website/docs/full_javadoc/constant-values.html

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   6 <title>Constant Field Values</title>
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  72 <div class="header">
  73 <h1 title="Constant Field Values" class="title">Constant Field Values</h1>
  74 <h2 title="Contents">Contents</h2>
  75 <ul>
  76 <li><a href="#compbio.data">compbio.data.*</a></li>
  77 <li><a href="#compbio.engine">compbio.engine.*</a></li>
  78 <li><a href="#compbio.metadata">compbio.metadata.*</a></li>
  79 <li><a href="#compbio.runner">compbio.runner.*</a></li>
  80 <li><a href="#compbio.stat">compbio.stat.*</a></li>
  81 <li><a href="#compbio.ws">compbio.ws.*</a></li>
  82 </ul>
  83 </div>
  84 <div class="constantValuesContainer"><a name="compbio.data">
  85 <!--   -->
  86 </a>
  87 <h2 title="compbio.data">compbio.data.*</h2>
  88 <ul class="blockList">
  89 <li class="blockList">
  90 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
  91 <caption><span>compbio.data.msa.<a href="compbio/data/msa/Category.html" title="class in compbio.data.msa">Category</a></span><span class="tabEnd">&nbsp;</span></caption>
  92 <tr>
  93 <th class="colFirst" scope="col">Modifier and Type</th>
  94 <th scope="col">Constant Field</th>
  95 <th class="colLast" scope="col">Value</th>
  96 </tr>
  97 <tbody>
  98 <tr class="altColor">
  99 <td class="colFirst"><a name="compbio.data.msa.Category.CATEGORY_ALIGNMENT">
 100 <!--   -->
 101 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 102 <td><code><a href="compbio/data/msa/Category.html#CATEGORY_ALIGNMENT">CATEGORY_ALIGNMENT</a></code></td>
 103 <td class="colLast"><code>"Alignment"</code></td>
 104 </tr>
 105 <tr class="rowColor">
 106 <td class="colFirst"><a name="compbio.data.msa.Category.CATEGORY_CONSERVATION">
 107 <!--   -->
 108 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 109 <td><code><a href="compbio/data/msa/Category.html#CATEGORY_CONSERVATION">CATEGORY_CONSERVATION</a></code></td>
 110 <td class="colLast"><code>"Conservation"</code></td>
 111 </tr>
 112 <tr class="altColor">
 113 <td class="colFirst"><a name="compbio.data.msa.Category.CATEGORY_DISORDER">
 114 <!--   -->
 115 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 116 <td><code><a href="compbio/data/msa/Category.html#CATEGORY_DISORDER">CATEGORY_DISORDER</a></code></td>
 117 <td class="colLast"><code>"Protein Disorder"</code></td>
 118 </tr>
 119 <tr class="rowColor">
 120 <td class="colFirst"><a name="compbio.data.msa.Category.CATEGORY_PREDICTION">
 121 <!--   -->
 122 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 123 <td><code><a href="compbio/data/msa/Category.html#CATEGORY_PREDICTION">CATEGORY_PREDICTION</a></code></td>
 124 <td class="colLast"><code>"Prediction"</code></td>
 125 </tr>
 126 </tbody>
 127 </table>
 128 </li>
 129 <li class="blockList">
 130 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 131 <caption><span>compbio.data.msa.<a href="compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a></span><span class="tabEnd">&nbsp;</span></caption>
 132 <tr>
 133 <th class="colFirst" scope="col">Modifier and Type</th>
 134 <th scope="col">Constant Field</th>
 135 <th class="colLast" scope="col">Value</th>
 136 </tr>
 137 <tbody>
 138 <tr class="altColor">
 139 <td class="colFirst"><a name="compbio.data.msa.JABAService.JABAWS_VERSION">
 140 <!--   -->
 141 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 142 <td><code><a href="compbio/data/msa/JABAService.html#JABAWS_VERSION">JABAWS_VERSION</a></code></td>
 143 <td class="colLast"><code>"2.1"</code></td>
 144 </tr>
 145 <tr class="rowColor">
 146 <td class="colFirst"><a name="compbio.data.msa.JABAService.SERVICE_NAMESPACE">
 147 <!--   -->
 148 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 149 <td><code><a href="compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</a></code></td>
 150 <td class="colLast"><code>"http://msa.data.compbio/01/01/2010/"</code></td>
 151 </tr>
 152 <tr class="altColor">
 153 <td class="colFirst"><a name="compbio.data.msa.JABAService.V2_SERVICE_NAMESPACE">
 154 <!--   -->
 155 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 156 <td><code><a href="compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</a></code></td>
 157 <td class="colLast"><code>"http://msa.data.compbio/01/12/2010/"</code></td>
 158 </tr>
 159 <tr class="rowColor">
 160 <td class="colFirst"><a name="compbio.data.msa.JABAService.V3_SERVICE_NAMESPACE">
 161 <!--   -->
 162 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 163 <td><code><a href="compbio/data/msa/JABAService.html#V3_SERVICE_NAMESPACE">V3_SERVICE_NAMESPACE</a></code></td>
 164 <td class="colLast"><code>"http://msa.data.compbio/01/12/2013/"</code></td>
 165 </tr>
 166 </tbody>
 167 </table>
 168 </li>
 169 </ul>
 170 <ul class="blockList">
 171 <li class="blockList">
 172 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 173 <caption><span>compbio.data.sequence.<a href="compbio/data/sequence/ClustalAlignmentUtil.html" title="class in compbio.data.sequence">ClustalAlignmentUtil</a></span><span class="tabEnd">&nbsp;</span></caption>
 174 <tr>
 175 <th class="colFirst" scope="col">Modifier and Type</th>
 176 <th scope="col">Constant Field</th>
 177 <th class="colLast" scope="col">Value</th>
 178 </tr>
 179 <tbody>
 180 <tr class="altColor">
 181 <td class="colFirst"><a name="compbio.data.sequence.ClustalAlignmentUtil.gapchar">
 182 <!--   -->
 183 </a><code>public&nbsp;static&nbsp;final&nbsp;char</code></td>
 184 <td><code><a href="compbio/data/sequence/ClustalAlignmentUtil.html#gapchar">gapchar</a></code></td>
 185 <td class="colLast"><code>45</code></td>
 186 </tr>
 187 <tr class="rowColor">
 188 <td class="colFirst"><a name="compbio.data.sequence.ClustalAlignmentUtil.maxNameLength">
 189 <!--   -->
 190 </a><code>private&nbsp;static&nbsp;final&nbsp;int</code></td>
 191 <td><code><a href="compbio/data/sequence/ClustalAlignmentUtil.html#maxNameLength">maxNameLength</a></code></td>
 192 <td class="colLast"><code>30</code></td>
 193 </tr>
 194 <tr class="altColor">
 195 <td class="colFirst"><a name="compbio.data.sequence.ClustalAlignmentUtil.minNameHolderLength">
 196 <!--   -->
 197 </a><code>private&nbsp;static&nbsp;final&nbsp;int</code></td>
 198 <td><code><a href="compbio/data/sequence/ClustalAlignmentUtil.html#minNameHolderLength">minNameHolderLength</a></code></td>
 199 <td class="colLast"><code>10</code></td>
 200 </tr>
 201 <tr class="rowColor">
 202 <td class="colFirst"><a name="compbio.data.sequence.ClustalAlignmentUtil.oneLineAlignmentLength">
 203 <!--   -->
 204 </a><code>private&nbsp;static&nbsp;final&nbsp;int</code></td>
 205 <td><code><a href="compbio/data/sequence/ClustalAlignmentUtil.html#oneLineAlignmentLength">oneLineAlignmentLength</a></code></td>
 206 <td class="colLast"><code>60</code></td>
 207 </tr>
 208 <tr class="altColor">
 209 <td class="colFirst"><a name="compbio.data.sequence.ClustalAlignmentUtil.spacer">
 210 <!--   -->
 211 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 212 <td><code><a href="compbio/data/sequence/ClustalAlignmentUtil.html#spacer">spacer</a></code></td>
 213 <td class="colLast"><code>"      "</code></td>
 214 </tr>
