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Make muscle executable compilation not static to fix problem on Macs
[jabaws.git] / website / dm_javadoc / index-files / index-8.html
diff --git a/website/dm_javadoc/index-files/index-8.html b/website/dm_javadoc/index-files/index-8.html
index 81d737f..2e45f4b 100644 (file)
--- a/website/dm_javadoc/index-files/index-8.html
+++ b/website/dm_javadoc/index-files/index-8.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
 I-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
@@ -82,6 +82,9 @@ function windowTitle()
 <A NAME="_I_"><!-- --></A><H2>\r
 <B>I</B></H2>\r
 <DL>\r
+<DT><A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client"><B>IOHelper</B></A> - Class in <A HREF="../compbio/ws/client/package-summary.html">compbio.ws.client</A><DD>&nbsp;<DT><A HREF="../compbio/ws/client/IOHelper.html#IOHelper()"><B>IOHelper()</B></A> - \r
+Constructor for class compbio.ws.client.<A HREF="../compbio/ws/client/IOHelper.html" title="class in compbio.ws.client">IOHelper</A>\r
+<DD>&nbsp;\r
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isAmbiguosProtein(java.lang.String)"><B>isAmbiguosProtein(String)</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>Check whether the sequence confirms to amboguous protein sequence\r
@@ -91,7 +94,7 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title=
 <DT><A HREF="../compbio/metadata/Limit.html#isExceeded(java.util.List)"><B>isExceeded(List&lt;FastaSequence&gt;)</B></A> - \r
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>\r
 <DD>Checks if the number of sequences or their average length in the dataset
- exceeds limits the values defined by this Limit\r
+ exceeds this limit.\r
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</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>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
@@ -108,7 +111,7 @@ Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title
  line for an executable to run\r
 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</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>&nbsp;\r
+<DD>Please note this method closes the input stream provided as a parameter\r
 </DL>\r
 <HR>\r
 \r