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  72 <div class="header">
  73 <h1 title="Package" class="title">Package&nbsp;compbio.data.sequence</h1>
  74 <div class="docSummary">
  75 <div class="block">A data model for multiple sequence alignment web services and utility methods
  76  that work on the objects of this model.</div>
  77 </div>
  78 <p>See:&nbsp;<a href="#package.description">Description</a></p>
  79 </div>
  80 <div class="contentContainer">
  81 <ul class="blockList">
  82 <li class="blockList">
  83 <table class="typeSummary" border="0" cellpadding="3" cellspacing="0" summary="Class Summary table, listing classes, and an explanation">
  84 <caption><span>Class Summary</span><span class="tabEnd">&nbsp;</span></caption>
  85 <tr>
  86 <th class="colFirst" scope="col">Class</th>
  87 <th class="colLast" scope="col">Description</th>
  88 </tr>
  89 <tbody>
  90 <tr class="altColor">
  91 <td class="colFirst"><a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></td>
  92 <td class="colLast">
  93 <div class="block">Multiple sequence alignment.</div>
  94 </td>
  95 </tr>
  96 <tr class="rowColor">
  97 <td class="colFirst"><a href="../../../compbio/data/sequence/AlignmentMetadata.html" title="class in compbio.data.sequence">AlignmentMetadata</a></td>
  98 <td class="colLast">
  99 <div class="block">Alignment metadata e.g.</div>
 100 </td>
 101 </tr>
 102 <tr class="altColor">
 103 <td class="colFirst"><a href="../../../compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></td>
 104 <td class="colLast">
 105 <div class="block">Tools to read and write clustal formated files</div>
 106 </td>
 107 </tr>
 108 <tr class="rowColor">
 109 <td class="colFirst"><a href="../../../compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></td>
 110 <td class="colLast">
 111 <div class="block">Reads files with FASTA formatted sequences.</div>
 112 </td>
 113 </tr>
 114 <tr class="altColor">
 115 <td class="colFirst"><a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a></td>
 116 <td class="colLast">
 117 <div class="block">A FASTA formatted sequence.</div>
 118 </td>
 119 </tr>
 120 <tr class="rowColor">
 121 <td class="colFirst"><a href="../../../compbio/data/sequence/Range.html" title="class in compbio.data.sequence">Range</a></td>
 122 <td class="colLast">&nbsp;</td>
 123 </tr>
 124 <tr class="altColor">
 125 <td class="colFirst"><a href="../../../compbio/data/sequence/RNAStructReader.html" title="class in compbio.data.sequence">RNAStructReader</a></td>
 126 <td class="colLast">&nbsp;</td>
 127 </tr>
 128 <tr class="rowColor">
 129 <td class="colFirst"><a href="../../../compbio/data/sequence/RNAStructScoreManager.html" title="class in compbio.data.sequence">RNAStructScoreManager</a></td>
 130 <td class="colLast">&nbsp;</td>
 131 </tr>
 132 <tr class="altColor">
 133 <td class="colFirst"><a href="../../../compbio/data/sequence/Score.html" title="class in compbio.data.sequence">Score</a></td>
 134 <td class="colLast">
 135 <div class="block">A value class for AACon annotation results storage.</div>
 136 </td>
 137 </tr>
 138 <tr class="rowColor">
 139 <td class="colFirst"><a href="../../../compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></td>
 140 <td class="colLast">&nbsp;</td>
 141 </tr>
 142 <tr class="altColor">
 143 <td class="colFirst"><a href="../../../compbio/data/sequence/ScoreManager.ScoreHolder.html" title="class in compbio.data.sequence">ScoreManager.ScoreHolder</a></td>
 144 <td class="colLast">&nbsp;</td>
 145 </tr>
 146 <tr class="rowColor">
 147 <td class="colFirst"><a href="../../../compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></td>
 148 <td class="colLast">
 149 <div class="block">Utility class for operations on sequences</div>
 150 </td>
 151 </tr>
 152 </tbody>
 153 </table>
 154 </li>
 155 <li class="blockList">
 156 <table class="typeSummary" border="0" cellpadding="3" cellspacing="0" summary="Enum Summary table, listing enums, and an explanation">
 157 <caption><span>Enum Summary</span><span class="tabEnd">&nbsp;</span></caption>
