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-Package compbio.data.sequence\r
-</H2>\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
- <A HREF="#package_description"><B>Description</B></A>\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Class Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></B></TD>\r
-<TD>Multiple sequence alignment.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></B></TD>\r
-<TD>Alignment metadata e.g.</TD>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></B></TD>\r
-<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> </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> </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> </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
-</TABLE>\r
- \r
-\r
-<P>\r
-\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
-<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> </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>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
- \r
-\r
-<P>\r
-\r
-<TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
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-<TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
-<B>Exception Summary</B></FONT></TH>\r
-</TR>\r
-<TR BGCOLOR="white" CLASS="TableRowColor">\r
-<TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></B></TD>\r
-<TD> </TD>\r
-</TR>\r
-</TABLE>\r
- \r
-\r
-<P>\r
-<A NAME="package_description"><!-- --></A><H2>\r
-Package compbio.data.sequence Description\r
-</H2>\r
-\r
-<P>\r
-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 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</DD>\r
-</DL>\r
-<HR>\r
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