT></TD>\r
<TD><CODE><B><A HREF="../../compbio/metadata/Option.html#getPossibleValues()">getPossibleValues</A></B>()</CODE>\r
\r
<BR>\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
+<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 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
+<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 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
+<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 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
+<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 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
+<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 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
+<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> 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
+<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> java.lang.String</CODE></FONT></TD>\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
<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>\r
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
<TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">\r
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
+<TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</CODE></TD>\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#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
-<!-- ============ FIELD DETAIL =========== -->\r
-\r
-<A NAME="field_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>Field Detail</B></FONT></TH>\r
-</TR>\r
-</TABLE>\r
-\r
-<A NAME="description"><!-- --></A><H3>\r
-description</H3>\r
-<PRE>\r
-protected java.lang.String <B>description</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="name"><!-- --></A><H3>\r
-name</H3>\r
-<PRE>\r
-protected java.lang.String <B>name</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="isRequired"><!-- --></A><H3>\r
-isRequired</H3>\r
-<PRE>\r
-protected boolean <B>isRequired</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="furtherDetails"><!-- --></A><H3>\r
-furtherDetails</H3>\r
-<PRE>\r
-protected java.net.URL <B>furtherDetails</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-<HR>\r
-\r
-<A NAME="defaultValue"><!-- --></A><H3>\r
-defaultValue</H3>\r
-<PRE>\r
-protected java.lang.String <B>defaultValue</B></PRE>\r
-<DL>\r
-<DL>\r
-</DL>\r
-</DL>\r
-\r
<!-- ========= CONSTRUCTOR DETAIL ======== -->\r
\r
<A NAME="constructor_detail"><!-- --></A>\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
+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
<A NAME="getName()"><!-- --></A><H3>\r
getName</H3>\r
<PRE>\r
-public java.lang.String <B>getName</B>()</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
<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
+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
<A NAME="getDescription()"><!-- --></A><H3>\r
getDescription</H3>\r
<PRE>\r
-public java.lang.String <B>getDescription</B>()</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
<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
+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
<A NAME="getFurtherDetails()"><!-- --></A><H3>\r
getFurtherDetails</H3>\r
<PRE>\r
-public java.net.URL <B>getFurtherDetails</B>()</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
<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
+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
<A NAME="getDefaultValue()"><!-- --></A><H3>\r
getDefaultValue</H3>\r
<PRE>\r
-public java.lang.String <B>getDefaultValue</B>()</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
<A NAME="setDefaultValue(java.lang.String)"><!-- --></A><H3>\r
setDefaultValue</H3>\r
<PRE>\r
-public void <B>setDefaultValue</B>(java.lang.String defaultVal)\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
<A NAME="getOptionNames()"><!-- --></A><H3>\r
getOptionNames</H3>\r
<PRE>\r
-public java.util.List<java.lang.String> <B>getOptionNames</B>()</PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getOptionNames</B>()</PRE>\r
<DL>\r
<DD><DL>\r
</DL>\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
+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
<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
+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
<A NAME="toString()"><!-- --></A><H3>\r
toString</H3>\r
<PRE>\r
-public java.lang.String <B>toString</B>()</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>toString</CODE> in class <CODE>java.lang.Object</CODE></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
<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
+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
<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
+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>equals</CODE> in class <CODE>java.lang.Object</CODE></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
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
+<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
<A NAME="getPossibleValues()"><!-- --></A><H3>\r
getPossibleValues</H3>\r
<PRE>\r
-public java.util.List<java.lang.String> <B>getPossibleValues</B>()</PRE>\r
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A><<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>> <B>getPossibleValues</B>()</PRE>\r
<DL>\r
<DD>List of possible optionNames\r
<P>\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
+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
</TR>\r
<TR>\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: <A HREF="#field_detail">FIELD</A> | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
+DETAIL: FIELD | <A HREF="#constructor_detail">CONSTR</A> | <A HREF="#method_detail">METHOD</A></FONT></TD>\r
</TR>\r
</TABLE>\r
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