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   6 <title>Uses of Package compbio.data.sequence</title>
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  72 <div class="header">
  73 <h1 title="Uses of Package compbio.data.sequence" class="title">Uses of Package<br>compbio.data.sequence</h1>
  74 </div>
  75 <div class="contentContainer">
  76 <ul class="blockList">
  77 <li class="blockList">
  78 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing packages, and an explanation">
  79 <caption><span>Packages that use <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></span><span class="tabEnd">&nbsp;</span></caption>
  80 <tr>
  81 <th class="colFirst" scope="col">Package</th>
  82 <th class="colLast" scope="col">Description</th>
  83 </tr>
  84 <tbody>
  85 <tr class="altColor">
  86 <td class="colFirst"><a href="#compbio.data.msa">compbio.data.msa</a></td>
  87 <td class="colLast">
  88 <div class="block">Web Service interfaces for JAva Bioinformatics Analysis Web Services.</div>
  89 </td>
  90 </tr>
  91 <tr class="rowColor">
  92 <td class="colFirst"><a href="#compbio.data.msa.jaxws">compbio.data.msa.jaxws</a></td>
  93 <td class="colLast">&nbsp;</td>
  94 </tr>
  95 <tr class="altColor">
  96 <td class="colFirst"><a href="#compbio.data.sequence">compbio.data.sequence</a></td>
  97 <td class="colLast">
  98 <div class="block">A data model for multiple sequence alignment web services and utility methods
  99  that work on the objects of this model.</div>
 100 </td>
 101 </tr>
 102 <tr class="rowColor">
 103 <td class="colFirst"><a href="#compbio.engine">compbio.engine</a></td>
 104 <td class="colLast">&nbsp;</td>
 105 </tr>
 106 <tr class="altColor">
 107 <td class="colFirst"><a href="#compbio.metadata">compbio.metadata</a></td>
 108 <td class="colLast">
 109 <div class="block">A meta-data model for multiple sequence alignment web services
 110  Classes in this package have no dependencies to other sources in the project.</div>
 111 </td>
 112 </tr>
 113 <tr class="rowColor">
 114 <td class="colFirst"><a href="#compbio.runner">compbio.runner</a></td>
 115 <td class="colLast">
 116 <div class="block">Utilities commonly used by all runners.</div>
 117 </td>
 118 </tr>
 119 <tr class="altColor">
 120 <td class="colFirst"><a href="#compbio.runner.conservation">compbio.runner.conservation</a></td>
 121 <td class="colLast">&nbsp;</td>
 122 </tr>
 123 <tr class="rowColor">
 124 <td class="colFirst"><a href="#compbio.runner.disorder">compbio.runner.disorder</a></td>
 125 <td class="colLast">&nbsp;</td>
 126 </tr>
 127 <tr class="altColor">
 128 <td class="colFirst"><a href="#compbio.runner.msa">compbio.runner.msa</a></td>
 129 <td class="colLast">
 130 <div class="block">Wrappers for native executables for multiple sequence alignment (msa)</div>
 131 </td>
 132 </tr>
 133 <tr class="rowColor">
 134 <td class="colFirst"><a href="#compbio.runner.structure">compbio.runner.structure</a></td>
 135 <td class="colLast">&nbsp;</td>
 136 </tr>
 137 <tr class="altColor">
 138 <td class="colFirst"><a href="#compbio.ws.client">compbio.ws.client</a></td>
 139 <td class="colLast">
 140 <div class="block">A command line client and web services testing client for
 141  JAva Bioinformatics Analysis Web Services.</div>
 142 </td>
 143 </tr>
 144 <tr class="rowColor">
 145 <td class="colFirst"><a href="#compbio.ws.server">compbio.ws.server</a></td>
 146 <td class="colLast">&nbsp;</td>
 147 </tr>
 148 </tbody>
 149 </table>
 150 </li>
 151 <li class="blockList"><a name="compbio.data.msa">
 152 <!--   -->
 153 </a>
 154 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 155 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/data/msa/package-summary.html">compbio.data.msa</a></span><span class="tabEnd">&nbsp;</span></caption>
 156 <tr>
 157 <th class="colOne" scope="col">Class and Description</th>
 158 </tr>
 159 <tbody>
 160 <tr class="altColor">
 161 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa">Alignment</a>
 162 <div class="block">Multiple sequence alignment.</div>
 163 </td>
 164 </tr>
 165 <tr class="rowColor">
 166 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa">FastaSequence</a>
 167 <div class="block">A FASTA formatted sequence.</div>
