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remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / compbio / metadata / class-use / Option.html
diff --git a/website/full_javadoc/compbio/metadata/class-use/Option.html b/website/full_javadoc/compbio/metadata/class-use/Option.html
index 1defb5a..faf2047 100644 (file)
--- a/website/full_javadoc/compbio/metadata/class-use/Option.html
+++ b/website/full_javadoc/compbio/metadata/class-use/Option.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
 <TITLE>\r
 Uses of Class compbio.metadata.Option\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -91,7 +91,7 @@ Packages that use <A HREF="../../../compbio/metadata/Option.html" title="class i
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD>&nbsp;&nbsp;</TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
@@ -99,7 +99,7 @@ Packages that use <A HREF="../../../compbio/metadata/Option.html" title="class i
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.engine.client"><B>compbio.engine.client</B></A></TD>\r
-<TD>Classes and interfaces representing an input for engines.&nbsp;</TD>\r
+<TD>&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>\r
@@ -133,13 +133,23 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
+<CODE>&nbsp;<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>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>\r
 </TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>SequenceAnnotation.</B><B><A HREF="../../../compbio/data/msa/SequenceAnnotation.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+              <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/data/msa/SequenceAnnotation.html" title="type parameter in SequenceAnnotation">T</A>&gt;&gt;&nbsp;options)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Analyse the sequences according to custom settings defined in options
+ list.</TD>\r
+</TR>\r
 </TABLE>\r
 &nbsp;\r
 <P>\r
@@ -159,7 +169,15 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;</CODE></FONT></TD>\r
+<CODE>&nbsp;<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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAnalize.html#getOptions()">getOptions</A></B>()</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;</CODE></FONT></TD>\r
 <TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#getOptions()">getOptions</A></B>()</CODE>\r
 \r
 <BR>\r
@@ -176,7 +194,15 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</CODE>\r
+<TD><CODE><B>CustomAnalize.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAnalize.html#setOptions(java.util.List)">setOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;void</CODE></FONT></TD>\r
+<TD><CODE><B>CustomAlign.</B><B><A HREF="../../../compbio/data/msa/jaxws/CustomAlign.html#setOptions(java.util.List)">setOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -208,8 +234,8 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 </TABLE>\r
 </CODE></FONT></TD>\r
-<TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\r
-                  java.lang.String&nbsp;nameValueSeparator)</CODE>\r
+<TD><CODE><B>CommandBuilder.</B><B><A HREF="../../../compbio/engine/client/CommandBuilder.html#newCommandBuilder(java.util.List, java.lang.String)">newCommandBuilder</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;arguments,\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>&nbsp;nameValueSeparator)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;This produces the same result as getCommands method.</TD>\r
@@ -237,7 +263,7 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 <TD><CODE><B><A HREF="../../../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter&lt;T&gt;</A></B></CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing option supported by the web service e.g.</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A single value containing an option supported by the web service e.g.</TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -250,15 +276,15 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(java.lang.String&nbsp;name)</CODE>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgument(java.lang.String)">getArgument</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;name)</CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by its name if found, NULL otherwise</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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>&nbsp;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(java.lang.String&nbsp;optionName)</CODE>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArgumentByOptionName(java.lang.String)">getArgumentByOptionName</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A>&nbsp;optionName)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the argument by option name, NULL if the argument is not found</TD>\r
@@ -273,15 +299,16 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
+<CODE>&nbsp;<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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getArguments()">getArguments</A></B>()</CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;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>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
+<CODE>&nbsp;<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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&gt;</CODE></FONT></TD>\r
 <TD><CODE><B>Preset.</B><B><A HREF="../../../compbio/metadata/Preset.html#getArguments(compbio.metadata.RunnerConfig)">getArguments</A></B>(<A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;<A HREF="../../../compbio/metadata/Preset.html" title="type parameter in Preset">T</A>&gt;&nbsp;rconfig)</CODE>\r
 \r
 <BR>\r
@@ -289,11 +316,11 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
+<CODE>&nbsp;<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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;</CODE></FONT></TD>\r
 <TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#getOptions()">getOptions</A></B>()</CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Returns the list of the Options supported by the executable of type T</TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -309,7 +336,7 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 <TD><CODE><B>RunnerConfig.</B><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>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&nbsp;option)</CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds Option to the internal list of options</TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -322,10 +349,10 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
