website/docs/full_javadoc/compbio/ws/server/ClustalOWS.html

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   6 <title>ClustalOWS</title>
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  42 <li class="navBarCell1Rev">Class</li>
  43 <li><a href="class-use/ClustalOWS.html">Use</a></li>
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  75 <ul class="subNavList">
  76 <li>Summary:&nbsp;</li>
  77 <li>Nested&nbsp;|&nbsp;</li>
  78 <li><a href="#field.summary">Field</a>&nbsp;|&nbsp;</li>
  79 <li><a href="#constructor.summary">Constr</a>&nbsp;|&nbsp;</li>
  80 <li><a href="#method.summary">Method</a></li>
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  83 <li>Detail:&nbsp;</li>
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  85 <li><a href="#constructor.detail">Constr</a>&nbsp;|&nbsp;</li>
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  94 <div class="header">
  95 <div class="subTitle">compbio.ws.server</div>
  96 <h2 title="Class ClustalOWS" class="title">Class ClustalOWS</h2>
  97 </div>
  98 <div class="contentContainer">
  99 <ul class="inheritance">
 100 <li>java.lang.Object</li>
 101 <li>
 102 <ul class="inheritance">
 103 <li>compbio.ws.server.ClustalOWS</li>
 104 </ul>
 105 </li>
 106 </ul>
 107 <div class="description">
 108 <ul class="blockList">
 109 <li class="blockList">
 110 <dl>
 111 <dt>All Implemented Interfaces:</dt>
 112 <dd><a href="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a>, <a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a>, <a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;, <a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</dd>
 113 </dl>
 114 <hr>
 115 <br>
 116 <pre>public class <span class="typeNameLabel">ClustalOWS</span>
 117 extends java.lang.Object
 118 implements <a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</pre>
 119 </li>
 120 </ul>
 121 </div>
 122 <div class="summary">
 123 <ul class="blockList">
 124 <li class="blockList">
 125 <!-- =========== FIELD SUMMARY =========== -->
 126 <ul class="blockList">
 127 <li class="blockList"><a name="field.summary">
 128 <!--   -->
 129 </a>
 130 <h3>Field Summary</h3>
 131 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Field Summary table, listing fields, and an explanation">
 132 <caption><span>Fields</span><span class="tabEnd">&nbsp;</span></caption>
 133 <tr>
 134 <th class="colFirst" scope="col">Modifier and Type</th>
 135 <th class="colLast" scope="col">Field and Description</th>
 136 </tr>
 137 <tr class="altColor">
 138 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 139 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#clustalOptions">clustalOptions</a></span></code>&nbsp;</td>
 140 </tr>
 141 <tr class="rowColor">
 142 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 143 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#clustalPresets">clustalPresets</a></span></code>&nbsp;</td>
 144 </tr>
 145 <tr class="altColor">
 146 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 147 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#limitMan">limitMan</a></span></code>&nbsp;</td>
 148 </tr>
 149 <tr class="rowColor">
 150 <td class="colFirst"><code>private static org.apache.log4j.Logger</code></td>
 151 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#log">log</a></span></code>&nbsp;</td>
 152 </tr>
 153 </table>
 154 <ul class="blockList">
 155 <li class="blockList"><a name="fields.inherited.from.class.compbio.data.msa.JABAService">
 156 <!--   -->
 157 </a>
 158 <h3>Fields inherited from interface&nbsp;compbio.data.msa.<a href="../../../compbio/data/msa/JABAService.html" title="interface in compbio.data.msa">JABAService</a></h3>
 159 <code><a href="../../../compbio/data/msa/JABAService.html#JABAWS_VERSION">JABAWS_VERSION</a>, <a href="../../../compbio/data/msa/JABAService.html#SERVICE_NAMESPACE">SERVICE_NAMESPACE</a>, <a href="../../../compbio/data/msa/JABAService.html#V2_SERVICE_NAMESPACE">V2_SERVICE_NAMESPACE</a>, <a href="../../../compbio/data/msa/JABAService.html#V3_SERVICE_NAMESPACE">V3_SERVICE_NAMESPACE</a></code></li>
 160 </ul>
 161 </li>
 162 </ul>
 163 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
