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remove old datamodel javadoc
[jabaws.git] / website / full_javadoc / index-files / index-22.html
diff --git a/website/full_javadoc/index-files/index-22.html b/website/full_javadoc/index-files/index-22.html
index 8537653..22c0b58 100644 (file)
--- a/website/full_javadoc/index-files/index-22.html
+++ b/website/full_javadoc/index-files/index-22.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:51 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:36 BST 2011 -->\r
 <TITLE>\r
 W-Index\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
@@ -109,6 +109,9 @@ Method in class compbio.engine.cluster.drmaa.<A HREF="../compbio/engine/cluster/
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#WHITE_SPACE"><B>WHITE_SPACE</B></A> - \r
 Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>A whitespace character: [\t\n\x0B\f\r]\r
+<DT><A HREF="../compbio/data/sequence/Score.html#write(java.util.TreeSet, java.io.Writer)"><B>write(TreeSet&lt;Score&gt;, Writer)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A>\r
+<DD>Outputs the List of Score objects into the Output stream.\r
 <DT><A HREF="../compbio/engine/client/RunConfiguration.html#write(compbio.engine.client.RunConfiguration)"><B>write(RunConfiguration)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/RunConfiguration.html" title="class in compbio.engine.client">RunConfiguration</A>\r
 <DD>&nbsp;\r
@@ -118,7 +121,7 @@ Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfig
 <DT><A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html#writeAndValidate(java.lang.Object, java.lang.String, java.io.OutputStream)"><B>writeAndValidate(Object, String, OutputStream)</B></A> - \r
 Method in class compbio.engine.conf.<A HREF="../compbio/engine/conf/RunnerConfigMarshaller.html" title="class in compbio.engine.conf">RunnerConfigMarshaller</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><B>writeClustalAlignment(OutputStream, Alignment)</B></A> - \r
+<DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)"><B>writeClustalAlignment(Writer, Alignment)</B></A> - \r
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>\r
 <DD>Write Clustal formatted alignment Limitations: does not record the
  consensus.\r
@@ -129,6 +132,9 @@ Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/S
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFasta(java.io.OutputStream, java.util.List)"><B>writeFasta(OutputStream, List&lt;FastaSequence&gt;)</B></A> - \r
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>Writes FastaSequence in the file, each sequence will take one line only\r
+<DT><A HREF="../compbio/data/sequence/SequenceUtil.html#writeFastaKeepTheStream(java.io.OutputStream, java.util.List, int)"><B>writeFastaKeepTheStream(OutputStream, List&lt;FastaSequence&gt;, int)</B></A> - \r
+Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/Util.html#writeFile(java.lang.String, java.lang.String, java.lang.String, boolean)"><B>writeFile(String, String, String, boolean)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 <DD>&nbsp;\r
@@ -138,6 +144,12 @@ Static method in class compbio.runner.<A HREF="../compbio/runner/Util.html" titl
 <DT><A HREF="../compbio/engine/client/Util.html#writeMarker(java.lang.String, compbio.metadata.JobStatus)"><B>writeMarker(String, JobStatus)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html#writeOut(java.io.Writer)"><B>writeOut(Writer)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#writeOut(java.io.Writer)"><B>writeOut(Writer)</B></A> - \r
+Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/engine/client/Util.html#writeStatFile(java.lang.String, java.lang.String)"><B>writeStatFile(String, String)</B></A> - \r
 Static method in class compbio.engine.client.<A HREF="../compbio/engine/client/Util.html" title="class in compbio.engine.client">Util</A>\r
 <DD>&nbsp;\r
@@ -158,9 +170,9 @@ Constructor for exception compbio.metadata.<A HREF="../compbio/metadata/WrongPar
 <DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws"><B>WrongParameterExceptionBean</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>This class was generated by the JAX-WS RI.<DT><A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html#WrongParameterExceptionBean()"><B>WrongParameterExceptionBean()</B></A> - \r
 Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/WrongParameterExceptionBean.html" title="class in compbio.data.msa.jaxws">WrongParameterExceptionBean</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>Class for testing web services<DT><A HREF="../compbio/ws/client/WSTester.html#WSTester()"><B>WSTester()</B></A> - \r
+<DT><A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client"><B>WSTester</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>Class for testing web services<DT><A HREF="../compbio/ws/client/WSTester.html#WSTester(java.lang.String, java.io.PrintWriter)"><B>WSTester(String, PrintWriter)</B></A> - \r
 Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</A>\r
-<DD>&nbsp;\r
+<DD>Construct an instance of JABAWS tester\r
 <DT><A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server"><B>WSUtil</B></A> - Class in <A HREF="../compbio/ws/server/package-summary.html">compbio.ws.server</A><DD>&nbsp;<DT><A HREF="../compbio/ws/server/WSUtil.html#WSUtil()"><B>WSUtil()</B></A> - \r
 Constructor for class compbio.ws.server.<A HREF="../compbio/ws/server/WSUtil.html" title="class in compbio.ws.server">WSUtil</A>\r
 <DD>&nbsp;\r