+<TD><CODE><B>RunnerConfig.</B><B><A HREF="../../../compbio/metadata/RunnerConfig.html#setOptions(java.util.List)">setOptions</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/metadata/RunnerConfig.html" title="type parameter in RunnerConfig">T</A>&gt;&gt;&nbsp;parameters)</CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Adds the list of options or parameters to the internal list of options</TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -360,7 +387,7 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
+<CODE>&nbsp;<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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;</CODE></FONT></TD>\r
 <TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#getAllOptions()">getAllOptions</A></B>()</CODE>\r
 \r
 <BR>\r
@@ -376,16 +403,16 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments)</CODE>\r
+<CODE>&nbsp;<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>&lt;<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>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List)">argumentsToCommandString</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>static&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(java.util.List&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
+<CODE>static&nbsp;<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>&lt;<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>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#argumentsToCommandString(java.util.List, compbio.metadata.RunnerConfig)">argumentsToCommandString</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;? extends <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;arguments,\r
                          <A HREF="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>&lt;? extends <A HREF="../../../compbio/engine/client/Executable.html" title="interface in compbio.engine.client">Executable</A>&lt;?&gt;&gt;&nbsp;rconfig)</CODE>\r
 \r
 <BR>\r
@@ -393,8 +420,8 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
-<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)">optionsToCommandString</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;options)</CODE>\r
+<CODE>&nbsp;<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>&lt;<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>&gt;</CODE></FONT></TD>\r
+<TD><CODE><B>OptionCombinator.</B><B><A HREF="../../../compbio/runner/OptionCombinator.html#optionsToCommandString(java.util.List)">optionsToCommandString</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;?&gt;&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -418,45 +445,90 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
+<CODE>&nbsp;<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>ClustalOWS.</B><B><A HREF="../../../compbio/ws/server/ClustalOWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</A>&gt;&gt;&nbsp;options)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>ClustalWS.</B><B><A HREF="../../../compbio/ws/server/ClustalWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/ClustalW.html" title="class in compbio.runner.msa">ClustalW</A>&gt;&gt;&nbsp;options)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
+<CODE>&nbsp;<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>_MsaService.</B><B><A HREF="../../../compbio/ws/server/_MsaService.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/ws/server/_MsaService.html" title="type parameter in _MsaService">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MafftWS.</B><B><A HREF="../../../compbio/ws/server/MafftWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</A>&gt;&gt;&nbsp;options)</CODE>\r
+<CODE>&nbsp;<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>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+            <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>MuscleWS.</B><B><A HREF="../../../compbio/ws/server/MuscleWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Muscle.html" title="class in compbio.runner.msa">Muscle</A>&gt;&gt;&nbsp;options)</CODE>\r
+<CODE>&nbsp;<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>DisemblWS.</B><B><A HREF="../../../compbio/ws/server/DisemblWS.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+              <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/disorder/Disembl.html" title="class in compbio.runner.disorder">Disembl</A>&gt;&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>ProbconsWS.</B><B><A HREF="../../../compbio/ws/server/ProbconsWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Probcons.html" title="class in compbio.runner.msa">Probcons</A>&gt;&gt;&nbsp;options)</CODE>\r
+<CODE>&nbsp;<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>GlobPlotWS.</B><B><A HREF="../../../compbio/ws/server/GlobPlotWS.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+              <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/disorder/GlobPlot.html" title="class in compbio.runner.disorder">GlobPlot</A>&gt;&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>\r
-<TD><CODE><B>TcoffeeWS.</B><B><A HREF="../../../compbio/ws/server/TcoffeeWS.html#customAlign(java.util.List, java.util.List)">customAlign</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
-            java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/runner/msa/Tcoffee.html" title="class in compbio.runner.msa">Tcoffee</A>&gt;&gt;&nbsp;options)</CODE>\r
+<CODE>&nbsp;<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>SequenceAnnotationService.</B><B><A HREF="../../../compbio/ws/server/SequenceAnnotationService.html#customAnalize(java.util.List, java.util.List)">customAnalize</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,\r
+              <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>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;<A HREF="../../../compbio/ws/server/SequenceAnnotationService.html" title="type parameter in SequenceAnnotationService">T</A>&gt;&gt;&nbsp;options)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
@@ -467,12 +539,12 @@ Uses of <A HREF="../../../compbio/metadata/Option.html" title="class in compbio.
 <TABLE BORDER="0" CELLPADDING="0" CELLSPACING="0" SUMMARY="">\r
 <TR ALIGN="right" VALIGN="">\r
 <TD NOWRAP><FONT SIZE="-1">\r
-<CODE>&lt;T&gt; java.util.List&lt;java.lang.String&gt;</CODE></FONT></TD>\r
+<CODE>&lt;T&gt; <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>&lt;<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>&gt;</CODE></FONT></TD>\r
 </TR>\r
 </TABLE>\r
 </CODE></FONT></TD>\r
-<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</A></B>(java.util.List&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\r
-            java.lang.String&nbsp;keyValueSeparator)</CODE>\r
+<TD><CODE><B>WSUtil.</B><B><A HREF="../../../compbio/ws/server/WSUtil.html#getCommands(java.util.List, java.lang.String)">getCommands</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>&lt;T&gt;&gt;&nbsp;options,\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>&nbsp;keyValueSeparator)</CODE>\r
 \r
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r