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