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[jabaws.git] / website / dm_javadoc / index-files / index-1.html
diff --git a/website/dm_javadoc/index-files/index-1.html b/website/dm_javadoc/index-files/index-1.html
index d6d9139..ea7a39c 100644 (file)
--- a/website/dm_javadoc/index-files/index-1.html
+++ b/website/dm_javadoc/index-files/index-1.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:59 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Wed Dec 07 12:08:25 GMT 2011 -->\r
 <TITLE>\r
 A-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-12-21">\r
+<META NAME="date" CONTENT="2011-12-07">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -85,10 +85,10 @@ function windowTitle()
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AA"><B>AA</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>Valid Amino acids\r
-<DT><A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html#addAnnotation(T, java.util.ArrayList)"><B>addAnnotation(T, ArrayList&lt;Float&gt;)</B></A> - \r
-Method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence">MultiAnnotatedSequence</A>\r
+<DT><A HREF="../compbio/ws/client/Services.html#AACON_INFO"><B>AACON_INFO</B></A> - \r
+Static variable in enum compbio.ws.client.<A HREF="../compbio/ws/client/Services.html" title="enum in compbio.ws.client">Services</A>\r
 <DD>&nbsp;\r
-<DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option&lt;T&gt;)</B></A> - \r
+<DT><A HREF="../compbio/ws/client/AAConClient.html" title="class in compbio.ws.client"><B>AAConClient</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>A command line client for AACon web service<DT><A HREF="../compbio/metadata/RunnerConfig.html#addOption(compbio.metadata.Option)"><B>addOption(Option&lt;T&gt;)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</A>\r
 <DD>Adds Option to the internal list of options\r
 <DT><A HREF="../compbio/metadata/Option.html#addOptionNames(java.lang.String...)"><B>addOptionNames(String...)</B></A> - \r
@@ -103,6 +103,9 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/RunnerConfig.html"
 <DT><A HREF="../compbio/metadata/Parameter.html#addPossibleValues(java.lang.String...)"><B>addPossibleValues(String...)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" title="class in compbio.metadata">Parameter</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws"><B>Align</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/Align.html#Align()"><B>Align()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Align.html" title="class in compbio.data.msa.jaxws">Align</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/msa/MsaWS.html#align(java.util.List)"><B>align(List&lt;FastaSequence&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 default settings.\r
@@ -115,23 +118,32 @@ Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Al
 <DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>AlignmentMetadata</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Alignment metadata e.g.<DT><A HREF="../compbio/data/sequence/AlignmentMetadata.html#AlignmentMetadata(compbio.data.sequence.Program, char)"><B>AlignmentMetadata(Program, char)</B></A> - \r
 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>\r
 <DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws"><B>AlignResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/AlignResponse.html#AlignResponse()"><B>AlignResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AlignResponse.html" title="class in compbio.data.msa.jaxws">AlignResponse</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_AA"><B>AMBIGUOUS_AA</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>Same as AA pattern but with two additional letters - XU\r
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#AMBIGUOUS_NUCLEOTIDE"><B>AMBIGUOUS_NUCLEOTIDE</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>Ambiguous nucleotide\r
-<DT><A HREF="../compbio/data/msa/Annotation.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&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
+<DT><A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws"><B>Analize</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/Analize.html#Analize()"><B>Analize()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/Analize.html" title="class in compbio.data.msa.jaxws">Analize</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/data/msa/SequenceAnnotation.html#analize(java.util.List)"><B>analize(List&lt;FastaSequence&gt;)</B></A> - \r
+Method in interface compbio.data.msa.<A HREF="../compbio/data/msa/SequenceAnnotation.html" title="interface in compbio.data.msa">SequenceAnnotation</A>\r
 <DD>Analyse the sequences.\r
-<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence"><B>AnnotatedSequence</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>&nbsp;<DT><A HREF="../compbio/data/sequence/AnnotatedSequence.html#AnnotatedSequence(java.lang.String, java.lang.String, float[])"><B>AnnotatedSequence(String, String, float[])</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws"><B>AnalizeResponse</B></A> - Class in <A HREF="../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</A><DD>&nbsp;<DT><A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html#AnalizeResponse()"><B>AnalizeResponse()</B></A> - \r
+Constructor for class compbio.data.msa.jaxws.<A HREF="../compbio/data/msa/jaxws/AnalizeResponse.html" title="class in compbio.data.msa.jaxws">AnalizeResponse</A>\r
+<DD>&nbsp;\r
+<DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A>&lt;<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>&gt; - Interface in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>An unmodifiable view for the options and parameters, with one exception - it
+ allows to set a value<DT><A HREF="../compbio/data/sequence/ScoreManager.html#asMap()"><B>asMap()</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/data/sequence/AnnotatedSequence.html#AnnotatedSequence(compbio.data.sequence.FastaSequence, float[])"><B>AnnotatedSequence(FastaSequence, float[])</B></A> - \r
-Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A>\r
+<DT><A HREF="../compbio/data/sequence/ScoreManager.html#asSet()"><B>asSet()</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/data/msa/Annotation.html" title="interface in compbio.data.msa"><B>Annotation</B></A>&lt;<A HREF="../compbio/data/msa/Annotation.html" title="type parameter in Annotation">T</A>&gt; - Interface in <A HREF="../compbio/data/msa/package-summary.html">compbio.data.msa</A><DD>Interface for tools that results to one or more annotation to sequence(s)<DT><A HREF="../compbio/metadata/Argument.html" title="interface in compbio.metadata"><B>Argument</B></A>&lt;<A HREF="../compbio/metadata/Argument.html" title="type parameter in Argument">T</A>&gt; - Interface in <A HREF="../compbio/metadata/package-summary.html">compbio.metadata</A><DD>An unmodifiable view for the options and parameters, with one exception - it
- allows to set a value</DL>\r
+</DL>\r
 <HR>\r
 \r
 \r