 164 <ul class="blockList">
 165 <li class="blockList"><a name="constructor.summary">
 166 <!--   -->
 167 </a>
 168 <h3>Constructor Summary</h3>
 169 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Constructor Summary table, listing constructors, and an explanation">
 170 <caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
 171 <tr>
 172 <th class="colOne" scope="col">Constructor and Description</th>
 173 </tr>
 174 <tr class="altColor">
 175 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#ClustalOWS--">ClustalOWS</a></span>()</code>&nbsp;</td>
 176 </tr>
 177 </table>
 178 </li>
 179 </ul>
 180 <!-- ========== METHOD SUMMARY =========== -->
 181 <ul class="blockList">
 182 <li class="blockList"><a name="method.summary">
 183 <!--   -->
 184 </a>
 185 <h3>Method Summary</h3>
 186 <table class="memberSummary" border="0" cellpadding="3" cellspacing="0" summary="Method Summary table, listing methods, and an explanation">
 187 <caption><span id="t0" class="activeTableTab"><span>All Methods</span><span class="tabEnd">&nbsp;</span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd">&nbsp;</span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd">&nbsp;</span></span></caption>
 188 <tr>
 189 <th class="colFirst" scope="col">Modifier and Type</th>
 190 <th class="colLast" scope="col">Method and Description</th>
 191 </tr>
 192 <tr id="i0" class="altColor">
 193 <td class="colFirst"><code>java.lang.String</code></td>
 194 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#align-java.util.List-">align</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)</code>
 195 <div class="block">Align a list of sequences with default settings.</div>
 196 </td>
 197 </tr>
 198 <tr id="i1" class="rowColor">
 199 <td class="colFirst"><code>boolean</code></td>
 200 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#cancelJob-java.lang.String-">cancelJob</a></span>(java.lang.String&nbsp;jobId)</code>
 201 <div class="block">Stop running the job <code>jobId</code> but leave its output untouched</div>
 202 </td>
 203 </tr>
 204 <tr id="i2" class="altColor">
 205 <td class="colFirst"><code>java.lang.String</code></td>
 206 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 207            java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&gt;&nbsp;options)</code>
 208 <div class="block">Align a list of sequences with options.</div>
 209 </td>
 210 </tr>
 211 <tr id="i3" class="rowColor">
 212 <td class="colFirst"><code><a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a></code></td>
 213 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#getJobStatus-java.lang.String-">getJobStatus</a></span>(java.lang.String&nbsp;jobId)</code>
 214 <div class="block">Return the status of the job.</div>
 215 </td>
 216 </tr>
 217 <tr id="i4" class="altColor">
 218 <td class="colFirst"><code><a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 219 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#getLimit-java.lang.String-">getLimit</a></span>(java.lang.String&nbsp;presetName)</code>
 220 <div class="block">Get a Limit for a preset.</div>
 221 </td>
 222 </tr>
 223 <tr id="i5" class="rowColor">
 224 <td class="colFirst"><code><a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 225 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#getLimits--">getLimits</a></span>()</code>
 226 <div class="block">List Limits supported by a web service.</div>
 227 </td>
 228 </tr>
 229 <tr id="i6" class="altColor">
 230 <td class="colFirst"><code><a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 231 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#getPresets--">getPresets</a></span>()</code>
 232 <div class="block">Get presets supported by a web service</div>
 233 </td>
 234 </tr>
 235 <tr id="i7" class="rowColor">
 236 <td class="colFirst"><code><a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a></code></td>
 237 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String&nbsp;jobId)</code>
 238 <div class="block">Return the result of the job.</div>
 239 </td>
 240 </tr>
 241 <tr id="i8" class="altColor">
 242 <td class="colFirst"><code><a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 243 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#getRunnerOptions--">getRunnerOptions</a></span>()</code>
