X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2FClustalAlignmentUtil.html;h=fd91235910b63b9258f8e8d09537ffe934ee357d;hb=bc3346bd7c1c518fad867d4c60a53779e7516588;hp=3cbace7ca0b6b701a0307c30941ec02d9014df4e;hpb=b413eee53fa3cc22a6bd4e03c9ac64bf26b7c834;p=jabaws.git

diff --git a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html
index 3cbace7..fd91235 100644
--- a/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html
+++ b/website/dm_javadoc/compbio/data/sequence/ClustalAlignmentUtil.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:18 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:03 BST 2011 -->
 <TITLE>
 ClustalAlignmentUtil
 </TITLE>
 
-<META NAME="date" CONTENT="2010-11-24">
+<META NAME="date" CONTENT="2011-08-12">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
 
@@ -56,7 +56,7 @@ function windowTitle()
 <TR>
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
 &nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;
-&nbsp;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
+&nbsp;<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
   <A HREF="../../../index.html?compbio/data/sequence/ClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;
 &nbsp;<A HREF="ClustalAlignmentUtil.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;
@@ -183,7 +183,7 @@ Tools to read and write clustal formated files
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
 <CODE>static&nbsp;void</CODE></FONT></TD>
-<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,
+<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,
                       <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)</CODE>
 
 <BR>
@@ -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>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
-<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>
+<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>
 </TR>
 </TABLE>
 &nbsp;
@@ -288,10 +288,10 @@ public static boolean <B>isValidClustalFile</B>(<A HREF="http://java.sun.com/jav
 </DL>
 <HR>
 
-<A NAME="writeClustalAlignment(java.io.OutputStream, compbio.data.sequence.Alignment)"><!-- --></A><H3>
+<A NAME="writeClustalAlignment(java.io.Writer, compbio.data.sequence.Alignment)"><!-- --></A><H3>
 writeClustalAlignment</H3>
 <PRE>
-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,
+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,
                                          <A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A>&nbsp;alignment)
                                   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>
 <DL>
@@ -300,7 +300,7 @@ public static void <B>writeClustalAlignment</B>(<A HREF="http://java.sun.com/jav
  Clustal would have recorded 50 chars.
 <P>
 <DD><DL>
-<DT><B>Parameters:</B><DD><CODE>outStream</CODE> - <DD><CODE>alignment</CODE> - 
+<DT><B>Parameters:</B><DD><CODE>out</CODE> - <DD><CODE>alignment</CODE> - 
 <DT><B>Throws:</B>
 <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>
 </DD>
@@ -353,7 +353,7 @@ public static <A HREF="../../../compbio/data/sequence/Alignment.html" title="cla
 <TR>
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
 &nbsp;<A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;
-&nbsp;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
+&nbsp;<A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
   <A HREF="../../../index.html?compbio/data/sequence/ClustalAlignmentUtil.html" target="_top"><B>FRAMES</B></A>  &nbsp;
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