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Adding changes from JWS2 branch. Fixes for Limit in particular
[jabaws.git] / website / dm_javadoc / compbio / data / sequence / ClustalAlignmentUtil.html
diff --git a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html
index 0bb55b0..39bba28 100644 (file)
--- a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html
+++ b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.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 Thu Nov 18 15:38:37 GMT 2010 -->\r
 <TITLE>\r
 ClustalAlignmentUtil\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2010-11-18">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -106,10 +106,10 @@ Tools to read and write clustal formated files
 \r
 <P>\r
 <DL>\r
+<DT><B>Version:</B></DT>\r
+  <DD>1.0 September 2009</DD>\r
 <DT><B>Author:</B></DT>\r
-  <DD>Petr Troshin based on jimp class
- 
-         Date September 2009</DD>\r
+  <DD>Petr Troshin based on jimp class</DD>\r
 </DL>\r
 <HR>\r
 \r
@@ -162,7 +162,7 @@ Tools to read and write clustal formated files
 <TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#isValidClustalFile(java.io.InputStream)">isValidClustalFile</A></B>(java.io.InputStream&nbsp;input)</CODE>\r
 \r
 <BR>\r
-&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>\r
+&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Please note this method closes the input stream provided as a parameter</TD>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
@@ -197,7 +197,7 @@ Tools to read and write clustal formated files
 <TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE>equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
+<TD><CODE>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</CODE></TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -278,6 +278,8 @@ isValidClustalFile</H3>
 <PRE>\r
 public static boolean <B>isValidClustalFile</B>(java.io.InputStream&nbsp;input)</PRE>\r
 <DL>\r
+<DD>Please note this method closes the input stream provided as a parameter\r
+<P>\r
 <DD><DL>\r
 <DT><B>Parameters:</B><DD><CODE>input</CODE> - \r
 <DT><B>Returns:</B><DD>true if the file is recognised as Clustal formatted alignment,