 244 <div class="block">Get options supported by a web service</div>
 245 </td>
 246 </tr>
 247 <tr id="i9" class="rowColor">
 248 <td class="colFirst"><code>(package private) <a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></td>
 249 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#init-java.util.List-">init</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;dataSet)</code>&nbsp;</td>
 250 </tr>
 251 <tr id="i10" class="altColor">
 252 <td class="colFirst"><code>java.lang.String</code></td>
 253 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></span>(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 254            <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;preset)</code>
 255 <div class="block">Align a list of sequences with preset.</div>
 256 </td>
 257 </tr>
 258 <tr id="i11" class="rowColor">
 259 <td class="colFirst"><code><a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a></code></td>
 260 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/ClustalOWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics</a></span>(java.lang.String&nbsp;jobId,
 261                   long&nbsp;position)</code>
 262 <div class="block">Reads 1kb chunk from the statistics file which is specific to a given web
 263  service from the <code>position</code>.</div>
 264 </td>
 265 </tr>
 266 </table>
 267 <ul class="blockList">
 268 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
 269 <!--   -->
 270 </a>
 271 <h3>Methods inherited from class&nbsp;java.lang.Object</h3>
 272 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
 273 </ul>
 274 </li>
 275 </ul>
 276 </li>
 277 </ul>
 278 </div>
 279 <div class="details">
 280 <ul class="blockList">
 281 <li class="blockList">
 282 <!-- ============ FIELD DETAIL =========== -->
 283 <ul class="blockList">
 284 <li class="blockList"><a name="field.detail">
 285 <!--   -->
 286 </a>
 287 <h3>Field Detail</h3>
 288 <a name="log">
 289 <!--   -->
 290 </a>
 291 <ul class="blockList">
 292 <li class="blockList">
 293 <h4>log</h4>
 294 <pre>private static&nbsp;org.apache.log4j.Logger log</pre>
 295 </li>
 296 </ul>
 297 <a name="clustalOptions">
 298 <!--   -->
 299 </a>
 300 <ul class="blockList">
 301 <li class="blockList">
 302 <h4>clustalOptions</h4>
 303 <pre>private static final&nbsp;<a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt; clustalOptions</pre>
 304 </li>
 305 </ul>
 306 <a name="clustalPresets">
 307 <!--   -->
 308 </a>
 309 <ul class="blockList">
 310 <li class="blockList">
 311 <h4>clustalPresets</h4>
 312 <pre>private static final&nbsp;<a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt; clustalPresets</pre>
 313 </li>
 314 </ul>
 315 <a name="limitMan">
 316 <!--   -->
 317 </a>
 318 <ul class="blockListLast">
 319 <li class="blockList">
 320 <h4>limitMan</h4>
 321 <pre>private static final&nbsp;<a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt; limitMan</pre>
 322 </li>
 323 </ul>
 324 </li>
 325 </ul>
 326 <!-- ========= CONSTRUCTOR DETAIL ======== -->
 327 <ul class="blockList">
 328 <li class="blockList"><a name="constructor.detail">
 329 <!--   -->
 330 </a>
 331 <h3>Constructor Detail</h3>
 332 <a name="ClustalOWS--">
 333 <!--   -->
 334 </a>
 335 <ul class="blockListLast">
 336 <li class="blockList">
 337 <h4>ClustalOWS</h4>
 338 <pre>public&nbsp;ClustalOWS()</pre>
 339 </li>
 340 </ul>
 341 </li>
 342 </ul>
 343 <!-- ============ METHOD DETAIL ========== -->
 344 <ul class="blockList">
 345 <li class="blockList"><a name="method.detail">
 346 <!--   -->
 347 </a>
 348 <h3>Method Detail</h3>
 349 <a name="align-java.util.List-">
 350 <!--   -->
 351 </a>
 352 <ul class="blockList">
 353 <li class="blockList">
 354 <h4>align</h4>
 355 <pre>public&nbsp;java.lang.String&nbsp;align(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences)
 356                        throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 357 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#align-java.util.List-">MsaWS</a></code></span></div>
 358 <div class="block">Align a list of sequences with default settings.