 215 </tbody>
 216 </table>
 217 </li>
 218 <li class="blockList">
 219 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 220 <caption><span>compbio.data.sequence.<a href="compbio/data/sequence/FastaReader.html" title="class in compbio.data.sequence">FastaReader</a></span><span class="tabEnd">&nbsp;</span></caption>
 221 <tr>
 222 <th class="colFirst" scope="col">Modifier and Type</th>
 223 <th scope="col">Constant Field</th>
 224 <th class="colLast" scope="col">Value</th>
 225 </tr>
 226 <tbody>
 227 <tr class="altColor">
 228 <td class="colFirst"><a name="compbio.data.sequence.FastaReader.DELIM">
 229 <!--   -->
 230 </a><code>private&nbsp;final&nbsp;java.lang.String</code></td>
 231 <td><code><a href="compbio/data/sequence/FastaReader.html#DELIM">DELIM</a></code></td>
 232 <td class="colLast"><code>"&gt;"</code></td>
 233 </tr>
 234 </tbody>
 235 </table>
 236 </li>
 237 <li class="blockList">
 238 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 239 <caption><span>compbio.data.sequence.<a href="compbio/data/sequence/ScoreManager.html" title="class in compbio.data.sequence">ScoreManager</a></span><span class="tabEnd">&nbsp;</span></caption>
 240 <tr>
 241 <th class="colFirst" scope="col">Modifier and Type</th>
 242 <th scope="col">Constant Field</th>
 243 <th class="colLast" scope="col">Value</th>
 244 </tr>
 245 <tbody>
 246 <tr class="altColor">
 247 <td class="colFirst"><a name="compbio.data.sequence.ScoreManager.SINGLE_ENTRY_KEY">
 248 <!--   -->
 249 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 250 <td><code><a href="compbio/data/sequence/ScoreManager.html#SINGLE_ENTRY_KEY">SINGLE_ENTRY_KEY</a></code></td>
 251 <td class="colLast"><code>"Alignment"</code></td>
 252 </tr>
 253 </tbody>
 254 </table>
 255 </li>
 256 <li class="blockList">
 257 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 258 <caption><span>compbio.data.sequence.<a href="compbio/data/sequence/SequenceUtil.html" title="class in compbio.data.sequence">SequenceUtil</a></span><span class="tabEnd">&nbsp;</span></caption>
 259 <tr>
 260 <th class="colFirst" scope="col">Modifier and Type</th>
 261 <th scope="col">Constant Field</th>
 262 <th class="colLast" scope="col">Value</th>
 263 </tr>
 264 <tbody>
 265 <tr class="altColor">
 266 <td class="colFirst"><a name="compbio.data.sequence.SequenceUtil.JRONN_WRONG_FORMAT_MESSAGE">
 267 <!--   -->
 268 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 269 <td><code><a href="compbio/data/sequence/SequenceUtil.html#JRONN_WRONG_FORMAT_MESSAGE">JRONN_WRONG_FORMAT_MESSAGE</a></code></td>
 270 <td class="colLast"><code>"Jronn file must be in the following format:\n&gt;sequence_name\n M\tV\tS\n0.43\t0.22\t0.65\nWhere first line is the sequence name,\nsecond line is the tab delimited sequence,\nthird line contains tab delimited disorder prediction values.\nNo lines are allowed between these three. Additionally, the number of  sequence residues must be equal to the number of the disorder values."</code></td>
 271 </tr>
 272 </tbody>
 273 </table>
 274 </li>
 275 <li class="blockList">
 276 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 277 <caption><span>compbio.data.sequence.<a href="compbio/data/sequence/SMERFSConstraints.html" title="enum in compbio.data.sequence">SMERFSConstraints</a></span><span class="tabEnd">&nbsp;</span></caption>
 278 <tr>
 279 <th class="colFirst" scope="col">Modifier and Type</th>
 280 <th scope="col">Constant Field</th>
 281 <th class="colLast" scope="col">Value</th>
 282 </tr>
 283 <tbody>
 284 <tr class="altColor">
 285 <td class="colFirst"><a name="compbio.data.sequence.SMERFSConstraints.DEFAULT_GAP_THRESHOLD">
 286 <!--   -->
 287 </a><code>public&nbsp;static&nbsp;final&nbsp;double</code></td>
 288 <td><code><a href="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_GAP_THRESHOLD">DEFAULT_GAP_THRESHOLD</a></code></td>
 289 <td class="colLast"><code>0.1</code></td>
 290 </tr>
 291 <tr class="rowColor">
 292 <td class="colFirst"><a name="compbio.data.sequence.SMERFSConstraints.DEFAULT_WINDOW_SIZE">
 293 <!--   -->
 294 </a><code>public&nbsp;static&nbsp;final&nbsp;int</code></td>
 295 <td><code><a href="compbio/data/sequence/SMERFSConstraints.html#DEFAULT_WINDOW_SIZE">DEFAULT_WINDOW_SIZE</a></code></td>
 296 <td class="colLast"><code>7</code></td>
 297 </tr>
 298 </tbody>
 299 </table>
 300 </li>
 301 <li class="blockList">
 302 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 303 <caption><span>compbio.data.sequence.<a href="compbio/data/sequence/UnknownFileFormatException.html" title="class in compbio.data.sequence">UnknownFileFormatException</a></span><span class="tabEnd">&nbsp;</span></caption>
 304 <tr>
 305 <th class="colFirst" scope="col">Modifier and Type</th>
 306 <th scope="col">Constant Field</th>
 307 <th class="colLast" scope="col">Value</th>
 308 </tr>
 309 <tbody>
 310 <tr class="altColor">
 311 <td class="colFirst"><a name="compbio.data.sequence.UnknownFileFormatException.serialVersionUID">
 312 <!--   -->
 313 </a><code>private&nbsp;static&nbsp;final&nbsp;long</code></td>
 314 <td><code><a href="compbio/data/sequence/UnknownFileFormatException.html#serialVersionUID">serialVersionUID</a></code></td>
 315 <td class="colLast"><code>196629543695636854L</code></td>
 316 </tr>
 317 </tbody>
 318 </table>
 319 </li>
 320 </ul>
 321 <a name="compbio.engine">
 322 <!--   -->
 323 </a>
 324 <h2 title="compbio.engine">compbio.engine.*</h2>
 325 <ul class="blockList">
 326 <li class="blockList">
 327 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 328 <caption><span>compbio.engine.client.compbio.engine.client.CommandBuilder.Parameter</span><span class="tabEnd">&nbsp;</span></caption>
 329 <tr>
 330 <th class="colFirst" scope="col">Modifier and Type</th>
 331 <th scope="col">Constant Field</th>
 332 <th class="colLast" scope="col">Value</th>
 333 </tr>
 334 <tbody>
 335 <tr class="altColor">
 336 <td class="colFirst"><a name="compbio.engine.client.CommandBuilder.Parameter.FIRST">
 337 <!--   -->
 338 </a><code>private&nbsp;static&nbsp;final&nbsp;int</code></td>
 339 <td><code><a href="compbio/engine/client/CommandBuilder.Parameter.html#FIRST">FIRST</a></code></td>
 340 <td class="colLast"><code>-200</code></td>
 341 </tr>
 342 <tr class="rowColor">
 343 <td class="colFirst"><a name="compbio.engine.client.CommandBuilder.Parameter.LAST">
 344 <!--   -->
 345 </a><code>private&nbsp;static&nbsp;final&nbsp;int</code></td>
 346 <td><code><a href="compbio/engine/client/CommandBuilder.Parameter.html#LAST">LAST</a></code></td>
 347 <td class="colLast"><code>-100</code></td>
 348 </tr>
 349 </tbody>
 350 </table>
 351 </li>
 352 <li class="blockList">
 353 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 354 <caption><span>compbio.engine.client.<a href="compbio/engine/client/ConfExecutable.html" title="class in compbio.engine.client">ConfExecutable</a>&lt;<a href="compbio/engine/client/ConfExecutable.html" title="type parameter in ConfExecutable">T</a>&gt;</span><span class="tabEnd">&nbsp;</span></caption>
 355 <tr>
 356 <th class="colFirst" scope="col">Modifier and Type</th>
 357 <th scope="col">Constant Field</th>
 358 <th class="colLast" scope="col">Value</th>
 359 </tr>
 360 <tbody>
 361 <tr class="altColor">