 168 </td>
 169 </tr>
 170 <tr class="altColor">
 171 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa">ScoreManager</a>&nbsp;</td>
 172 </tr>
 173 </tbody>
 174 </table>
 175 </li>
 176 <li class="blockList"><a name="compbio.data.msa.jaxws">
 177 <!--   -->
 178 </a>
 179 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 180 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/data/msa/jaxws/package-summary.html">compbio.data.msa.jaxws</a></span><span class="tabEnd">&nbsp;</span></caption>
 181 <tr>
 182 <th class="colOne" scope="col">Class and Description</th>
 183 </tr>
 184 <tbody>
 185 <tr class="altColor">
 186 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.msa.jaxws">Alignment</a>
 187 <div class="block">Multiple sequence alignment.</div>
 188 </td>
 189 </tr>
 190 <tr class="rowColor">
 191 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.msa.jaxws">FastaSequence</a>
 192 <div class="block">A FASTA formatted sequence.</div>
 193 </td>
 194 </tr>
 195 <tr class="altColor">
 196 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.msa.jaxws">ScoreManager</a>&nbsp;</td>
 197 </tr>
 198 </tbody>
 199 </table>
 200 </li>
 201 <li class="blockList"><a name="compbio.data.sequence">
 202 <!--   -->
 203 </a>
 204 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 205 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a></span><span class="tabEnd">&nbsp;</span></caption>
 206 <tr>
 207 <th class="colOne" scope="col">Class and Description</th>
 208 </tr>
 209 <tbody>
 210 <tr class="altColor">
 211 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Alignment.html#compbio.data.sequence">Alignment</a>
 212 <div class="block">Multiple sequence alignment.</div>
 213 </td>
 214 </tr>
 215 <tr class="rowColor">
 216 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/AlignmentMetadata.html#compbio.data.sequence">AlignmentMetadata</a>
 217 <div class="block">Alignment metadata e.g.</div>
 218 </td>
 219 </tr>
 220 <tr class="altColor">
 221 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ConservationMethod.html#compbio.data.sequence">ConservationMethod</a>
 222 <div class="block">Enumeration listing of all the supported methods.</div>
 223 </td>
 224 </tr>
 225 <tr class="rowColor">
 226 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/DisemblResult.html#compbio.data.sequence">DisemblResult</a>&nbsp;</td>
 227 </tr>
 228 <tr class="altColor">
 229 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/DisorderMethod.html#compbio.data.sequence">DisorderMethod</a>&nbsp;</td>
 230 </tr>
 231 <tr class="rowColor">
 232 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.data.sequence">FastaSequence</a>
 233 <div class="block">A FASTA formatted sequence.</div>
 234 </td>
 235 </tr>
 236 <tr class="altColor">
 237 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/GlobProtResult.html#compbio.data.sequence">GlobProtResult</a>&nbsp;</td>
 238 </tr>
 239 <tr class="rowColor">
 240 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/IUPredResult.html#compbio.data.sequence">IUPredResult</a>&nbsp;</td>
 241 </tr>
 242 <tr class="altColor">
 243 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Program.html#compbio.data.sequence">Program</a>
 244 <div class="block">The list of programmes that can produce alignments</div>
 245 </td>
 246 </tr>
 247 <tr class="rowColor">
 248 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Range.html#compbio.data.sequence">Range</a>&nbsp;</td>
 249 </tr>
 250 <tr class="altColor">
 251 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/RNAStructReader.AlifoldLine.html#compbio.data.sequence">RNAStructReader.AlifoldLine</a>&nbsp;</td>
 252 </tr>
 253 <tr class="rowColor">
 254 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/RNAStructReader.AlifoldResult.html#compbio.data.sequence">RNAStructReader.AlifoldResult</a>&nbsp;</td>
 255 </tr>
 256 <tr class="altColor">
 257 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/RNAStructReader.RNAOut.html#compbio.data.sequence">RNAStructReader.RNAOut</a>&nbsp;</td>
 258 </tr>
 259 <tr class="rowColor">
 260 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/RNAStructScoreManager.html#compbio.data.sequence">RNAStructScoreManager</a>&nbsp;</td>