 359
 360  Any dataset containing a greater number of sequences or when the average
 361  length of the sequences are greater then defined in the default Limit,
 362  will not be accepted for an alignment operation and
 363  JobSubmissionException will be thrown.</div>
 364 <dl>
 365 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 366 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#align-java.util.List-">align</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 367 <dt><span class="paramLabel">Parameters:</span></dt>
 368 <dd><code>sequences</code> - List of FastaSequence objects. The program does not perform
 369             any sequence validity checks. Nor does it checks whether the
 370             sequences names are unique. It is responsibility of the caller
 371             to make sure of this</dd>
 372 <dt><span class="returnLabel">Returns:</span></dt>
 373 <dd>jobId - unique identifier for the job</dd>
 374 <dt><span class="throwsLabel">Throws:</span></dt>
 375 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 376              following reasons: 1) The number of sequences in the
 377              submission or their average length is greater then defined by
 378              the default Limit. 2) Any problems on the server side e.g. it
 379              is misconfigured or malfunction, is reported via this
 380              exception. In the first case the information on the limit
 381              could be obtained from an exception.</dd>
 382 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 383              given web service, e.g. JABAWS is deployed on Windows and
 384              Mafft service is called</dd>
 385 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or their average
 386              length exceeds what is defined by the limit</dd>
 387 </dl>
 388 </li>
 389 </ul>
 390 <a name="init-java.util.List-">
 391 <!--   -->
 392 </a>
 393 <ul class="blockList">
 394 <li class="blockList">
 395 <h4>init</h4>
 396 <pre><a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;init(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;dataSet)
 397                              throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
 398 <dl>
 399 <dt><span class="throwsLabel">Throws:</span></dt>
 400 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code></dd>
 401 </dl>
 402 </li>
 403 </ul>
 404 <a name="presetAlign-java.util.List-compbio.metadata.Preset-">
 405 <!--   -->
 406 </a>
 407 <ul class="blockList">
 408 <li class="blockList">
 409 <h4>presetAlign</h4>
 410 <pre>public&nbsp;java.lang.String&nbsp;presetAlign(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 411                                     <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;preset)
 412                              throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a>,
 413                                     <a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 414 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">MsaWS</a></code></span></div>
 415 <div class="block">Align a list of sequences with preset.
 416
 417  Limit for a presetName is used whether the calculation will be permitted
 418  or denied. If no Limit was defined for a presetName, than default limit
 419  is used.</div>
 420 <dl>
 421 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 422 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 423 <dt><span class="paramLabel">Parameters:</span></dt>
 424 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
 425             any sequence validity checks. Nor does it checks whether the
 426             sequences names are unique. It is responsibility of the caller
 427             to validate this information</dd>
 428 <dd><code>preset</code> - A list of Options</dd>
 429 <dt><span class="returnLabel">Returns:</span></dt>
 430 <dd>String - jobId - unique identifier for the job</dd>
 431 <dt><span class="throwsLabel">Throws:</span></dt>
 432 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 433              following reasons: 1) The number of sequences in the
 434              submission or their average length is greater then defined by
 435              the default Limit. 2) Any problems on the server side e.g. it
 436              is misconfigured or malfunction, is reported via this
 437              exception. In the first case the information on the limit
 438              could be obtained from an exception.</dd>
 439 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 440              given web service, e.g. JABAWS is deployed on Windows and
 441              Mafft service is called</dd>
 442 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or average length
 443              exceeds what is defined by the limit</dd>
 444 <dd><code><a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - is throws when 1) One of the Options provided is not
 445              supported, 2) The value of the option is defined outside the
 446              boundaries. In both cases exception object contain the
 447              information on the violating Option.</dd>
 448 <dt><span class="seeLabel">See Also:</span></dt>
 449 <dd><a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><code>Preset</code></a></dd>
 450 </dl>
 451 </li>
 452 </ul>
 453 <a name="customAlign-java.util.List-java.util.List-">
 454 <!--   -->
 455 </a>
 456 <ul class="blockList">
 457 <li class="blockList">
 458 <h4>customAlign</h4>
 459 <pre>public&nbsp;java.lang.String&nbsp;customAlign(java.util.List&lt;<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>&gt;&nbsp;sequences,
 460                                     java.util.List&lt;<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&gt;&nbsp;options)