 362 <td class="colFirst"><a name="compbio.engine.client.ConfExecutable.CLUSTER_TASK_ID_PREFIX">
 363 <!--   -->
 364 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 365 <td><code><a href="compbio/engine/client/ConfExecutable.html#CLUSTER_TASK_ID_PREFIX">CLUSTER_TASK_ID_PREFIX</a></code></td>
 366 <td class="colLast"><code>"@"</code></td>
 367 </tr>
 368 </tbody>
 369 </table>
 370 </li>
 371 <li class="blockList">
 372 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 373 <caption><span>compbio.engine.client.<a href="compbio/engine/client/EnvVariableProcessor.html" title="class in compbio.engine.client">EnvVariableProcessor</a></span><span class="tabEnd">&nbsp;</span></caption>
 374 <tr>
 375 <th class="colFirst" scope="col">Modifier and Type</th>
 376 <th scope="col">Constant Field</th>
 377 <th class="colLast" scope="col">Value</th>
 378 </tr>
 379 <tbody>
 380 <tr class="altColor">
 381 <td class="colFirst"><a name="compbio.engine.client.EnvVariableProcessor.fasta4mafft">
 382 <!--   -->
 383 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 384 <td><code><a href="compbio/engine/client/EnvVariableProcessor.html#fasta4mafft">fasta4mafft</a></code></td>
 385 <td class="colLast"><code>"FASTA_4_MAFFT"</code></td>
 386 </tr>
 387 <tr class="rowColor">
 388 <td class="colFirst"><a name="compbio.engine.client.EnvVariableProcessor.iupred_path">
 389 <!--   -->
 390 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 391 <td><code><a href="compbio/engine/client/EnvVariableProcessor.html#iupred_path">iupred_path</a></code></td>
 392 <td class="colLast"><code>"IUPred_PATH"</code></td>
 393 </tr>
 394 <tr class="altColor">
 395 <td class="colFirst"><a name="compbio.engine.client.EnvVariableProcessor.mafft_binaries">
 396 <!--   -->
 397 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 398 <td><code><a href="compbio/engine/client/EnvVariableProcessor.html#mafft_binaries">mafft_binaries</a></code></td>
 399 <td class="colLast"><code>"MAFFT_BINARIES"</code></td>
 400 </tr>
 401 <tr class="rowColor">
 402 <td class="colFirst"><a name="compbio.engine.client.EnvVariableProcessor.NEXT_ENV_PROPERTY_DELIMITER">
 403 <!--   -->
 404 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 405 <td><code><a href="compbio/engine/client/EnvVariableProcessor.html#NEXT_ENV_PROPERTY_DELIMITER">NEXT_ENV_PROPERTY_DELIMITER</a></code></td>
 406 <td class="colLast"><code>";"</code></td>
 407 </tr>
 408 <tr class="altColor">
 409 <td class="colFirst"><a name="compbio.engine.client.EnvVariableProcessor.PATH">
 410 <!--   -->
 411 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 412 <td><code><a href="compbio/engine/client/EnvVariableProcessor.html#PATH">PATH</a></code></td>
 413 <td class="colLast"><code>"PATH"</code></td>
 414 </tr>
 415 <tr class="rowColor">
 416 <td class="colFirst"><a name="compbio.engine.client.EnvVariableProcessor.PROP_NAME_VALUE_SEPARATOR">
 417 <!--   -->
 418 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 419 <td><code><a href="compbio/engine/client/EnvVariableProcessor.html#PROP_NAME_VALUE_SEPARATOR">PROP_NAME_VALUE_SEPARATOR</a></code></td>
 420 <td class="colLast"><code>"#"</code></td>
 421 </tr>
 422 </tbody>
 423 </table>
 424 </li>
 425 <li class="blockList">
 426 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
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 428 <tr>
 429 <th class="colFirst" scope="col">Modifier and Type</th>
 430 <th scope="col">Constant Field</th>
 431 <th class="colLast" scope="col">Value</th>
 432 </tr>
 433 <tbody>
 434 <tr class="altColor">
 435 <td class="colFirst"><a name="compbio.engine.client.RunConfiguration.rconfigFile">
 436 <!--   -->
 437 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 438 <td><code><a href="compbio/engine/client/RunConfiguration.html#rconfigFile">rconfigFile</a></code></td>
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 440 </tr>
 441 </tbody>
 442 </table>
 443 </li>
 444 <li class="blockList">
 445 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
 446 <caption><span>compbio.engine.client.<a href="compbio/engine/client/SkeletalExecutable.html" title="class in compbio.engine.client">SkeletalExecutable</a>&lt;<a href="compbio/engine/client/SkeletalExecutable.html" title="type parameter in SkeletalExecutable">T</a>&gt;</span><span class="tabEnd">&nbsp;</span></caption>
 447 <tr>
 448 <th class="colFirst" scope="col">Modifier and Type</th>
 449 <th scope="col">Constant Field</th>
 450 <th class="colLast" scope="col">Value</th>
 451 </tr>
 452 <tbody>
 453 <tr class="altColor">
 454 <td class="colFirst"><a name="compbio.engine.client.SkeletalExecutable.ERROR">
 455 <!--   -->
 456 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 457 <td><code><a href="compbio/engine/client/SkeletalExecutable.html#ERROR">ERROR</a></code></td>
 458 <td class="colLast"><code>"error.txt"</code></td>
 459 </tr>
 460 <tr class="rowColor">
 461 <td class="colFirst"><a name="compbio.engine.client.SkeletalExecutable.INPUT">
 462 <!--   -->
 463 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 464 <td><code><a href="compbio/engine/client/SkeletalExecutable.html#INPUT">INPUT</a></code></td>
 465 <td class="colLast"><code>"input.txt"</code></td>
 466 </tr>
 467 <tr class="altColor">
 468 <td class="colFirst"><a name="compbio.engine.client.SkeletalExecutable.OUTPUT">
 469 <!--   -->
 470 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 471 <td><code><a href="compbio/engine/client/SkeletalExecutable.html#OUTPUT">OUTPUT</a></code></td>
 472 <td class="colLast"><code>"result.txt"</code></td>
 473 </tr>
 474 </tbody>
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 476 </li>
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 478 <ul class="blockList">
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 482 <tr>
 483 <th class="colFirst" scope="col">Modifier and Type</th>
 484 <th scope="col">Constant Field</th>
 485 <th class="colLast" scope="col">Value</th>
 486 </tr>
 487 <tbody>
 488 <tr class="altColor">
 489 <td class="colFirst"><a name="compbio.engine.cluster.drmaa.ClusterSession.JOBID">
 490 <!--   -->
 491 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 492 <td><code><a href="compbio/engine/cluster/drmaa/ClusterSession.html#JOBID">JOBID</a></code></td>
 493 <td class="colLast"><code>"JOBID"</code></td>
 494 </tr>
 495 </tbody>
 496 </table>
 497 </li>
 498 </ul>
 499 <ul class="blockList">
 500 <li class="blockList">
 501 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
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 503 <tr>
 504 <th class="colFirst" scope="col">Modifier and Type</th>
 505 <th scope="col">Constant Field</th>
 506 <th class="colLast" scope="col">Value</th>
 507 </tr>
 508 <tbody>
 509 <tr class="altColor">
 510 <td class="colFirst"><a name="compbio.engine.conf.DirectoryManager.DELIM">
 511 <!--   -->
 512 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 513 <td><code><a href="compbio/engine/conf/DirectoryManager.html#DELIM">DELIM</a></code></td>
 514 <td class="colLast"><code>"#"</code></td>
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 516 </tbody>
 517 </table>
 518 </li>
 519 </ul>
 520 <ul class="blockList">
 521 <li class="blockList">
