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Make muscle executable compilation not static to fix problem on Macs
[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 70eb380..d6d9139 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_14) on Wed Feb 17 16:46:28 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:59 GMT 2010 -->\r
 <TITLE>\r
 A-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2010-12-21">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -85,9 +85,12 @@ 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
+<DD>&nbsp;\r
 <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>&nbsp;\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
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>\r
 <DD>Adds an option to the optionName list\r
@@ -96,10 +99,13 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Parameter.html" ti
 <DD>&nbsp;\r
 <DT><A HREF="../compbio/metadata/RunnerConfig.html#addParameter(compbio.metadata.Parameter)"><B>addParameter(Parameter&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>&nbsp;\r
+<DD>Adds parameter to the internal parameter list\r
 <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/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
 <DT><A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence"><B>Alignment</B></A> - Class in <A HREF="../compbio/data/sequence/package-summary.html">compbio.data.sequence</A><DD>Multiple sequence alignment.<DT><A HREF="../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)"><B>Alignment(List&lt;FastaSequence&gt;, Program, char)</B></A> - \r
 Constructor for class compbio.data.sequence.<A HREF="../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>\r
 <DD>&nbsp;\r
@@ -115,7 +121,16 @@ Static variable in class compbio.data.sequence.<A HREF="../compbio/data/sequence
 <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/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
+<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
+<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
+<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
+<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
 <HR>\r
 \r