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Make muscle executable compilation not static to fix problem on Macs
[jabaws.git] / website / dm_javadoc / index-files / index-3.html
diff --git a/website/dm_javadoc/index-files/index-3.html b/website/dm_javadoc/index-files/index-3.html
index 454eebc..9c7e4f1 100644 (file)
--- a/website/dm_javadoc/index-files/index-3.html
+++ b/website/dm_javadoc/index-files/index-3.html
@@ -2,12 +2,12 @@
 <!--NewPage-->\r
 <HTML>\r
 <HEAD>\r
-<!-- Generated by javadoc (build 1.6.0_21) on Thu Dec 09 12:00:29 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:59 GMT 2010 -->\r
 <TITLE>\r
 D-Index\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-12-09">\r
+<META NAME="date" CONTENT="2010-12-21">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">\r
 \r
@@ -86,6 +86,15 @@ function windowTitle()
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>\r
 <DD>Removes all special characters and digits as well as whitespace chars
  from the sequence\r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_COLUMN_SCORE"><B>DEFAULT_COLUMN_SCORE</B></A> - \r
+Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>Default column scoring schema\r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD"><B>DEFAULT_GAP_THRESHOLD</B></A> - \r
+Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>Default gap threshold value for SMERFS algorithm\r
+<DT><A HREF="../compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE"><B>DEFAULT_WINDOW_SIZE</B></A> - \r
+Static variable in enum compbio.data.sequence.<A HREF="../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A>\r
+<DD>Default window size value for SMERFS algorithm\r
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#DIGIT"><B>DIGIT</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 digit\r