X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Findex-files%2Findex-8.html;h=6bd28cf05851c79c984b080032a82522cf4344c1;hb=1178f388e4d4e64387704a751fd9c77ccb773a27;hp=81d737fa8fe43b3fcc48f7e77bd3ea105ff67bee;hpb=535359a3d592ee41bda72e7356f0181f6cee9d07;p=jabaws.git

diff --git a/website/dm_javadoc/index-files/index-8.html b/website/dm_javadoc/index-files/index-8.html
index 81d737f..6bd28cf 100644
--- a/website/dm_javadoc/index-files/index-8.html
+++ b/website/dm_javadoc/index-files/index-8.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:28 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:19 GMT 2010 -->
 <TITLE>
 I-Index
 </TITLE>
 
-<META NAME="date" CONTENT="2010-02-17">
+<META NAME="date" CONTENT="2010-11-24">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../stylesheet.css" TITLE="Style">
 
@@ -91,7 +91,7 @@ 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> - 
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</A>
 <DD>Checks if the number of sequences or their average length in the dataset
- exceeds limits the values defined by this Limit
+ exceeds this limit.
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isNonAmbNucleotideSequence(java.lang.String)"><B>isNonAmbNucleotideSequence(String)</B></A> - 
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
 <DD>Ambiguous DNA chars : AGTCRYMKSWHBVDN // differs from protein in only one
@@ -102,13 +102,16 @@ Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/S
 <DT><A HREF="../compbio/data/sequence/SequenceUtil.html#isProteinSequence(java.lang.String)"><B>isProteinSequence(String)</B></A> - 
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A>
 <DD>&nbsp;
+<DT><A HREF="../compbio/metadata/Option.html#isRequired"><B>isRequired</B></A> - 
+Variable in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
+<DD>&nbsp;
 <DT><A HREF="../compbio/metadata/Option.html#isRequired()"><B>isRequired()</B></A> - 
 Method in class compbio.metadata.<A HREF="../compbio/metadata/Option.html" title="class in compbio.metadata">Option</A>
 <DD>Flag that indicated that this option must be specified in the command
  line for an executable to run
 <DT><A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)"><B>isValidClustalFile(InputStream)</B></A> - 
 Static method in class compbio.data.sequence.<A HREF="../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A>
-<DD>&nbsp;
+<DD>Please note this method closes the input stream provided as a parameter
 </DL>
 <HR>
 