 261 </tr>
 262 <tr class="altColor">
 263 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Score.html#compbio.data.sequence">Score</a>
 264 <div class="block">A value class for AACon annotation results storage.</div>
 265 </td>
 266 </tr>
 267 <tr class="rowColor">
 268 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.data.sequence">ScoreManager</a>&nbsp;</td>
 269 </tr>
 270 <tr class="altColor">
 271 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.ScoreHolder.html#compbio.data.sequence">ScoreManager.ScoreHolder</a>&nbsp;</td>
 272 </tr>
 273 <tr class="rowColor">
 274 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/SMERFSConstraints.html#compbio.data.sequence">SMERFSConstraints</a>
 275 <div class="block">Enumeration defining two constraints for SMERFS columns score calculation.</div>
 276 </td>
 277 </tr>
 278 <tr class="altColor">
 279 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.data.sequence">UnknownFileFormatException</a>&nbsp;</td>
 280 </tr>
 281 </tbody>
 282 </table>
 283 </li>
 284 <li class="blockList"><a name="compbio.engine">
 285 <!--   -->
 286 </a>
 287 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 288 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/engine/package-summary.html">compbio.engine</a></span><span class="tabEnd">&nbsp;</span></caption>
 289 <tr>
 290 <th class="colOne" scope="col">Class and Description</th>
 291 </tr>
 292 <tbody>
 293 <tr class="altColor">
 294 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.engine">FastaSequence</a>
 295 <div class="block">A FASTA formatted sequence.</div>
 296 </td>
 297 </tr>
 298 </tbody>
 299 </table>
 300 </li>
 301 <li class="blockList"><a name="compbio.metadata">
 302 <!--   -->
 303 </a>
 304 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 305 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/metadata/package-summary.html">compbio.metadata</a></span><span class="tabEnd">&nbsp;</span></caption>
 306 <tr>
 307 <th class="colOne" scope="col">Class and Description</th>
 308 </tr>
 309 <tbody>
 310 <tr class="altColor">
 311 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.metadata">FastaSequence</a>
 312 <div class="block">A FASTA formatted sequence.</div>
 313 </td>
 314 </tr>
 315 </tbody>
 316 </table>
 317 </li>
 318 <li class="blockList"><a name="compbio.runner">
 319 <!--   -->
 320 </a>
 321 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 322 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/runner/package-summary.html">compbio.runner</a></span><span class="tabEnd">&nbsp;</span></caption>
 323 <tr>
 324 <th class="colOne" scope="col">Class and Description</th>
 325 </tr>
 326 <tbody>
 327 <tr class="altColor">
 328 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner">Alignment</a>
 329 <div class="block">Multiple sequence alignment.</div>
 330 </td>
 331 </tr>
 332 <tr class="rowColor">
 333 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.runner">FastaSequence</a>
 334 <div class="block">A FASTA formatted sequence.</div>
 335 </td>
 336 </tr>
 337 <tr class="altColor">
 338 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/RNAStructScoreManager.html#compbio.runner">RNAStructScoreManager</a>&nbsp;</td>
 339 </tr>
 340 <tr class="rowColor">
 341 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Score.html#compbio.runner">Score</a>
 342 <div class="block">A value class for AACon annotation results storage.</div>
 343 </td>
 344 </tr>
 345 <tr class="altColor">
 346 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/UnknownFileFormatException.html#compbio.runner">UnknownFileFormatException</a>&nbsp;</td>
 347 </tr>
 348 </tbody>
 349 </table>
 350 </li>
 351 <li class="blockList"><a name="compbio.runner.conservation">
 352 <!--   -->
 353 </a>
 354 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 355 <caption><span>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></span><span class="tabEnd">&nbsp;</span></caption>
 356 <tr>
 357 <th class="colOne" scope="col">Class and Description</th>
 358 </tr>
 359 <tbody>
 360 <tr class="altColor">
 361 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.conservation">ScoreManager</a>&nbsp;</td>
 362 </tr>
 363 </tbody>