 461                              throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a>,
 462                                     <a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
 463 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">MsaWS</a></code></span></div>
 464 <div class="block">Align a list of sequences with options.</div>
 465 <dl>
 466 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 467 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 468 <dt><span class="paramLabel">Parameters:</span></dt>
 469 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
 470             any sequence validity checks. Nor does it checks whether the
 471             sequences names are unique. It is responsibility of the caller
 472             to validate this information</dd>
 473 <dd><code>options</code> - A list of Options</dd>
 474 <dt><span class="returnLabel">Returns:</span></dt>
 475 <dd>jobId - unique identifier for the job</dd>
 476 <dt><span class="throwsLabel">Throws:</span></dt>
 477 <dd><code><a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></code> - is thrown when the job could not be submitted due to the
 478              following reasons: 1) The number of sequences in the
 479              submission or their average length is greater then defined by
 480              the default Limit. 2) Any problems on the server side e.g. it
 481              is misconfigured or malfunction, is reported via this
 482              exception. In the first case the information on the limit
 483              could be obtained from an exception.</dd>
 484 <dd><code><a href="../../../compbio/metadata/UnsupportedRuntimeException.html" title="class in compbio.metadata">UnsupportedRuntimeException</a></code> - thrown if server OS does not support native executables for a
 485              given web service, e.g. JABAWS is deployed on Windows and
 486              Mafft service is called</dd>
 487 <dd><code><a href="../../../compbio/metadata/LimitExceededException.html" title="class in compbio.metadata">LimitExceededException</a></code> - is throw if the input sequences number or their average
 488              length exceeds what is defined by the limit</dd>
 489 <dd><code><a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></code> - is throws when 1) One of the Options provided is not
 490              supported, 2) The value of the option is defined outside the
 491              boundaries. In both cases exception object contain the
 492              information on the violating Option.</dd>
 493 <dt><span class="seeLabel">See Also:</span></dt>
 494 <dd><a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><code>Default Limit is used to decide whether the calculation will be
 495       permitted or denied</code></a></dd>
 496 </dl>
 497 </li>
 498 </ul>
 499 <a name="getRunnerOptions--">
 500 <!--   -->
 501 </a>
 502 <ul class="blockList">
 503 <li class="blockList">
 504 <h4>getRunnerOptions</h4>
 505 <pre>public&nbsp;<a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;getRunnerOptions()</pre>
 506 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getRunnerOptions--">Metadata</a></code></span></div>
 507 <div class="block">Get options supported by a web service</div>
 508 <dl>
 509 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 510 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getRunnerOptions--">getRunnerOptions</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 511 <dt><span class="returnLabel">Returns:</span></dt>
 512 <dd>RunnerConfig the list of options and parameters supported by a
 513          web service.</dd>
 514 </dl>
 515 </li>
 516 </ul>
 517 <a name="getResult-java.lang.String-">
 518 <!--   -->
 519 </a>
 520 <ul class="blockList">
 521 <li class="blockList">
 522 <h4>getResult</h4>
 523 <pre>public&nbsp;<a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a>&nbsp;getResult(java.lang.String&nbsp;jobId)
 524                     throws <a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
 525 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">MsaWS</a></code></span></div>
 526 <div class="block">Return the result of the job. This method waits for the job
 527  <code>jobId</code> to complete before return.</div>
 528 <dl>
 529 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 530 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">getResult</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 531 <dt><span class="paramLabel">Parameters:</span></dt>
 532 <dd><code>jobId</code> - a unique job identifier</dd>
 533 <dt><span class="returnLabel">Returns:</span></dt>
 534 <dd>Alignment</dd>
 535 <dt><span class="throwsLabel">Throws:</span></dt>
 536 <dd><code><a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></code> - this exception is throw if the job execution was not
 537              successful or the result of the execution could not be found.
 538              (e.g. removed). Exception could also be thrown due to the
 539              lower level problems on the server i.e. IOException,
 540              FileNotFoundException problems as well as
 541              UnknownFileFormatException.</dd>
 542 </dl>
 543 </li>
 544 </ul>
 545 <a name="getLimit-java.lang.String-">
 546 <!--   -->
 547 </a>
 548 <ul class="blockList">
 549 <li class="blockList">
 550 <h4>getLimit</h4>
 551 <pre>public&nbsp;<a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;getLimit(java.lang.String&nbsp;presetName)</pre>
 552 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">Metadata</a></code></span></div>
 553 <div class="block">Get a Limit for a preset.</div>
 554 <dl>
 555 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 556 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">getLimit</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 557 <dt><span class="paramLabel">Parameters:</span></dt>
