X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fmetadata%2Fclass-use%2FWrongParameterException.html;h=8af9a17d0296ae33b8e9613ad965f598aec30914;hb=5ca8c6a56369ea884670666cddcc5f1d3a09bc10;hp=a71011cb1bb7ad9e29528a0d748a18b8454c09ea;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html b/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html
index a71011c..8af9a17 100644
--- a/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html
+++ b/website/dm_javadoc/compbio/metadata/class-use/WrongParameterException.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:28 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:18 GMT 2010 -->
 <TITLE>
 Uses of Class compbio.metadata.WrongParameterException
 </TITLE>
 
-<META NAME="date" CONTENT="2010-02-17">
+<META NAME="date" CONTENT="2010-11-24">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
 
@@ -90,6 +90,10 @@ function windowTitle()
 Packages that use <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
+<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.&nbsp;</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
 <TD><A HREF="#compbio.metadata"><B>compbio.metadata</B></A></TD>
 <TD>A meta-data model for multiple sequence alignment web services 
  Classes in this package have no dependencies to other sources in the project.&nbsp;</TD>
@@ -97,6 +101,41 @@ Packages that use <A HREF="../../../compbio/metadata/WrongParameterException.htm
 </TABLE>
 &nbsp;
 <P>
+<A NAME="compbio.data.msa"><!-- --></A>
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">
+Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A> in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A></FONT></TH>
+</TR>
+</TABLE>
+&nbsp;
+<P>
+
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
+<TR BGCOLOR="#CCCCFF" CLASS="TableSubHeadingColor">
+<TH ALIGN="left" COLSPAN="2">Methods in <A HREF="../../../compbio/data/msa/package-summary.html">compbio.data.msa</A> that throw <A HREF="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</A></FONT></TH>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<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>
+<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,
+            <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>
+
+<BR>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with options.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
+<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>
+<TD><CODE><B>MsaWS.</B><B><A HREF="../../../compbio/data/msa/MsaWS.html#presetAlign(java.util.List, compbio.metadata.Preset)">presetAlign</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,
+            <A HREF="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</A>&lt;<A HREF="../../../compbio/data/msa/MsaWS.html" title="type parameter in MsaWS">T</A>&gt;&nbsp;preset)</CODE>
+
+<BR>
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Align a list of sequences with preset.</TD>
+</TR>
+</TABLE>
+&nbsp;
+<P>
 <A NAME="compbio.metadata"><!-- --></A>
 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">
@@ -113,7 +152,7 @@ Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<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>
+<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>
 <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>
 
 <BR>
@@ -122,7 +161,7 @@ Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
 <CODE>&nbsp;void</CODE></FONT></TD>
-<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(java.lang.String&nbsp;defaultVal)</CODE>
+<TD><CODE><B>Parameter.</B><B><A HREF="../../../compbio/metadata/Parameter.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>&nbsp;defaultVal)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
@@ -130,7 +169,7 @@ Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
 <CODE>&nbsp;void</CODE></FONT></TD>
-<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setDefaultValue(java.lang.String)">setDefaultValue</A></B>(java.lang.String&nbsp;defaultVal)</CODE>
+<TD><CODE><B>Option.</B><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>&nbsp;defaultVal)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Sets one of the values defined in optionList as default.</TD>
@@ -138,7 +177,7 @@ Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
 <CODE>&nbsp;void</CODE></FONT></TD>
-<TD><CODE><B>Argument.</B><B><A HREF="../../../compbio/metadata/Argument.html#setValue(java.lang.String)">setValue</A></B>(java.lang.String&nbsp;defaultValue)</CODE>
+<TD><CODE><B>Argument.</B><B><A HREF="../../../compbio/metadata/Argument.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>&nbsp;defaultValue)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Set default values for the parameter or an option</TD>
@@ -146,7 +185,7 @@ Uses of <A HREF="../../../compbio/metadata/WrongParameterException.html" title="
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
 <CODE>&nbsp;void</CODE></FONT></TD>
-<TD><CODE><B>Option.</B><B><A HREF="../../../compbio/metadata/Option.html#setValue(java.lang.String)">setValue</A></B>(java.lang.String&nbsp;dValue)</CODE>
+<TD><CODE><B>Option.</B><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>&nbsp;dValue)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>

Methods in compbio.data.msa that throw WrongParameterException
+ `String`	`MsaWS.customAlign(List<FastaSequence> sequences, + List<Option<T>> options)` + + + Align a list of sequences with options.
+ `String`	`MsaWS.presetAlign(List<FastaSequence> sequences, + Preset<T> preset)` + + + Align a list of sequences with preset.