 364 </table>
 365 </li>
 366 <li class="blockList"><a name="compbio.runner.disorder">
 367 <!--   -->
 368 </a>
 369 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 370 <caption><span>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></span><span class="tabEnd">&nbsp;</span></caption>
 371 <tr>
 372 <th class="colOne" scope="col">Class and Description</th>
 373 </tr>
 374 <tbody>
 375 <tr class="altColor">
 376 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Score.html#compbio.runner.disorder">Score</a>
 377 <div class="block">A value class for AACon annotation results storage.</div>
 378 </td>
 379 </tr>
 380 <tr class="rowColor">
 381 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.runner.disorder">ScoreManager</a>&nbsp;</td>
 382 </tr>
 383 </tbody>
 384 </table>
 385 </li>
 386 <li class="blockList"><a name="compbio.runner.msa">
 387 <!--   -->
 388 </a>
 389 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 390 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/runner/msa/package-summary.html">compbio.runner.msa</a></span><span class="tabEnd">&nbsp;</span></caption>
 391 <tr>
 392 <th class="colOne" scope="col">Class and Description</th>
 393 </tr>
 394 <tbody>
 395 <tr class="altColor">
 396 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Alignment.html#compbio.runner.msa">Alignment</a>
 397 <div class="block">Multiple sequence alignment.</div>
 398 </td>
 399 </tr>
 400 </tbody>
 401 </table>
 402 </li>
 403 <li class="blockList"><a name="compbio.runner.structure">
 404 <!--   -->
 405 </a>
 406 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 407 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/runner/structure/package-summary.html">compbio.runner.structure</a></span><span class="tabEnd">&nbsp;</span></caption>
 408 <tr>
 409 <th class="colOne" scope="col">Class and Description</th>
 410 </tr>
 411 <tbody>
 412 <tr class="altColor">
 413 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/RNAStructScoreManager.html#compbio.runner.structure">RNAStructScoreManager</a>&nbsp;</td>
 414 </tr>
 415 </tbody>
 416 </table>
 417 </li>
 418 <li class="blockList"><a name="compbio.ws.client">
 419 <!--   -->
 420 </a>
 421 <table class="useSummary" border="0" cellpadding="3" cellspacing="0" summary="Use table, listing classes, and an explanation">
 422 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/ws/client/package-summary.html">compbio.ws.client</a></span><span class="tabEnd">&nbsp;</span></caption>
 423 <tr>
 424 <th class="colOne" scope="col">Class and Description</th>
 425 </tr>
 426 <tbody>
 427 <tr class="altColor">
 428 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Alignment.html#compbio.ws.client">Alignment</a>
 429 <div class="block">Multiple sequence alignment.</div>
 430 </td>
 431 </tr>
 432 <tr class="rowColor">
 433 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.ws.client">FastaSequence</a>
 434 <div class="block">A FASTA formatted sequence.</div>
 435 </td>
 436 </tr>
 437 <tr class="altColor">
 438 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.ws.client">ScoreManager</a>&nbsp;</td>
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 447 <caption><span>Classes in <a href="../../../compbio/data/sequence/package-summary.html">compbio.data.sequence</a> used by <a href="../../../compbio/ws/server/package-summary.html">compbio.ws.server</a></span><span class="tabEnd">&nbsp;</span></caption>
 448 <tr>
 449 <th class="colOne" scope="col">Class and Description</th>
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 452 <tr class="altColor">
 453 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/Alignment.html#compbio.ws.server">Alignment</a>
 454 <div class="block">Multiple sequence alignment.</div>
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 458 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/FastaSequence.html#compbio.ws.server">FastaSequence</a>
 459 <div class="block">A FASTA formatted sequence.</div>
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 463 <td class="colOne"><a href="../../../compbio/data/sequence/class-use/ScoreManager.html#compbio.ws.server">ScoreManager</a>&nbsp;</td>
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