X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fdm_javadoc%2Fcompbio%2Fdata%2Fsequence%2FFastaSequence.html;h=1975623e0633c0788d4b58eda0083ccb457dcc00;hb=5f582fe1adafda5df440d1d1b3955b2bca7fbc88;hp=c9a97f652916223134691c1e442add7a8435d099;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git

diff --git a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html
index c9a97f6..1975623 100644
--- a/website/dm_javadoc/compbio/data/sequence/FastaSequence.html
+++ b/website/dm_javadoc/compbio/data/sequence/FastaSequence.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_21) on Thu Nov 18 15:38:37 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_21) on Tue Dec 21 18:32:58 GMT 2010 -->
 <TITLE>
 FastaSequence
 </TITLE>
 
-<META NAME="date" CONTENT="2010-11-18">
+<META NAME="date" CONTENT="2010-12-21">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
 
@@ -55,8 +55,8 @@ function windowTitle()
 
 <TR>
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
-&nbsp;<A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;
-&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
+&nbsp;<A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;
+&nbsp;<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class 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/FastaSequence.html" target="_top"><B>FRAMES</B></A>  &nbsp;
 &nbsp;<A HREF="FastaSequence.html" target="_top"><B>NO FRAMES</B></A>  &nbsp;
@@ -92,13 +92,16 @@ compbio.data.sequence</FONT>
 <BR>
 Class FastaSequence</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.FastaSequence</B>
 </PRE>
+<DL>
+<DT><B>Direct Known Subclasses:</B> <DD><A HREF="../../../compbio/data/sequence/AnnotatedSequence.html" title="class in compbio.data.sequence">AnnotatedSequence</A></DD>
+</DL>
 <HR>
 <DL>
 <DT><PRE><FONT SIZE="-1">@Immutable
-</FONT>public class <B>FastaSequence</B><DT>extends java.lang.Object</DL>
+</FONT>public class <B>FastaSequence</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>
@@ -129,8 +132,8 @@ A FASTA formatted sequence. Please note that this class does not make any
 <B>Constructor Summary</B></FONT></TH>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</A></B>(java.lang.String&nbsp;id,
-              java.lang.String&nbsp;sequence)</CODE>
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#FastaSequence(java.lang.String, java.lang.String)">FastaSequence</A></B>(<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>&nbsp;id,
+              <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>&nbsp;sequence)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Upon construction the any whitespace characters are removed from the
@@ -149,8 +152,8 @@ A FASTA formatted sequence. Please note that this class does not make any
 <TR BGCOLOR="white" CLASS="TableRowColor">
 <TD ALIGN="right" VALIGN="top" WIDTH="1%"><FONT SIZE="-1">
 <CODE>static&nbsp;int</CODE></FONT></TD>
-<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A></B>(java.lang.String&nbsp;theString,
-                       java.lang.String&nbsp;theRegExp)</CODE>
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.html#countMatchesInSequence(java.lang.String, java.lang.String)">countMatchesInSequence</A></B>(<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>&nbsp;theString,
+                       <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>&nbsp;theRegExp)</CODE>
 
 <BR>
 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</TD>
@@ -158,14 +161,14 @@ A FASTA formatted sequence. Please note that this class does not make any
 <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/FastaSequence.html#equals(java.lang.Object)">equals</A></B>(java.lang.Object&nbsp;obj)</CODE>
+<TD><CODE><B><A HREF="../../../compbio/data/sequence/FastaSequence.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;&nbsp;</TD>
 </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/FastaSequence.html#getFormatedSequence(int)">getFormatedSequence</A></B>(int&nbsp;width)</CODE>
 
 <BR>
@@ -173,7 +176,7 @@ A FASTA formatted sequence. Please note that this class does not make any
 </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/FastaSequence.html#getFormattedFasta()">getFormattedFasta</A></B>()</CODE>
 
 <BR>
@@ -181,7 +184,7 @@ A FASTA formatted sequence. Please note that this class does not make any
 </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/FastaSequence.html#getId()">getId</A></B>()</CODE>
 
 <BR>
@@ -197,7 +200,7 @@ A FASTA formatted sequence. Please note that this class does not make any
 </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/FastaSequence.html#getOnelineFasta()">getOnelineFasta</A></B>()</CODE>
 
 <BR>
@@ -205,7 +208,7 @@ A FASTA formatted sequence. Please note that this class does not make any
 </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/FastaSequence.html#getSequence()">getSequence</A></B>()</CODE>
 
