<!--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 Wed Dec 07 12:30:43 GMT 2011 -->\r
<TITLE>\r
Uses of Package compbio.data.sequence\r
</TITLE>\r
\r
-<META NAME="date" CONTENT="2010-02-17">\r
+<META NAME="date" CONTENT="2011-12-07">\r
\r
<LINK REL ="stylesheet" TYPE="text/css" HREF="../../../stylesheet.css" TITLE="Style">\r
\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.data.msa"><B>compbio.data.msa</B></A></TD>\r
-<TD> </TD>\r
+<TD>Web Service interfaces for JAva Bioinformatics Analysis Web Services. </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.data.msa.jaxws"><B>compbio.data.msa.jaxws</B></A></TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.data.sequence"><B>compbio.data.sequence</B></A></TD>\r
-<TD>A data model for multiple sequence alignment web services
- Classes in this package have no dependencies to other sources in the project. </TD>\r
+<TD>A data model for multiple sequence alignment web services and utility methods
+ that work on the objects of this model. </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.engine"><B>compbio.engine</B></A></TD>\r
<TD>Utilities commonly used by all runners. </TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.runner.conservation"><B>compbio.runner.conservation</B></A></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><A HREF="#compbio.runner.disorder"><B>compbio.runner.disorder</B></A></TD>\r
+<TD> </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><A HREF="#compbio.runner.msa"><B>compbio.runner.msa</B></A></TD>\r
<TD>Wrappers for native executables for multiple sequence alignment (msa) </TD>\r
</TR>\r
<BR>\r
A FASTA formatted sequence.</TD>\r
</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa"><B>ScoreManager</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
</TABLE>\r
\r
<P>\r
<BR>\r
A FASTA formatted sequence.</TD>\r
</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa.jaxws"><B>ScoreManager</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
</TABLE>\r
\r
<P>\r
Alignment metadata e.g.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ConservationMethod.html#compbio.data.sequence"><B>ConservationMethod</B></A></B>\r
+\r
+<BR>\r
+ Enumeration listing of all the supported methods.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/DisorderMethod.html#compbio.data.sequence"><B>DisorderMethod</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence"><B>FastaSequence</B></A></B>\r
\r
<BR>\r
<TD><B><A HREF="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence"><B>Program</B></A></B>\r
\r
<BR>\r
- Programmes that can produce alignments</TD>\r
+ The list of programmes that can produce alignments</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Range.html#compbio.data.sequence"><B>Range</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence"><B>Score</B></A></B>\r
+\r
+<BR>\r
+ A value class for AACon annotation results storage.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.sequence"><B>ScoreManager</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.ScoreHolder.html#compbio.data.sequence"><B>ScoreManager.ScoreHolder</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/SMERFSConstraints.html#compbio.data.sequence"><B>SMERFSConstraints</B></A></B>\r
+\r
+<BR>\r
+ Enumeration defining two constraints for SMERFS columns score calculation.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence"><B>UnknownFileFormatException</B></A></B>\r
A FASTA formatted sequence.</TD>\r
</TR>\r
<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/Score.html#compbio.runner"><B>Score</B></A></B>\r
+\r
+<BR>\r
+ A value class for AACon annotation results storage.</TD>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
<TD><B><A HREF="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.runner"><B>UnknownFileFormatException</B></A></B>\r
\r
<BR>\r
</TABLE>\r
\r
<P>\r
+<A NAME="compbio.runner.conservation"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/conservation/package-summary.html">compbio.runner.conservation</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.conservation"><B>ScoreManager</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
+<A NAME="compbio.runner.disorder"><!-- --></A>\r
+<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
+<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
+<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
+Classes in <A HREF="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</A> used by <A HREF="../../../compbio/runner/disorder/package-summary.html">compbio.runner.disorder</A></FONT></TH>\r
+</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.disorder"><B>ScoreManager</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
+</TABLE>\r
+ \r
+<P>\r
<A NAME="compbio.runner.msa"><!-- --></A>\r
<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
<TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
<BR>\r
A FASTA formatted sequence.</TD>\r
</TR>\r
+<TR BGCOLOR="white" CLASS="TableRowColor">\r
+<TD><B><A HREF="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.ws.server"><B>ScoreManager</B></A></B>\r
+\r
+<BR>\r
+ </TD>\r
+</TR>\r
</TABLE>\r
\r
<P>\r
git://source.jalview.org / jabaws.git / blobdiff