 522 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
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 524 <tr>
 525 <th class="colFirst" scope="col">Modifier and Type</th>
 526 <th scope="col">Constant Field</th>
 527 <th class="colLast" scope="col">Value</th>
 528 </tr>
 529 <tbody>
 530 <tr class="altColor">
 531 <td class="colFirst"><a name="compbio.engine.local.ExecutableWrapper.PROC_ERR_FILE">
 532 <!--   -->
 533 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 534 <td><code><a href="compbio/engine/local/ExecutableWrapper.html#PROC_ERR_FILE">PROC_ERR_FILE</a></code></td>
 535 <td class="colLast"><code>"procError.txt"</code></td>
 536 </tr>
 537 <tr class="rowColor">
 538 <td class="colFirst"><a name="compbio.engine.local.ExecutableWrapper.PROC_IN_FILE">
 539 <!--   -->
 540 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 541 <td><code><a href="compbio/engine/local/ExecutableWrapper.html#PROC_IN_FILE">PROC_IN_FILE</a></code></td>
 542 <td class="colLast"><code>"procInput.txt"</code></td>
 543 </tr>
 544 <tr class="altColor">
 545 <td class="colFirst"><a name="compbio.engine.local.ExecutableWrapper.PROC_OUT_FILE">
 546 <!--   -->
 547 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 548 <td><code><a href="compbio/engine/local/ExecutableWrapper.html#PROC_OUT_FILE">PROC_OUT_FILE</a></code></td>
 549 <td class="colLast"><code>"procOutput.txt"</code></td>
 550 </tr>
 551 </tbody>
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 557 <tr>
 558 <th class="colFirst" scope="col">Modifier and Type</th>
 559 <th scope="col">Constant Field</th>
 560 <th class="colLast" scope="col">Value</th>
 561 </tr>
 562 <tbody>
 563 <tr class="altColor">
 564 <td class="colFirst"><a name="compbio.engine.local.LocalExecutorService.threadNumPropName">
 565 <!--   -->
 566 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 567 <td><code><a href="compbio/engine/local/LocalExecutorService.html#threadNumPropName">threadNumPropName</a></code></td>
 568 <td class="colLast"><code>"engine.local.thread.number"</code></td>
 569 </tr>
 570 </tbody>
 571 </table>
 572 </li>
 573 </ul>
 574 <a name="compbio.metadata">
 575 <!--   -->
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 577 <h2 title="compbio.metadata">compbio.metadata.*</h2>
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 582 <tr>
 583 <th class="colFirst" scope="col">Modifier and Type</th>
 584 <th scope="col">Constant Field</th>
 585 <th class="colLast" scope="col">Value</th>
 586 </tr>
 587 <tbody>
 588 <tr class="altColor">
 589 <td class="colFirst"><a name="compbio.metadata.JobExecutionException.serialVersionUID">
 590 <!--   -->
 591 </a><code>private&nbsp;static&nbsp;final&nbsp;long</code></td>
 592 <td><code><a href="compbio/metadata/JobExecutionException.html#serialVersionUID">serialVersionUID</a></code></td>
 593 <td class="colLast"><code>-5477751361755778769L</code></td>
 594 </tr>
 595 </tbody>
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 598 <li class="blockList">
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 600 <caption><span>compbio.metadata.<a href="compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></span><span class="tabEnd">&nbsp;</span></caption>
 601 <tr>
 602 <th class="colFirst" scope="col">Modifier and Type</th>
 603 <th scope="col">Constant Field</th>
 604 <th class="colLast" scope="col">Value</th>
 605 </tr>
 606 <tbody>
 607 <tr class="altColor">
 608 <td class="colFirst"><a name="compbio.metadata.JobSubmissionException.serialVersionUID">
 609 <!--   -->
 610 </a><code>private&nbsp;static&nbsp;final&nbsp;long</code></td>
 611 <td><code><a href="compbio/metadata/JobSubmissionException.html#serialVersionUID">serialVersionUID</a></code></td>
 612 <td class="colLast"><code>607986894357895572L</code></td>
 613 </tr>
 614 </tbody>
 615 </table>
 616 </li>
 617 <li class="blockList">
 618 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
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 620 <tr>
 621 <th class="colFirst" scope="col">Modifier and Type</th>
 622 <th scope="col">Constant Field</th>
 623 <th class="colLast" scope="col">Value</th>
 624 </tr>
 625 <tbody>
 626 <tr class="altColor">
 627 <td class="colFirst"><a name="compbio.metadata.LimitExceededException.serialVersionUID">
 628 <!--   -->
 629 </a><code>private&nbsp;static&nbsp;final&nbsp;long</code></td>
 630 <td><code><a href="compbio/metadata/LimitExceededException.html#serialVersionUID">serialVersionUID</a></code></td>
 631 <td class="colLast"><code>15066952180013505L</code></td>
 632 </tr>
 633 </tbody>
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 636 <li class="blockList">
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 639 <tr>
 640 <th class="colFirst" scope="col">Modifier and Type</th>
 641 <th scope="col">Constant Field</th>
 642 <th class="colLast" scope="col">Value</th>
 643 </tr>
 644 <tbody>
 645 <tr class="altColor">
 646 <td class="colFirst"><a name="compbio.metadata.Preset.SPACE">
 647 <!--   -->
 648 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 649 <td><code><a href="compbio/metadata/Preset.html#SPACE">SPACE</a></code></td>
 650 <td class="colLast"><code>" "</code></td>
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 655 <li class="blockList">
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 658 <tr>
 659 <th class="colFirst" scope="col">Modifier and Type</th>
 660 <th scope="col">Constant Field</th>
 661 <th class="colLast" scope="col">Value</th>
 662 </tr>
 663 <tbody>
 664 <tr class="altColor">
 665 <td class="colFirst"><a name="compbio.metadata.PresetManager.LOCAL_ENGINE_LIMIT_PRESET">
 666 <!--   -->
 667 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 668 <td><code><a href="compbio/metadata/PresetManager.html#LOCAL_ENGINE_LIMIT_PRESET">LOCAL_ENGINE_LIMIT_PRESET</a></code></td>
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 677 <tr>
 678 <th class="colFirst" scope="col">Modifier and Type</th>
 679 <th scope="col">Constant Field</th>
 680 <th class="colLast" scope="col">Value</th>
 681 </tr>
 682 <tbody>
 683 <tr class="altColor">
 684 <td class="colFirst"><a name="compbio.metadata.ResultNotAvailableException.serialVersionUID">
 685 <!--   -->
 686 </a><code>private&nbsp;static&nbsp;final&nbsp;long</code></td>
 687 <td><code><a href="compbio/metadata/ResultNotAvailableException.html#serialVersionUID">serialVersionUID</a></code></td>
 688 <td class="colLast"><code>-5475613614578761L</code></td>
 689 </tr>
 690 </tbody>
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 696 <tr>
 697 <th class="colFirst" scope="col">Modifier and Type</th>
 698 <th scope="col">Constant Field</th>
 699 <th class="colLast" scope="col">Value</th>
 700 </tr>
 701 <tbody>
 702 <tr class="altColor">
 703 <td class="colFirst"><a name="compbio.metadata.UnsupportedRuntimeException.serialVersionUID">
 704 <!--   -->
 705 </a><code>private&nbsp;static&nbsp;final&nbsp;long</code></td>
 706 <td><code><a href="compbio/metadata/UnsupportedRuntimeException.html#serialVersionUID">serialVersionUID</a></code></td>
 707 <td class="colLast"><code>-86624836785110293L</code></td>
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 715 <tr>