 158 <tr>
 159 <th class="colFirst" scope="col">Enum</th>
 160 <th class="colLast" scope="col">Description</th>
 161 </tr>
 162 <tbody>
 163 <tr class="altColor">
 164 <td class="colFirst"><a href="../../../compbio/data/sequence/ConservationMethod.html" title="enum in compbio.data.sequence">ConservationMethod</a></td>
 165 <td class="colLast">
 166 <div class="block">Enumeration listing of all the supported methods.</div>
 167 </td>
 168 </tr>
 169 <tr class="rowColor">
 170 <td class="colFirst"><a href="../../../compbio/data/sequence/DisemblResult.html" title="enum in compbio.data.sequence">DisemblResult</a></td>
 171 <td class="colLast">&nbsp;</td>
 172 </tr>
 173 <tr class="altColor">
 174 <td class="colFirst"><a href="../../../compbio/data/sequence/DisorderMethod.html" title="enum in compbio.data.sequence">DisorderMethod</a></td>
 175 <td class="colLast">&nbsp;</td>
 176 </tr>
 177 <tr class="rowColor">
 178 <td class="colFirst"><a href="../../../compbio/data/sequence/GlobProtResult.html" title="enum in compbio.data.sequence">GlobProtResult</a></td>
 179 <td class="colLast">&nbsp;</td>
 180 </tr>
 181 <tr class="altColor">
 182 <td class="colFirst"><a href="../../../compbio/data/sequence/IUPredResult.html" title="enum in compbio.data.sequence">IUPredResult</a></td>
 183 <td class="colLast">&nbsp;</td>
 184 </tr>
 185 <tr class="rowColor">
 186 <td class="colFirst"><a href="../../../compbio/data/sequence/Program.html" title="enum in compbio.data.sequence">Program</a></td>
 187 <td class="colLast">
 188 <div class="block">The list of programmes that can produce alignments</div>
 189 </td>
 190 </tr>
 191 <tr class="altColor">
 192 <td class="colFirst"><a href="../../../compbio/data/sequence/RNAStructReader.AlifoldLine.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldLine</a></td>
 193 <td class="colLast">&nbsp;</td>
 194 </tr>
 195 <tr class="rowColor">
 196 <td class="colFirst"><a href="../../../compbio/data/sequence/RNAStructReader.AlifoldResult.html" title="enum in compbio.data.sequence">RNAStructReader.AlifoldResult</a></td>
 197 <td class="colLast">&nbsp;</td>
 198 </tr>
 199 <tr class="altColor">
 200 <td class="colFirst"><a href="../../../compbio/data/sequence/RNAStructReader.RNAOut.html" title="enum in compbio.data.sequence">RNAStructReader.RNAOut</a></td>
 201 <td class="colLast">&nbsp;</td>
 202 </tr>
 203 <tr class="rowColor">
 204 <td class="colFirst"><a href="../../../compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></td>
 205 <td class="colLast">
 206 <div class="block">Enumeration defining two constraints for SMERFS columns score calculation.</div>
 207 </td>
 208 </tr>
 209 </tbody>
 210 </table>
 211 </li>
 212 <li class="blockList">
 213 <table class="typeSummary" border="0" cellpadding="3" cellspacing="0" summary="Exception Summary table, listing exceptions, and an explanation">
 214 <caption><span>Exception Summary</span><span class="tabEnd">&nbsp;</span></caption>
 215 <tr>
 216 <th class="colFirst" scope="col">Exception</th>
 217 <th class="colLast" scope="col">Description</th>
 218 </tr>
 219 <tbody>
 220 <tr class="altColor">
 221 <td class="colFirst"><a href="../../../compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></td>
 222 <td class="colLast">&nbsp;</td>
 223 </tr>
 224 </tbody>
 225 </table>
 226 </li>
 227 </ul>
 228 <a name="package.description">
 229 <!--   -->
 230 </a>
 231 <h2 title="Package compbio.data.sequence Description">Package compbio.data.sequence Description</h2>
 232 <div class="block">A data model for multiple sequence alignment web services and utility methods
 233  that work on the objects of this model.
 234  Classes in this package have no dependencies to other sources in the project.
 235  They form a base layer of JAva Bioinformatics Analysis Web Services.</div>
 236 <dl>
 237 <dt><span class="simpleTagLabel">Version:</span></dt>
 238 <dd>1.0     January 2010</dd>
 239 <dt><span class="simpleTagLabel">Author:</span></dt>
 240 <dd>Petr Troshin</dd>
 241 </dl>
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