 558 <dd><code>presetName</code> - the name of the preset. if no name is provided, then the
 559             default preset is returned. If no limit for a particular
 560             preset is defined then the default preset is returned</dd>
 561 <dt><span class="returnLabel">Returns:</span></dt>
 562 <dd>Limit</dd>
 563 </dl>
 564 </li>
 565 </ul>
 566 <a name="getLimits--">
 567 <!--   -->
 568 </a>
 569 <ul class="blockList">
 570 <li class="blockList">
 571 <h4>getLimits</h4>
 572 <pre>public&nbsp;<a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;getLimits()</pre>
 573 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getLimits--">Metadata</a></code></span></div>
 574 <div class="block">List Limits supported by a web service.</div>
 575 <dl>
 576 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 577 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getLimits--">getLimits</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 578 <dt><span class="returnLabel">Returns:</span></dt>
 579 <dd>LimitManager</dd>
 580 </dl>
 581 </li>
 582 </ul>
 583 <a name="cancelJob-java.lang.String-">
 584 <!--   -->
 585 </a>
 586 <ul class="blockList">
 587 <li class="blockList">
 588 <h4>cancelJob</h4>
 589 <pre>public&nbsp;boolean&nbsp;cancelJob(java.lang.String&nbsp;jobId)</pre>
 590 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">JManagement</a></code></span></div>
 591 <div class="block">Stop running the job <code>jobId</code> but leave its output untouched</div>
 592 <dl>
 593 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 594 <dd><code><a href="../../../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">cancelJob</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
 595 <dt><span class="returnLabel">Returns:</span></dt>
 596 <dd>true if job was cancelled successfully, false otherwise</dd>
 597 </dl>
 598 </li>
 599 </ul>
 600 <a name="getJobStatus-java.lang.String-">
 601 <!--   -->
 602 </a>
 603 <ul class="blockList">
 604 <li class="blockList">
 605 <h4>getJobStatus</h4>
 606 <pre>public&nbsp;<a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a>&nbsp;getJobStatus(java.lang.String&nbsp;jobId)</pre>
 607 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">JManagement</a></code></span></div>
 608 <div class="block">Return the status of the job.</div>
 609 <dl>
 610 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 611 <dd><code><a href="../../../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">getJobStatus</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
 612 <dt><span class="paramLabel">Parameters:</span></dt>
 613 <dd><code>jobId</code> - - unique job identifier</dd>
 614 <dt><span class="returnLabel">Returns:</span></dt>
 615 <dd>JobStatus - status of the job</dd>
 616 <dt><span class="seeLabel">See Also:</span></dt>
 617 <dd><a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><code>JobStatus</code></a></dd>
 618 </dl>
 619 </li>
 620 </ul>
 621 <a name="getPresets--">
 622 <!--   -->
 623 </a>
 624 <ul class="blockList">
 625 <li class="blockList">
 626 <h4>getPresets</h4>
 627 <pre>public&nbsp;<a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;&nbsp;getPresets()</pre>
 628 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html#getPresets--">Metadata</a></code></span></div>
 629 <div class="block">Get presets supported by a web service</div>
 630 <dl>
 631 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 632 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getPresets--">getPresets</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a>&lt;<a href="../../../compbio/runner/msa/ClustalO.html" title="class in compbio.runner.msa">ClustalO</a>&gt;</code></dd>
 633 <dt><span class="returnLabel">Returns:</span></dt>
 634 <dd>PresetManager the object contains information about presets
 635          supported by a web service</dd>
 636 </dl>
 637 </li>
 638 </ul>
 639 <a name="pullExecStatistics-java.lang.String-long-">
 640 <!--   -->
 641 </a>
 642 <ul class="blockListLast">
 643 <li class="blockList">
 644 <h4>pullExecStatistics</h4>
 645 <pre>public&nbsp;<a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a>&nbsp;pullExecStatistics(java.lang.String&nbsp;jobId,
 646                                       long&nbsp;position)</pre>
 647 <div class="block"><span class="descfrmTypeLabel">Description copied from interface:&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">JManagement</a></code></span></div>
 648 <div class="block">Reads 1kb chunk from the statistics file which is specific to a given web
 649  service from the <code>position</code>. If in time of a request less then
 650  1kb data is available from the position to the end of the file, then it
 651  returns all the data available from the position to the end of the file.</div>
 652 <dl>
 653 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
 654 <dd><code><a href="../../../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics</a></code>&nbsp;in interface&nbsp;<code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
 655 <dt><span class="paramLabel">Parameters:</span></dt>
 656 <dd><code>jobId</code> - - unique job identifier</dd>
 657 <dd><code>position</code> - - next position within the file to read</dd>
 658 <dt><span class="returnLabel">Returns:</span></dt>
 659 <dd>ChunkHolder - which contains a chunk of data and a next position
 660          within the file from which no data has been read</dd>
 661 <dt><span class="seeLabel">See Also:</span></dt>
 662 <dd><a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><code>ChunkHolder</code></a></dd>
 663 </dl>
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