 716 <th class="colFirst" scope="col">Modifier and Type</th>
 717 <th scope="col">Constant Field</th>
 718 <th class="colLast" scope="col">Value</th>
 719 </tr>
 720 <tbody>
 721 <tr class="altColor">
 722 <td class="colFirst"><a name="compbio.metadata.WrongParameterException.serialVersionUID">
 723 <!--   -->
 724 </a><code>private&nbsp;static&nbsp;final&nbsp;long</code></td>
 725 <td><code><a href="compbio/metadata/WrongParameterException.html#serialVersionUID">serialVersionUID</a></code></td>
 726 <td class="colLast"><code>-547775417557345769L</code></td>
 727 </tr>
 728 </tbody>
 729 </table>
 730 </li>
 731 </ul>
 732 <a name="compbio.runner">
 733 <!--   -->
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 740 <tr>
 741 <th class="colFirst" scope="col">Modifier and Type</th>
 742 <th scope="col">Constant Field</th>
 743 <th class="colLast" scope="col">Value</th>
 744 </tr>
 745 <tbody>
 746 <tr class="altColor">
 747 <td class="colFirst"><a name="compbio.runner.OptionCombinator.MAXVALUE">
 748 <!--   -->
 749 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 750 <td><code><a href="compbio/runner/OptionCombinator.html#MAXVALUE">MAXVALUE</a></code></td>
 751 <td class="colLast"><code>"100"</code></td>
 752 </tr>
 753 <tr class="rowColor">
 754 <td class="colFirst"><a name="compbio.runner.OptionCombinator.MINVALUE">
 755 <!--   -->
 756 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 757 <td><code><a href="compbio/runner/OptionCombinator.html#MINVALUE">MINVALUE</a></code></td>
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 759 </tr>
 760 </tbody>
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 766 <tr>
 767 <th class="colFirst" scope="col">Modifier and Type</th>
 768 <th scope="col">Constant Field</th>
 769 <th class="colLast" scope="col">Value</th>
 770 </tr>
 771 <tbody>
 772 <tr class="altColor">
 773 <td class="colFirst"><a name="compbio.runner.Util.SPACE">
 774 <!--   -->
 775 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 776 <td><code><a href="compbio/runner/Util.html#SPACE">SPACE</a></code></td>
 777 <td class="colLast"><code>" "</code></td>
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 787 <tr>
 788 <th class="colFirst" scope="col">Modifier and Type</th>
 789 <th scope="col">Constant Field</th>
 790 <th class="colLast" scope="col">Value</th>
 791 </tr>
 792 <tbody>
 793 <tr class="altColor">
 794 <td class="colFirst"><a name="compbio.runner.conservation.AACon.KEY_VALUE_SEPARATOR">
 795 <!--   -->
 796 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 797 <td><code><a href="compbio/runner/conservation/AACon.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></code></td>
 798 <td class="colLast"><code>"="</code></td>
 799 </tr>
 800 <tr class="rowColor">
 801 <td class="colFirst"><a name="compbio.runner.conservation.AACon.ncorePrm">
 802 <!--   -->
 803 </a><code>private&nbsp;final&nbsp;java.lang.String</code></td>
 804 <td><code><a href="compbio/runner/conservation/AACon.html#ncorePrm">ncorePrm</a></code></td>
 805 <td class="colLast"><code>"-t="</code></td>
 806 </tr>
 807 <tr class="altColor">
 808 <td class="colFirst"><a name="compbio.runner.conservation.AACon.STAT_FILE">
 809 <!--   -->
 810 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
 811 <td><code><a href="compbio/runner/conservation/AACon.html#STAT_FILE">STAT_FILE</a></code></td>
 812 <td class="colLast"><code>"stat.txt"</code></td>
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 823 <th class="colFirst" scope="col">Modifier and Type</th>
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 828 <tr class="altColor">
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 889 <th class="colFirst" scope="col">Modifier and Type</th>
 890 <th scope="col">Constant Field</th>
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 894 <tr class="altColor">
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 916 <tr>
 917 <th class="colFirst" scope="col">Modifier and Type</th>
 918 <th scope="col">Constant Field</th>
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 987 <tbody>
 988 <tr class="altColor">
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1008 <tr>
1009 <th class="colFirst" scope="col">Modifier and Type</th>
1010 <th scope="col">Constant Field</th>
1011 <th class="colLast" scope="col">Value</th>
1012 </tr>
1013 <tbody>
1014 <tr class="altColor">
1015 <td class="colFirst"><a name="compbio.runner.msa.Mafft.KEY_VALUE_SEPARATOR">
1016 <!--   -->
1017 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1018 <td><code><a href="compbio/runner/msa/Mafft.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></code></td>
1019 <td class="colLast"><code>" "</code></td>
1020 </tr>
1021 <tr class="rowColor">
1022 <td class="colFirst"><a name="compbio.runner.msa.Mafft.MATRIX_PAR_NAME">
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1024 </a><code>private&nbsp;final&nbsp;java.lang.String</code></td>
1025 <td><code><a href="compbio/runner/msa/Mafft.html#MATRIX_PAR_NAME">MATRIX_PAR_NAME</a></code></td>
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1034 <tr>
1035 <th class="colFirst" scope="col">Modifier and Type</th>
1036 <th scope="col">Constant Field</th>
1037 <th class="colLast" scope="col">Value</th>
1038 </tr>
1039 <tbody>
1040 <tr class="altColor">
1041 <td class="colFirst"><a name="compbio.runner.msa.MSAprobs.ANNOTATION">
1042 <!--   -->
1043 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1044 <td><code><a href="compbio/runner/msa/MSAprobs.html#ANNOTATION">ANNOTATION</a></code></td>
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1047 <tr class="rowColor">
1048 <td class="colFirst"><a name="compbio.runner.msa.MSAprobs.KEY_VALUE_SEPARATOR">
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1050 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1051 <td><code><a href="compbio/runner/msa/MSAprobs.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></code></td>
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1061 <th class="colFirst" scope="col">Modifier and Type</th>
1062 <th scope="col">Constant Field</th>
1063 <th class="colLast" scope="col">Value</th>
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1065 <tbody>
1066 <tr class="altColor">
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1073 <tr class="rowColor">
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1077 <td><code><a href="compbio/runner/msa/Muscle.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></code></td>
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1086 <tr>
1087 <th class="colFirst" scope="col">Modifier and Type</th>
1088 <th scope="col">Constant Field</th>
1089 <th class="colLast" scope="col">Value</th>
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1091 <tbody>
1092 <tr class="altColor">
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1099 <tr class="rowColor">
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1102 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1103 <td><code><a href="compbio/runner/msa/Probcons.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></code></td>
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1112 <tr>
1113 <th class="colFirst" scope="col">Modifier and Type</th>
