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  82 <H2>\r
  83 Package compbio.data.sequence\r
  84 </H2>\r
  85 A data model for multiple sequence alignment web services and utility methods
  86  that work on the objects of this model.\r
  87 <P>\r
  88 <B>See:</B>\r
  89 <BR>\r
  90 &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<A HREF="#package_description"><B>Description</B></A>\r
  91 <P>\r
  92 \r
  93 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
  94 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
  95 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
  96 <B>Class Summary</B></FONT></TH>\r
  97 </TR>\r
  98 <TR BGCOLOR="white" CLASS="TableRowColor">\r
  99 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</A></B></TD>\r
 100 <TD>Multiple sequence alignment.</TD>\r
 101 </TR>\r
 102 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 103 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</A></B></TD>\r
 104 <TD>Alignment metadata e.g.</TD>\r
 105 </TR>\r
 106 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 107 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</A></B></TD>\r
 108 <TD>Tools to read and write clustal formated files</TD>\r
 109 </TR>\r
 110 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 111 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</A></B></TD>\r
 112 <TD>Reads files with FASTA formatted sequences.</TD>\r
 113 </TR>\r
 114 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 115 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</A></B></TD>\r
 116 <TD>A FASTA formatted sequence.</TD>\r
 117 </TR>\r
 118 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 119 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</A></B></TD>\r
 120 <TD>&nbsp;</TD>\r
 121 </TR>\r
 122 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 123 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</A></B></TD>\r
 124 <TD>A value class for AACon annotation results storage.</TD>\r
 125 </TR>\r
 126 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 127 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</A></B></TD>\r
 128 <TD>&nbsp;</TD>\r
 129 </TR>\r
 130 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 131 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</A></B></TD>\r
 132 <TD>&nbsp;</TD>\r
 133 </TR>\r
 134 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 135 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</A></B></TD>\r
 136 <TD>Utility class for operations on sequences</TD>\r
 137 </TR>\r
 138 </TABLE>\r
 139 &nbsp;\r
 140 \r
 141 <P>\r
 142 \r
 143 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 144 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 145 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 146 <B>Enum Summary</B></FONT></TH>\r
 147 </TR>\r
 148 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 149 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</A></B></TD>\r
 150 <TD>Enumeration listing of all the supported methods.</TD>\r
 151 </TR>\r
 152 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 153 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence">DisorderMethod</A></B></TD>\r
 154 <TD>&nbsp;</TD>\r
 155 </TR>\r
 156 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 157 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</A></B></TD>\r
 158 <TD>The list of programmes that can produce alignments</TD>\r
 159 </TR>\r
 160 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 161 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</A></B></TD>\r
 162 <TD>Enumeration defining two constraints for SMERFS columns score calculation.</TD>\r
 163 </TR>\r
 164 </TABLE>\r
 165 &nbsp;\r
 166 \r
 167 <P>\r
 168 \r
 169 <TABLE BORDER="1" WIDTH="100%" CELLPADDING="3" CELLSPACING="0" SUMMARY="">\r
 170 <TR BGCOLOR="#CCCCFF" CLASS="TableHeadingColor">\r
 171 <TH ALIGN="left" COLSPAN="2"><FONT SIZE="+2">\r
 172 <B>Exception Summary</B></FONT></TH>\r
 173 </TR>\r
 174 <TR BGCOLOR="white" CLASS="TableRowColor">\r
 175 <TD WIDTH="15%"><B><A HREF="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</A></B></TD>\r
 176 <TD>&nbsp;</TD>\r
 177 </TR>\r
 178 </TABLE>\r
 179 &nbsp;\r
 180 \r
 181 <P>\r
 182 <A NAME="package_description"><!-- --></A><H2>\r
 183 Package compbio.data.sequence Description\r
 184 </H2>\r
 185 \r
 186 <P>\r
 187 A data model for multiple sequence alignment web services and utility methods
 188  that work on the objects of this model.
 189  Classes in this package have no dependencies to other sources in the project.
 190  They form a base layer of JAva Bioinformatics Analysis Web Services.\r
 191 <P>\r
 192 \r
 193 <P>\r
 194 <DL>\r
 195 <DT><B>Version:</B></DT>\r
 196   <DD>1.0     January 2010</DD>\r
 197 <DT><B>Author:</B></DT>\r
 198   <DD>Petr Troshin</DD>\r
 199 </DL>\r
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