X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2FAlignment.html;h=5f14d3062bad96eb6f92bbaf67e282ac1432af66;hb=6e1c873d0879f462b1fb1a1efa444cf993a9e76a;hp=b2f0dc5882486a4043315a2053660fe86138a0e4;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git

diff --git a/website/dm_javadoc/compbio/data/sequence/Alignment.html b/website/dm_javadoc/compbio/data/sequence/Alignment.html
index b2f0dc5..5f14d30 100644
--- a/website/dm_javadoc/compbio/data/sequence/Alignment.html
+++ b/website/dm_javadoc/compbio/data/sequence/Alignment.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_21) on Thu Nov 18 15:38:36 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_21) on Wed Nov 24 12:17:18 GMT 2010 -->
 <TITLE>
 Alignment
 </TITLE>
 
-<META NAME="date" CONTENT="2010-11-18">
+<META NAME="date" CONTENT="2010-11-24">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
 
@@ -92,13 +92,13 @@ compbio.data.sequence</FONT>
 <BR>
 Class Alignment</H2>
 <PRE>
-java.lang.Object
+<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</A>
   <IMG SRC="../../../resources/inherit.gif" ALT="extended by "><B>compbio.data.sequence.Alignment</B>
 </PRE>
 <HR>
 <DL>
 <DT><PRE><FONT SIZE="-1">@Immutable
-</FONT>public final class <B>Alignment</B><DT>extends java.lang.Object</DL>
+</FONT>public final class <B>Alignment</B><DT>extends <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></DL>
 </PRE>
 
 <P>
@@ -130,14 +130,14 @@ Multiple sequence alignment.
 <B>Constructor Summary</B></FONT></TH>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
           <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#Alignment(java.util.List, compbio.data.sequence.Program, char)">Alignment</A></B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
           <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,
           char&nbsp;gapchar)</CODE>
 
@@ -157,7 +157,7 @@ Multiple sequence alignment.
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
 <CODE>&nbsp;boolean</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#equals(java.lang.Object)">equals</A></B>(<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>&nbsp;obj)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Please note that this implementation does not take the order of sequences
@@ -173,7 +173,7 @@ Multiple sequence alignment.
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE>&nbsp;java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>
+<CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;</CODE></FONT></TD>
 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#getSequences()">getSequences</A></B>()</CODE>
 
 <BR>
@@ -197,7 +197,7 @@ Multiple sequence alignment.
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
-<CODE>&nbsp;java.lang.String</CODE></FONT></TD>
+<CODE>&nbsp;<A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A></CODE></FONT></TD>
 <TD><CODE><B><A HREF="../../../compbio/data/sequence/Alignment.html#toString()">toString</A></B>()</CODE>
 
 <BR>
@@ -207,10 +207,10 @@ Multiple sequence alignment.
 &nbsp;<A NAME="methods_inherited_from_class_java.lang.Object"><!-- --></A>
 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">
 <TR BGCOLOR="#EEEEFF" CLASS="TableSubHeadingColor">
-<TH ALIGN="left"><B>Methods inherited from class java.lang.Object</B></TH>
+<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>clone, finalize, getClass, notify, notifyAll, wait, wait, wait</CODE></TD>
+<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#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#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#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;
@@ -229,7 +229,7 @@ Multiple sequence alignment.
 <A NAME="Alignment(java.util.List, compbio.data.sequence.Program, char)"><!-- --></A><H3>
 Alignment</H3>
 <PRE>
-public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
+public <B>Alignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
                  <A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A>&nbsp;program,
                  char&nbsp;gapchar)</PRE>
 <DL>
@@ -241,7 +241,7 @@ public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequenc
 <A NAME="Alignment(java.util.List, compbio.data.sequence.AlignmentMetadata)"><!-- --></A><H3>
 Alignment</H3>
 <PRE>
-public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
+public <B>Alignment</B>(<A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt;&nbsp;sequences,
                  <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A>&nbsp;metadata)</PRE>
 <DL>
 <DL>
@@ -261,7 +261,7 @@ public <B>Alignment</B>(java.util.List&lt;<A HREF="../../../compbio/data/sequenc
 <A NAME="getSequences()"><!-- --></A><H3>
 getSequences</H3>
 <PRE>
-public java.util.List&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>getSequences</B>()</PRE>
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/util/List.html?is-external=true" title="class or interface in java.util">List</A>&lt;<A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A>&gt; <B>getSequences</B>()</PRE>
 <DL>
 <DD><DL>
 
@@ -297,10 +297,10 @@ public <A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="cl
 <A NAME="toString()"><!-- --></A><H3>
 toString</H3>
 <PRE>
-public java.lang.String <B>toString</B>()</PRE>
+public <A HREF="http://java.sun.com/javase/6/docs/api/java/lang/String.html?is-external=true" title="class or interface in java.lang">String</A> <B>toString</B>()</PRE>
 <DL>
 <DD><DL>
-<DT><B>Overrides:</B><DD><CODE>toString</CODE> in class <CODE>java.lang.Object</CODE></DL>
+<DT><B>Overrides:</B><DD><CODE><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></CODE> in class <CODE><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></CODE></DL>
 </DD>
 <DD><DL>
 </DL>
@@ -314,7 +314,7 @@ hashCode</H3>
 public int <B>hashCode</B>()</PRE>
 <DL>
 <DD><DL>
-<DT><B>Overrides:</B><DD><CODE>hashCode</CODE> in class <CODE>java.lang.Object</CODE></DL>
+<DT><B>Overrides:</B><DD><CODE><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></CODE> in class <CODE><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></CODE></DL>
 </DD>
 <DD><DL>
 </DL>
@@ -325,13 +325,13 @@ public int <B>hashCode</B>()</PRE>
 <A NAME="equals(java.lang.Object)"><!-- --></A><H3>
 equals</H3>
 <PRE>
-public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>
+public boolean <B>equals</B>(<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>&nbsp;obj)</PRE>
 <DL>
 <DD>Please note that this implementation does not take the order of sequences
  into account!
 <P>
 <DD><DL>
-<DT><B>Overrides:</B><DD><CODE>equals</CODE> in class <CODE>java.lang.Object</CODE></DL>
+<DT><B>Overrides:</B><DD><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></CODE> in class <CODE><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></CODE></DL>
 </DD>
 <DD><DL>
 </DL>