1114 <th scope="col">Constant Field</th>
1115 <th class="colLast" scope="col">Value</th>
1116 </tr>
1117 <tbody>
1118 <tr class="altColor">
1119 <td class="colFirst"><a name="compbio.runner.msa.Tcoffee.KEY_VALUE_SEPARATOR">
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1121 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1122 <td><code><a href="compbio/runner/msa/Tcoffee.html#KEY_VALUE_SEPARATOR">KEY_VALUE_SEPARATOR</a></code></td>
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1125 <tr class="rowColor">
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1129 <td><code><a href="compbio/runner/msa/Tcoffee.html#ncorePrm">ncorePrm</a></code></td>
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1140 <tr>
1141 <th class="colFirst" scope="col">Modifier and Type</th>
1142 <th scope="col">Constant Field</th>
1143 <th class="colLast" scope="col">Value</th>
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1145 <tbody>
1146 <tr class="altColor">
1147 <td class="colFirst"><a name="compbio.runner.structure.RNAalifold.KEY_VALUE_SEPARATOR">
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1167 <th scope="col">Constant Field</th>
1168 <th class="colLast" scope="col">Value</th>
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1170 <tbody>
1171 <tr class="altColor">
1172 <td class="colFirst"><a name="compbio.stat.collector.DirCleaner.UNDEFINED">
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1202 <caption><span>compbio.stat.collector.<a href="compbio/stat/collector/JobDirectory.html" title="class in compbio.stat.collector">JobDirectory</a></span><span class="tabEnd">&nbsp;</span></caption>
1203 <tr>
1204 <th class="colFirst" scope="col">Modifier and Type</th>
1205 <th scope="col">Constant Field</th>
1206 <th class="colLast" scope="col">Value</th>
1207 </tr>
1208 <tbody>
1209 <tr class="altColor">
1210 <td class="colFirst"><a name="compbio.stat.collector.JobDirectory.UNDEFINED">
1211 <!--   -->
1212 </a><code>static&nbsp;final&nbsp;int</code></td>
1213 <td><code><a href="compbio/stat/collector/JobDirectory.html#UNDEFINED">UNDEFINED</a></code></td>
1214 <td class="colLast"><code>-1</code></td>
1215 </tr>
1216 </tbody>
1217 </table>
1218 </li>
1219 <li class="blockList">
1220 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
1221 <caption><span>compbio.stat.collector.<a href="compbio/stat/collector/StatDB.html" title="class in compbio.stat.collector">StatDB</a></span><span class="tabEnd">&nbsp;</span></caption>
1222 <tr>
1223 <th class="colFirst" scope="col">Modifier and Type</th>
1224 <th scope="col">Constant Field</th>
1225 <th class="colLast" scope="col">Value</th>
1226 </tr>
1227 <tbody>
1228 <tr class="altColor">
1229 <td class="colFirst"><a name="compbio.stat.collector.StatDB.driver">
1230 <!--   -->
1231 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1232 <td><code><a href="compbio/stat/collector/StatDB.html#driver">driver</a></code></td>
1233 <td class="colLast"><code>"org.apache.derby.jdbc.EmbeddedDriver"</code></td>
1234 </tr>
1235 <tr class="rowColor">
1236 <td class="colFirst"><a name="compbio.stat.collector.StatDB.protocol">
1237 <!--   -->
1238 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1239 <td><code><a href="compbio/stat/collector/StatDB.html#protocol">protocol</a></code></td>
1240 <td class="colLast"><code>"jdbc:derby:"</code></td>
1241 </tr>
1242 <tr class="altColor">
1243 <td class="colFirst"><a name="compbio.stat.collector.StatDB.statDBName">
1244 <!--   -->
1245 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1246 <td><code><a href="compbio/stat/collector/StatDB.html#statDBName">statDBName</a></code></td>
1247 <td class="colLast"><code>"ExecutionStatistic"</code></td>
1248 </tr>
1249 </tbody>
1250 </table>
1251 </li>
1252 </ul>
1253 <ul class="blockList">
1254 <li class="blockList">
1255 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
1256 <caption><span>compbio.stat.servlet.<a href="compbio/stat/servlet/Joblist.html" title="class in compbio.stat.servlet">Joblist</a></span><span class="tabEnd">&nbsp;</span></caption>
1257 <tr>
1258 <th class="colFirst" scope="col">Modifier and Type</th>
1259 <th scope="col">Constant Field</th>
1260 <th class="colLast" scope="col">Value</th>
1261 </tr>
1262 <tbody>
1263 <tr class="altColor">
1264 <td class="colFirst"><a name="compbio.stat.servlet.Joblist.JT_ABANDONED">
1265 <!--   -->
1266 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1267 <td><code><a href="compbio/stat/servlet/Joblist.html#JT_ABANDONED">JT_ABANDONED</a></code></td>
1268 <td class="colLast"><code>"abandoned"</code></td>
1269 </tr>
1270 <tr class="rowColor">
1271 <td class="colFirst"><a name="compbio.stat.servlet.Joblist.JT_ALL">
1272 <!--   -->
1273 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1274 <td><code><a href="compbio/stat/servlet/Joblist.html#JT_ALL">JT_ALL</a></code></td>
1275 <td class="colLast"><code>"all"</code></td>
1276 </tr>
1277 <tr class="altColor">
1278 <td class="colFirst"><a name="compbio.stat.servlet.Joblist.JT_CANCELLED">
1279 <!--   -->
1280 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1281 <td><code><a href="compbio/stat/servlet/Joblist.html#JT_CANCELLED">JT_CANCELLED</a></code></td>
1282 <td class="colLast"><code>"cancelled"</code></td>
1283 </tr>
1284 <tr class="rowColor">
1285 <td class="colFirst"><a name="compbio.stat.servlet.Joblist.JT_FAILED">
1286 <!--   -->
1287 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1288 <td><code><a href="compbio/stat/servlet/Joblist.html#JT_FAILED">JT_FAILED</a></code></td>
1289 <td class="colLast"><code>"failed"</code></td>
1290 </tr>
1291 <tr class="altColor">
1292 <td class="colFirst"><a name="compbio.stat.servlet.Joblist.JT_INCOMPLETE">
1293 <!--   -->
1294 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1295 <td><code><a href="compbio/stat/servlet/Joblist.html#JT_INCOMPLETE">JT_INCOMPLETE</a></code></td>
1296 <td class="colLast"><code>"incomplete"</code></td>
1297 </tr>
1298 </tbody>
1299 </table>
1300 </li>
1301 </ul>
1302 <a name="compbio.ws">
1303 <!--   -->
1304 </a>
1305 <h2 title="compbio.ws">compbio.ws.*</h2>
1306 <ul class="blockList">
1307 <li class="blockList">
1308 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
1309 <caption><span>compbio.ws.client.<a href="compbio/ws/client/AAConClient.html" title="class in compbio.ws.client">AAConClient</a></span><span class="tabEnd">&nbsp;</span></caption>
1310 <tr>
1311 <th class="colFirst" scope="col">Modifier and Type</th>
1312 <th scope="col">Constant Field</th>
1313 <th class="colLast" scope="col">Value</th>
1314 </tr>
1315 <tbody>
1316 <tr class="altColor">
1317 <td class="colFirst"><a name="compbio.ws.client.AAConClient.hostname">
1318 <!--   -->
1319 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1320 <td><code><a href="compbio/ws/client/AAConClient.html#hostname">hostname</a></code></td>
1321 <td class="colLast"><code>"http://www.compbio.dundee.ac.uk/aacon"</code></td>
1322 </tr>
1323 <tr class="rowColor">
1324 <td class="colFirst"><a name="compbio.ws.client.AAConClient.QUALIFIED_SERVICE_NAME">
1325 <!--   -->
1326 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1327 <td><code><a href="compbio/ws/client/AAConClient.html#QUALIFIED_SERVICE_NAME">QUALIFIED_SERVICE_NAME</a></code></td>
