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Make muscle executable compilation not static to fix problem on Macs
[jabaws.git] / website / dm_javadoc / index-files / index-2.html
diff --git a/website/dm_javadoc/index-files/index-2.html b/website/dm_javadoc/index-files/index-2.html
index 864900b..e5740c5 100644 (file)
--- a/website/dm_javadoc/index-files/index-2.html
+++ b/website/dm_javadoc/index-files/index-2.html
@@ -2,12 +2,12 @@
 <!--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
 C-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-11-18">\r
+<META NAME="date" CONTENT="2010-12-21">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -82,8 +82,8 @@ function windowTitle()
 <A NAME="_C_"><!-- --></A><H2>\r
 <B>C</B></H2>\r
 <DL>\r
-<DT><A HREF="../compbio/data/msa/MsaWS.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
-Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
+<DT><A HREF="../compbio/data/msa/JManagement.html#cancelJob(java.lang.String)"><B>cancelJob(String)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</A>\r
 <DD>Stop running the job <code>jobId</code> but leave its output untouched\r
 <DT><A HREF="../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><B>ChunkHolder</B></A> - Class in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>Represents a chunk of a string data together with the position in a file for
  the next read operation.<DT><A HREF="../compbio/metadata/ChunkHolder.html#ChunkHolder(java.lang.String, long)"><B>ChunkHolder(String, long)</B></A> - \r
@@ -98,11 +98,10 @@ Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/S
 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>ClustalAlignmentUtil</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Tools to read and write clustal formated files<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#ClustalAlignmentUtil()"><B>ClustalAlignmentUtil()</B></A> - \r
 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.<DT><A HREF="../compbio/ws/client/package-summary.html"><B>compbio.ws.client</B></A> - package compbio.ws.client<DD>A command line client and web services testing client for    
- JAva Bioinformatics Analysis Web Services.<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)"><B>connect(String, Services)</B></A> - \r
+<DT><A HREF="../compbio/data/msa/package-summary.html"><B>compbio.data.msa</B></A> - package compbio.data.msa<DD>Web Service interfaces for JAva Bioinformatics Analysis Web Services.<DT><A HREF="../compbio/ws/client/Jws2Client.html#connect(java.lang.String, compbio.ws.client.Services)"><B>connect(String, Services)</B></A> - \r
 Static method in class compbio.ws.client.<A HREF="../compbio/ws/client/Jws2Client.html" title="class in compbio.ws.client">Jws2Client</A>\r
 <DD>Connects to a web service by the host and the service name\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig&lt;?&gt;)</B></A> - \r
+<DT><A HREF="../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>ConservationMethod</B></A> - Enum in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Enumeration listing of all the supported methods.<DT><A HREF="../compbio/metadata/RunnerConfig.html#copyAndValidateRConfig(compbio.metadata.RunnerConfig)"><B>copyAndValidateRConfig(RunnerConfig&lt;?&gt;)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)"><B>countMatchesInSequence(String, String)</B></A> - \r
@@ -111,6 +110,10 @@ Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/F
 <DT><A HREF="../compbio/data/msa/MsaWS.html#customAlign(java.util.List, java.util.List)"><B>customAlign(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
 Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</A>\r
 <DD>Align a list of sequences with options.\r
+<DT><A HREF="../compbio/data/msa/Annotation.html#customAnalize(java.util.List, java.util.List)"><B>customAnalize(List&lt;FastaSequence&gt;, List&lt;Option&lt;T&gt;&gt;)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/Annotation.html" title="interface in compbio.data.msa">Annotation</A>\r
+<DD>Analyse the sequences according to custom settings defined in options
+ list.\r
 </DL>\r
 <HR>\r
 \r