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web pages updates to point to new download location also the redirect servlet
[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 3cbace7..fd91235 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_21) on Wed Nov 24 12:17:18 GMT 2010 -->\r
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:03 BST 2011 -->\r
 <TITLE>\r
 ClustalAlignmentUtil\r
 </TITLE>\r
 \r
-<META NAME="date" CONTENT="2010-11-24">\r
+<META NAME="date" CONTENT="2011-08-12">\r
 \r
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
 \r
@@ -56,7 +56,7 @@ function windowTitle()
 <TR>\r
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 &nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+&nbsp;<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
   <A HREF="../../../index.html?compbio/data/sequence/ClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 &nbsp;<A HREF="ClustalAlignmentUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r
@@ -183,7 +183,7 @@ Tools to read and write clustal formated files
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">\r
 <CODE>static&nbsp;void</CODE></FONT></TD>\r
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outStream,\r
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html#writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)">writeClustalAlignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A>&nbsp;out,\r
                       <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>\r
 \r
 <BR>\r
@@ -197,7 +197,7 @@ Tools to read and write clustal formated files
 <TH ALIGN="left"><B>Methods inherited from class java.lang.<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">Object</A></B></TH>\r
 </TR>\r
 <TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#clone()" title="class or interface in java.lang">clone</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#finalize()" title="class or interface in java.lang">finalize</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
+<TD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#equals(java.lang.Object)" title="class or interface in java.lang">equals</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#getClass()" title="class or interface in java.lang">getClass</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#hashCode()" title="class or interface in java.lang">hashCode</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notify()" title="class or interface in java.lang">notify</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#notifyAll()" title="class or interface in java.lang">notifyAll</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#toString()" title="class or interface in java.lang">toString</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait()" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long)" title="class or interface in java.lang">wait</A>, <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true#wait(long, int)" title="class or interface in java.lang">wait</A></CODE></TD>\r
 </TR>\r
 </TABLE>\r
 &nbsp;\r
@@ -288,10 +288,10 @@ public static boolean <B>isValidClustalFile</B>(<A HREF="http://java.sun.com/jav
 </DL>\r
 <HR>\r
 \r
-<A NAME="writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
+<A NAME="writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)"><!-- --></A><H3>\r
 writeClustalAlignment</H3>\r
 <PRE>\r
-public static void <B>writeClustalAlignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/OutputStream.html?is-external=true" title="class or interface in java.io">OutputStream</A>&nbsp;outStream,\r
+public static void <B>writeClustalAlignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/io/Writer.html?is-external=true" title="class or interface in java.io">Writer</A>&nbsp;out,\r
                                          <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)\r
                                   throws <A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></PRE>\r
 <DL>\r
@@ -300,7 +300,7 @@ public static void <B>writeClustalAlignment</B>(<A HREF="http://java.sun.com/jav
  Clustal would have recorded 50 chars.\r
 <P>\r
 <DD><DL>\r
-<DT><B>Parameters:</B><DD><CODE>outStream</CODE> - <DD><CODE>alignment</CODE> - \r
+<DT><B>Parameters:</B><DD><CODE>out</CODE> - <DD><CODE>alignment</CODE> - \r
 <DT><B>Throws:</B>\r
 <DD><CODE><A HREF="http://java.sun.com/javase/6/docs/api/java/io/IOException.html?is-external=true" title="class or interface in java.io">IOException</A></CODE></DL>\r
 </DD>\r
@@ -353,7 +353,7 @@ public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="cla
 <TR>\r
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
 &nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;\r
-&nbsp;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
+&nbsp;<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>\r
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">\r
   <A HREF="../../../index.html?compbio/data/sequence/ClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;\r
 &nbsp;<A HREF="ClustalAlignmentUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;\r