1328 <td class="colLast"><code>"http://msa.data.compbio/01/12/2010/"</code></td>
1329 </tr>
1330 <tr class="altColor">
1331 <td class="colFirst"><a name="compbio.ws.client.AAConClient.serviceName">
1332 <!--   -->
1333 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1334 <td><code><a href="compbio/ws/client/AAConClient.html#serviceName">serviceName</a></code></td>
1335 <td class="colLast"><code>"AAConWS"</code></td>
1336 </tr>
1337 </tbody>
1338 </table>
1339 </li>
1340 <li class="blockList">
1341 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
1342 <caption><span>compbio.ws.client.compbio.ws.client.Constraints</span><span class="tabEnd">&nbsp;</span></caption>
1343 <tr>
1344 <th class="colFirst" scope="col">Modifier and Type</th>
1345 <th scope="col">Constant Field</th>
1346 <th class="colLast" scope="col">Value</th>
1347 </tr>
1348 <tbody>
1349 <tr class="altColor">
1350 <td class="colFirst"><a name="compbio.ws.client.Constraints.help_text">
1351 <!--   -->
1352 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1353 <td><code><a href="compbio/ws/client/Constraints.html#help_text">help_text</a></code></td>
1354 <td class="colLast"><code>"\r\nUsage: java -jar &lt;JAR file name&gt; -h=host_and_context &lt;-s=serviceName&gt; ACTION [OPTIONS] \r\n\r\n       -h=&lt;host_context&gt; - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws\r\n       -s=&lt;ServiceName&gt;  - a name of servise (the full list can be obtain with the option -list)\r\n                           &lt;serviceName&gt; is required for all ACTIONS except -list\r\n\r\nACTIONS: \r\n        -i=&lt;inputFile&gt;  - defines an input file. For most services this is a FASTA file with initial sequences\r\n        -list           - lists all available web services\r\n        -test           - tests functioning of &lt;ServiceName&gt; \r\n        -parameters     - lists parameters supported by &lt;ServiceName&gt;\r\n        -presets        - lists presets supported by &lt;ServiceName&gt;\r\n        -limits         - lists limits of &lt;ServiceName&gt;\r\n\r\nN.B. If an input file is specified with -i other actions are ignored!\r\n\r\nOPTIONS (used with the -i action only):\r\n        -r=&lt;presetName&gt;  - name of the preset to use\r\n        -o=&lt;outputFile&gt;  - file with output results\r\n        -f=&lt;paramFile&gt;   - file with the list of parameters to use.\r\n\r\nPlease note that -r and -f options cannot be used together. \r\nAlignment/Prediction is done with either preset or a parameters from the file, but not both!\r\n\r\nEXAMPLES: \r\n&lt;THECLIENT&gt; is java -jar &lt;JAR file name&gt;\r\n\r\n1) List all available services on the host:\r\n   &lt;THECLIENT&gt; -h=http://www.compbio.dundee.ac.uk/jabaws -list\r\n\r\n2) Test Clustal web service:\r\n   &lt;THECLIENT&gt; -h=http://www.compbio.dundee.ac.uk/jabaws -s=ClustalWS -test \r\n\r\n3) Align sequence from file input.txt with Probcons. Record resulting alignment \r\n   into the output.txt:\r\n   &lt;THECLIENT&gt; -h=http://www.compbio.dundee.ac.uk/jabaws -s=ProbconsWS -i=input.txt -o=output.txt\r\n\r\n4) Calculate disorder with Disembl take input from input.txt with output results\r\n    to be printed out to the standard output:\r\n    &lt;THECLIENT&gt; -h=http://www.compbio.dundee.ac.uk/jabaws -s=DisemblWS -i=input.txt \r\n\r\n5) List all parameters available for AAconWS service:\r\n   &lt;THECLIENT&gt; -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -parameters\r\n\r\n6) Calculate conservation with AAConWS using LANDGRAF method, for Clustal alignment \r\n   from input.txt and report the scores to the standard output:\r\n   &lt;THECLIENT&gt; -h=http://www.compbio.dundee.ac.uk/jabaws -s=AAconWS -i=input.txt -f=prm.txt \r\n\r\n   Where the content of prm.txt file is -m=LANDGRAF\r\nN.B. The list of the supported parameters can be obtained as shown in the example 5.\r\n"</code></td>
1355 </tr>
1356 <tr class="rowColor">
1357 <td class="colFirst"><a name="compbio.ws.client.Constraints.hostkey">
1358 <!--   -->
1359 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1360 <td><code><a href="compbio/ws/client/Constraints.html#hostkey">hostkey</a></code></td>
1361 <td class="colLast"><code>"-h"</code></td>
1362 </tr>
1363 <tr class="altColor">
1364 <td class="colFirst"><a name="compbio.ws.client.Constraints.inputkey">
1365 <!--   -->
1366 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1367 <td><code><a href="compbio/ws/client/Constraints.html#inputkey">inputkey</a></code></td>
1368 <td class="colLast"><code>"-i"</code></td>
1369 </tr>
1370 <tr class="rowColor">
1371 <td class="colFirst"><a name="compbio.ws.client.Constraints.limitList">
1372 <!--   -->
1373 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1374 <td><code><a href="compbio/ws/client/Constraints.html#limitList">limitList</a></code></td>
1375 <td class="colLast"><code>"-limits"</code></td>
1376 </tr>
1377 <tr class="altColor">
1378 <td class="colFirst"><a name="compbio.ws.client.Constraints.listServices">
1379 <!--   -->
1380 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1381 <td><code><a href="compbio/ws/client/Constraints.html#listServices">listServices</a></code></td>
1382 <td class="colLast"><code>"-list"</code></td>
1383 </tr>
1384 <tr class="rowColor">
1385 <td class="colFirst"><a name="compbio.ws.client.Constraints.listServicesOld">
1386 <!--   -->
1387 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1388 <td><code><a href="compbio/ws/client/Constraints.html#listServicesOld">listServicesOld</a></code></td>
1389 <td class="colLast"><code>"-list_services"</code></td>
1390 </tr>
1391 <tr class="altColor">
1392 <td class="colFirst"><a name="compbio.ws.client.Constraints.outputkey">
1393 <!--   -->
1394 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1395 <td><code><a href="compbio/ws/client/Constraints.html#outputkey">outputkey</a></code></td>
1396 <td class="colLast"><code>"-o"</code></td>
1397 </tr>
1398 <tr class="rowColor">
1399 <td class="colFirst"><a name="compbio.ws.client.Constraints.parameterkey">
1400 <!--   -->
1401 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1402 <td><code><a href="compbio/ws/client/Constraints.html#parameterkey">parameterkey</a></code></td>
1403 <td class="colLast"><code>"-p"</code></td>
1404 </tr>
1405 <tr class="altColor">
1406 <td class="colFirst"><a name="compbio.ws.client.Constraints.paramFile">
1407 <!--   -->
1408 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1409 <td><code><a href="compbio/ws/client/Constraints.html#paramFile">paramFile</a></code></td>
1410 <td class="colLast"><code>"-f"</code></td>
1411 </tr>
1412 <tr class="rowColor">
1413 <td class="colFirst"><a name="compbio.ws.client.Constraints.paramList">
1414 <!--   -->
1415 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1416 <td><code><a href="compbio/ws/client/Constraints.html#paramList">paramList</a></code></td>
1417 <td class="colLast"><code>"-parameters"</code></td>
1418 </tr>
1419 <tr class="altColor">
1420 <td class="colFirst"><a name="compbio.ws.client.Constraints.presetkey">
1421 <!--   -->
1422 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1423 <td><code><a href="compbio/ws/client/Constraints.html#presetkey">presetkey</a></code></td>
