X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Ffull_javadoc%2Fcompbio%2Fdata%2Fsequence%2Fpackage-summary.html;h=bd7d97ae6a0db5383928ae83047629ff193a7d58;hb=5be600c3985aa7bcb8d8b51d77d773c76e6802bb;hp=04cec6a9e7920187ebffff949fc138ffa38b81e2;hpb=cb02e8a08893701386c270a8bf9d0f08b9cbc4db;p=jabaws.git

diff --git a/website/full_javadoc/compbio/data/sequence/package-summary.html b/website/full_javadoc/compbio/data/sequence/package-summary.html
index 04cec6a..bd7d97a 100644
--- a/website/full_javadoc/compbio/data/sequence/package-summary.html
+++ b/website/full_javadoc/compbio/data/sequence/package-summary.html
@@ -2,12 +2,12 @@
 <!--NewPage-->
 <HTML>
 <HEAD>
-<!-- Generated by javadoc (build 1.6.0_14) on Wed Feb 17 16:46:50 GMT 2010 -->
+<!-- Generated by javadoc (build 1.6.0_24) on Fri Aug 12 14:32:35 BST 2011 -->
 <TITLE>
 compbio.data.sequence
 </TITLE>
 
-<META NAME="date" CONTENT="2010-02-17">
+<META NAME="date" CONTENT="2011-08-12">
 
 <LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">
 
@@ -82,8 +82,8 @@ function windowTitle()
 <H2>
 Package compbio.data.sequence
 </H2>
-A data model for multiple sequence alignment web services 
- Classes in this package have no dependencies to other sources in the project.
+A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model.
 <P>
 <B>See:</B>
 <BR>
@@ -108,10 +108,30 @@ A data model for multiple sequence alignment web services
 <TD>Tools to read and write clustal formated files</TD>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A></B></TD>
+<TD>Reads files with FASTA formatted sequences.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></B></TD>
 <TD>A FASTA formatted sequence.</TD>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A></B></TD>
+<TD>&nbsp;</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></B></TD>
+<TD>A value class for AACon annotation results storage.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></B></TD>
+<TD>&nbsp;</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></B></TD>
+<TD>&nbsp;</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A></B></TD>
 <TD>Utility class for operations on sequences</TD>
 </TR>
@@ -126,8 +146,20 @@ A data model for multiple sequence alignment web services
 <B>Enum Summary</B></FONT></TH>
 </TR>
 <TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A></B></TD>
+<TD>Enumeration listing of all the supported methods.</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence">DisorderMethod</A></B></TD>
+<TD>&nbsp;</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></B></TD>
-<TD>Programmes that can produce alignments</TD>
+<TD>The list of programmes that can produce alignments</TD>
+</TR>
+<TR BGCOLOR="white" CLASS="TableRowColor">
+<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></B></TD>
+<TD>Enumeration defining two constraints for SMERFS columns score calculation.</TD>
 </TR>
 </TABLE>
 &nbsp;
@@ -152,17 +184,18 @@ Package compbio.data.sequence Description
 </H2>
 
 <P>
-A data model for multiple sequence alignment web services 
+A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model.  
  Classes in this package have no dependencies to other sources in the project. 
- They form a base layer of Jalview Web Services v2.
+ They form a base layer of JAva Bioinformatics Analysis Web Services.
 <P>
 
 <P>
 <DL>
+<DT><B>Version:</B></DT>
+  <DD>1.0     January 2010</DD>
 <DT><B>Author:</B></DT>
-  <DD>Petr Troshin 
- 
-        Date January 2010</DD>
+  <DD>Petr Troshin</DD>
 </DL>
 <HR>
 