 <BR>
@@ -221,7 +224,7 @@ A FASTA formatted sequence. Please note that this class does not make any
 </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/FastaSequence.html#toString()">toString</A></B>()</CODE>
 
 <BR>
@@ -231,10 +234,10 @@ A FASTA formatted sequence. Please note that this class does not make any
 &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#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;
@@ -253,8 +256,8 @@ A FASTA formatted sequence. Please note that this class does not make any
 <A NAME="FastaSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
 FastaSequence</H3>
 <PRE>
-public <B>FastaSequence</B>(java.lang.String&nbsp;id,
-                     java.lang.String&nbsp;sequence)</PRE>
+public <B>FastaSequence</B>(<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>&nbsp;id,
+                     <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>&nbsp;sequence)</PRE>
 <DL>
 <DD>Upon construction the any whitespace characters are removed from the
  sequence
@@ -276,7 +279,7 @@ public <B>FastaSequence</B>(java.lang.String&nbsp;id,
 <A NAME="getId()"><!-- --></A><H3>
 getId</H3>
 <PRE>
-public java.lang.String <B>getId</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>getId</B>()</PRE>
 <DL>
 <DD>Gets the value of id
 <P>
@@ -290,7 +293,7 @@ public java.lang.String <B>getId</B>()</PRE>
 <A NAME="getSequence()"><!-- --></A><H3>
 getSequence</H3>
 <PRE>
-public java.lang.String <B>getSequence</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>getSequence</B>()</PRE>
 <DL>
 <DD>Gets the value of sequence
 <P>
@@ -304,8 +307,8 @@ public java.lang.String <B>getSequence</B>()</PRE>
 <A NAME="countMatchesInSequence(java.lang.String, java.lang.String)"><!-- --></A><H3>
 countMatchesInSequence</H3>
 <PRE>
-public static int <B>countMatchesInSequence</B>(java.lang.String&nbsp;theString,
-                                         java.lang.String&nbsp;theRegExp)</PRE>
+public static int <B>countMatchesInSequence</B>(<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>&nbsp;theString,
+                                         <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>&nbsp;theRegExp)</PRE>
 <DL>
 <DD><DL>
 </DL>
@@ -316,7 +319,7 @@ public static int <B>countMatchesInSequence</B>(java.lang.String&nbsp;theString,
 <A NAME="getFormattedFasta()"><!-- --></A><H3>
 getFormattedFasta</H3>
 <PRE>
-public java.lang.String <B>getFormattedFasta</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>getFormattedFasta</B>()</PRE>
 <DL>
 <DD><DL>
 </DL>
@@ -327,7 +330,7 @@ public java.lang.String <B>getFormattedFasta</B>()</PRE>
 <A NAME="getOnelineFasta()"><!-- --></A><H3>
 getOnelineFasta</H3>
 <PRE>
-public java.lang.String <B>getOnelineFasta</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>getOnelineFasta</B>()</PRE>
 <DL>
 <DD><DL>
 
@@ -340,7 +343,7 @@ public java.lang.String <B>getOnelineFasta</B>()</PRE>
 <A NAME="getFormatedSequence(int)"><!-- --></A><H3>
 getFormatedSequence</H3>
 <PRE>
-public java.lang.String <B>getFormatedSequence</B>(int&nbsp;width)</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>getFormatedSequence</B>(int&nbsp;width)</PRE>
 <DL>
 <DD>Format sequence per width letter in one string. Without spaces.
 <P>
@@ -366,12 +369,12 @@ public int <B>getLength</B>()</PRE>
 <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>Same as oneLineFasta
 <P>
 <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>
@@ -385,7 +388,7 @@ 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>
@@ -396,10 +399,10 @@ 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><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>
@@ -436,8 +439,8 @@ public boolean <B>equals</B>(java.lang.Object&nbsp;obj)</PRE>
 
 <TR>
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
-&nbsp;<A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;
-&nbsp;<A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
+&nbsp;<A HREF="../../../compbio/data/sequence/DisemblResultAnnot.html" title="enum in compbio.data.sequence"><B>PREV CLASS</B></A>&nbsp;
+&nbsp;<A HREF="../../../compbio/data/sequence/MultiAnnotatedSequence.html" title="class in compbio.data.sequence"><B>NEXT CLASS</B></A></FONT></TD>
 <TD BGCOLOR="white" CLASS="NavBarCell2"><FONT SIZE="-2">
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