1424 <td class="colLast"><code>"-r"</code></td>
1425 </tr>
1426 <tr class="rowColor">
1427 <td class="colFirst"><a name="compbio.ws.client.Constraints.presetList">
1428 <!--   -->
1429 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1430 <td><code><a href="compbio/ws/client/Constraints.html#presetList">presetList</a></code></td>
1431 <td class="colLast"><code>"-presets"</code></td>
1432 </tr>
1433 <tr class="altColor">
1434 <td class="colFirst"><a name="compbio.ws.client.Constraints.pseparator">
1435 <!--   -->
1436 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1437 <td><code><a href="compbio/ws/client/Constraints.html#pseparator">pseparator</a></code></td>
1438 <td class="colLast"><code>"="</code></td>
1439 </tr>
1440 <tr class="rowColor">
1441 <td class="colFirst"><a name="compbio.ws.client.Constraints.servicekey">
1442 <!--   -->
1443 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1444 <td><code><a href="compbio/ws/client/Constraints.html#servicekey">servicekey</a></code></td>
1445 <td class="colLast"><code>"-s"</code></td>
1446 </tr>
1447 <tr class="altColor">
1448 <td class="colFirst"><a name="compbio.ws.client.Constraints.testKey">
1449 <!--   -->
1450 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1451 <td><code><a href="compbio/ws/client/Constraints.html#testKey">testKey</a></code></td>
1452 <td class="colLast"><code>"-test"</code></td>
1453 </tr>
1454 </tbody>
1455 </table>
1456 </li>
1457 <li class="blockList">
1458 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
1459 <caption><span>compbio.ws.client.compbio.ws.client.Services.ServiceInfo</span><span class="tabEnd">&nbsp;</span></caption>
1460 <tr>
1461 <th class="colFirst" scope="col">Modifier and Type</th>
1462 <th scope="col">Constant Field</th>
1463 <th class="colLast" scope="col">Value</th>
1464 </tr>
1465 <tbody>
1466 <tr class="altColor">
1467 <td class="colFirst"><a name="compbio.ws.client.Services.ServiceInfo.line_delimiter">
1468 <!--   -->
1469 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1470 <td><code><a href="compbio/ws/client/Services.ServiceInfo.html#line_delimiter">line_delimiter</a></code></td>
1471 <td class="colLast"><code>"\n"</code></td>
1472 </tr>
1473 </tbody>
1474 </table>
1475 </li>
1476 <li class="blockList">
1477 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
1478 <caption><span>compbio.ws.client.<a href="compbio/ws/client/WSTester.html" title="class in compbio.ws.client">WSTester</a></span><span class="tabEnd">&nbsp;</span></caption>
1479 <tr>
1480 <th class="colFirst" scope="col">Modifier and Type</th>
1481 <th scope="col">Constant Field</th>
1482 <th class="colLast" scope="col">Value</th>
1483 </tr>
1484 <tbody>
1485 <tr class="altColor">
1486 <td class="colFirst"><a name="compbio.ws.client.WSTester.clustalRNAAlignment">
1487 <!--   -->
1488 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1489 <td><code><a href="compbio/ws/client/WSTester.html#clustalRNAAlignment">clustalRNAAlignment</a></code></td>
1490 <td class="colLast"><code>"CLUSTAL\nFoo             C-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGA\nBar             G-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGA\nFoo             UGGUUG----GCAAC\nBar             U-UACGAUUAACCAC"</code></td>
1491 </tr>
1492 <tr class="rowColor">
1493 <td class="colFirst"><a name="compbio.ws.client.WSTester.FAILED">
1494 <!--   -->
1495 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1496 <td><code><a href="compbio/ws/client/WSTester.html#FAILED">FAILED</a></code></td>
1497 <td class="colLast"><code>"FAILED"</code></td>
1498 </tr>
1499 <tr class="altColor">
1500 <td class="colFirst"><a name="compbio.ws.client.WSTester.fastaAlignment">
1501 <!--   -->
1502 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1503 <td><code><a href="compbio/ws/client/WSTester.html#fastaAlignment">fastaAlignment</a></code></td>
1504 <td class="colLast"><code>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n&gt;Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"</code></td>
1505 </tr>
1506 <tr class="rowColor">
1507 <td class="colFirst"><a name="compbio.ws.client.WSTester.fastaInput1record">
1508 <!--   -->
1509 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1510 <td><code><a href="compbio/ws/client/WSTester.html#fastaInput1record">fastaInput1record</a></code></td>
1511 <td class="colLast"><code>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"</code></td>
1512 </tr>
1513 <tr class="altColor">
1514 <td class="colFirst"><a name="compbio.ws.client.WSTester.fastaInput2records">
1515 <!--   -->
1516 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1517 <td><code><a href="compbio/ws/client/WSTester.html#fastaInput2records">fastaInput2records</a></code></td>
1518 <td class="colLast"><code>"&gt;Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n&gt;Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n"</code></td>
1519 </tr>
1520 <tr class="rowColor">
1521 <td class="colFirst"><a name="compbio.ws.client.WSTester.fastaRNAAlignment">
1522 <!--   -->
1523 </a><code>public&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1524 <td><code><a href="compbio/ws/client/WSTester.html#fastaRNAAlignment">fastaRNAAlignment</a></code></td>
1525 <td class="colLast"><code>"&gt;Foo\nC-UUGCGUUAAUGAGAACAGAAACG-UAAA--CUAUAA-CCUAG-G-GGUUUCUGUUGGAUGGUUG----GCAAC\n&gt;Bar\nG-UGGCGCUUAUGACGCAGUUGUCU-UAAA-CUCGAAC--UCGA-GCGGGCAAUUGCUGAU-UACGAUUAACCAC\n"</code></td>
1526 </tr>
1527 <tr class="altColor">
1528 <td class="colFirst"><a name="compbio.ws.client.WSTester.OK">
1529 <!--   -->
1530 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1531 <td><code><a href="compbio/ws/client/WSTester.html#OK">OK</a></code></td>
1532 <td class="colLast"><code>"OK"</code></td>
1533 </tr>
1534 <tr class="rowColor">
1535 <td class="colFirst"><a name="compbio.ws.client.WSTester.UNSUPPORTED">
1536 <!--   -->
1537 </a><code>private&nbsp;static&nbsp;final&nbsp;java.lang.String</code></td>
1538 <td><code><a href="compbio/ws/client/WSTester.html#UNSUPPORTED">UNSUPPORTED</a></code></td>
1539 <td class="colLast"><code>"UNSUPPORTED"</code></td>
1540 </tr>
1541 </tbody>
1542 </table>
1543 </li>
1544 </ul>
1545 <ul class="blockList">
1546 <li class="blockList">
1547 <table class="constantsSummary" border="0" cellpadding="3" cellspacing="0" summary="Constant Field Values table, listing constant fields, and values">
1548 <caption><span>compbio.ws.server.<a href="compbio/ws/server/GAUtils.html" title="class in compbio.ws.server">GAUtils</a></span><span class="tabEnd">&nbsp;</span></caption>
1549 <tr>
1550 <th class="colFirst" scope="col">Modifier and Type</th>
1551 <th scope="col">Constant Field</th>
1552 <th class="colLast" scope="col">Value</th>
1553 </tr>
1554 <tbody>
1555 <tr class="altColor">
1556 <td class="colFirst"><a name="compbio.ws.server.GAUtils.VERSION_TYPE">
1557 <!--   -->
1558 </a><code>static&nbsp;final&nbsp;java.lang.String</code></td>
1559 <td><code><a href="compbio/ws/server/GAUtils.html#VERSION_TYPE">VERSION_TYPE</a></code></td>
1560 <td class="colLast"><code>"WAR"</code></td>
1561 </tr>
1562 </tbody>
1563 </table>
1564 </li>
1565 </ul>
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