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Make muscle executable compilation not static to fix problem on Macs
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / package-use.html
diff --git a/website/dm_javadoc/compbio/data/sequence/package-use.html b/website/dm_javadoc/compbio/data/sequence/package-use.html
index 89c7cbb..e2f2c39 100644 (file)
--- a/website/dm_javadoc/compbio/data/sequence/package-use.html
+++ b/website/dm_javadoc/compbio/data/sequence/package-use.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
 Uses of Package compbio.data.sequence\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
@@ -124,6 +124,12 @@ Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio
 <BR>\r
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A FASTA formatted sequence.</TD>\r
 </TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.msa"><B>Score</B></A></B>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value class for AACon annotation results storage</TD>\r
+</TR>\r
 </TABLE>\r
 &nbsp;\r
 <P>\r
@@ -146,6 +152,24 @@ Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Alignment metadata e.g.</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/AnnotatedSequence.html#compbio.data.sequence"><B>AnnotatedSequence</B></A></B>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ConservationMethod.html#compbio.data.sequence"><B>ConservationMethod</B></A></B>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Enumeration listing of all the supported methods.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/DisemblResultAnnot.html#compbio.data.sequence"><B>DisemblResultAnnot</B></A></B>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
 \r
 <BR>\r
@@ -158,6 +182,18 @@ Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The list of programmes that can produce alignments</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence"><B>Score</B></A></B>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;A value class for AACon annotation results storage</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/SMERFSConstraints.html#compbio.data.sequence"><B>SMERFSConstraints</B></A></B>\r
+\r
+<BR>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Enumeration defining two constraints for SMERFS columns score calculation.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
 \r
 <BR>\r