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76 <li>Summary: </li>
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78 <li><a href="#field.summary">Field</a> | </li>
79 <li><a href="#constructor.summary">Constr</a> | </li>
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95 <div class="subTitle">compbio.ws.server</div>
96 <h2 title="Class MafftWS" class="title">Class MafftWS</h2>
98 <div class="contentContainer">
99 <ul class="inheritance">
100 <li>java.lang.Object</li>
102 <ul class="inheritance">
103 <li>compbio.ws.server.MafftWS</li>
107 <div class="description">
108 <ul class="blockList">
109 <li class="blockList">
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><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>>, <a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></dd>
116 <pre>public class <span class="typeNameLabel">MafftWS</span>
117 extends java.lang.Object
118 implements <a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></pre>
122 <div class="summary">
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127 <li class="blockList"><a name="field.summary">
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"> </span></caption>
134 <th class="colFirst" scope="col">Modifier and Type</th>
135 <th class="colLast" scope="col">Field and Description</th>
137 <tr class="altColor">
138 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
139 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#limitMan">limitMan</a></span></code> </td>
141 <tr class="rowColor">
142 <td class="colFirst"><code>private static org.apache.log4j.Logger</code></td>
143 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#log">log</a></span></code> </td>
145 <tr class="altColor">
146 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
147 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#mafftOptions">mafftOptions</a></span></code> </td>
149 <tr class="rowColor">
150 <td class="colFirst"><code>private static <a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
151 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#mafftPresets">mafftPresets</a></span></code> </td>
154 <ul class="blockList">
155 <li class="blockList"><a name="fields.inherited.from.class.compbio.data.msa.JABAService">
158 <h3>Fields inherited from interface 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>
163 <!-- ======== CONSTRUCTOR SUMMARY ======== -->
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165 <li class="blockList"><a name="constructor.summary">
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"> </span></caption>
172 <th class="colOne" scope="col">Constructor and Description</th>
174 <tr class="altColor">
175 <td class="colOne"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#MafftWS--">MafftWS</a></span>()</code> </td>
180 <!-- ========== METHOD SUMMARY =========== -->
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182 <li class="blockList"><a name="method.summary">
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"> </span></span><span id="t2" class="tableTab"><span><a href="javascript:show(2);">Instance Methods</a></span><span class="tabEnd"> </span></span><span id="t4" class="tableTab"><span><a href="javascript:show(8);">Concrete Methods</a></span><span class="tabEnd"> </span></span></caption>
189 <th class="colFirst" scope="col">Modifier and Type</th>
190 <th class="colLast" scope="col">Method and Description</th>
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/MafftWS.html#align-java.util.List-">align</a></span>(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences)</code>
195 <div class="block">Align a list of sequences with default settings.</div>
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/MafftWS.html#cancelJob-java.lang.String-">cancelJob</a></span>(java.lang.String jobId)</code>
201 <div class="block">Stop running the job <code>jobId</code> but leave its output untouched</div>
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/MafftWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></span>(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
207 java.util.List<<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>>> options)</code>
208 <div class="block">Align a list of sequences with options.</div>
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/MafftWS.html#getJobStatus-java.lang.String-">getJobStatus</a></span>(java.lang.String jobId)</code>
214 <div class="block">Return the status of the job.</div>
217 <tr id="i4" class="altColor">
218 <td class="colFirst"><code><a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
219 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#getLimit-java.lang.String-">getLimit</a></span>(java.lang.String presetName)</code>
220 <div class="block">Get a Limit for a preset.</div>
223 <tr id="i5" class="rowColor">
224 <td class="colFirst"><code><a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
225 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#getLimits--">getLimits</a></span>()</code>
226 <div class="block">List Limits supported by a web service.</div>
229 <tr id="i6" class="altColor">
230 <td class="colFirst"><code><a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
231 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#getPresets--">getPresets</a></span>()</code>
232 <div class="block">Get presets supported by a web service</div>
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/MafftWS.html#getResult-java.lang.String-">getResult</a></span>(java.lang.String jobId)</code>
238 <div class="block">Return the result of the job.</div>
241 <tr id="i8" class="altColor">
242 <td class="colFirst"><code><a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
243 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#getRunnerOptions--">getRunnerOptions</a></span>()</code>
244 <div class="block">Get options supported by a web service</div>
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><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></td>
249 <td class="colLast"><code><span class="memberNameLink"><a href="../../../compbio/ws/server/MafftWS.html#init-java.util.List-">init</a></span>(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> dataSet)</code> </td>
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/MafftWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></span>(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
254 <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> preset)</code>
255 <div class="block">Align a list of sequences with preset.</div>
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/MafftWS.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics</a></span>(java.lang.String jobId,
261 long 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>
267 <ul class="blockList">
268 <li class="blockList"><a name="methods.inherited.from.class.java.lang.Object">
271 <h3>Methods inherited from class java.lang.Object</h3>
272 <code>clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait</code></li>
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">
287 <h3>Field Detail</h3>
291 <ul class="blockList">
292 <li class="blockList">
294 <pre>private static org.apache.log4j.Logger log</pre>
297 <a name="mafftOptions">
300 <ul class="blockList">
301 <li class="blockList">
302 <h4>mafftOptions</h4>
303 <pre>private static final <a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> mafftOptions</pre>
306 <a name="mafftPresets">
309 <ul class="blockList">
310 <li class="blockList">
311 <h4>mafftPresets</h4>
312 <pre>private static final <a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> mafftPresets</pre>
318 <ul class="blockListLast">
319 <li class="blockList">
321 <pre>private static final <a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> limitMan</pre>
326 <!-- ========= CONSTRUCTOR DETAIL ======== -->
327 <ul class="blockList">
328 <li class="blockList"><a name="constructor.detail">
331 <h3>Constructor Detail</h3>
335 <ul class="blockListLast">
336 <li class="blockList">
338 <pre>public MafftWS()</pre>
343 <!-- ============ METHOD DETAIL ========== -->
344 <ul class="blockList">
345 <li class="blockList"><a name="method.detail">
348 <h3>Method Detail</h3>
349 <a name="align-java.util.List-">
352 <ul class="blockList">
353 <li class="blockList">
355 <pre>public java.lang.String align(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> 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: <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.
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>
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> in interface <code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></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>
390 <a name="init-java.util.List-">
393 <ul class="blockList">
394 <li class="blockList">
396 <pre><a href="../../../compbio/engine/client/ConfiguredExecutable.html" title="interface in compbio.engine.client">ConfiguredExecutable</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> init(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> dataSet)
397 throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a></pre>
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>
404 <a name="customAlign-java.util.List-java.util.List-">
407 <ul class="blockList">
408 <li class="blockList">
410 <pre>public java.lang.String customAlign(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
411 java.util.List<<a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata">Option</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>>> options)
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: <code><a href="../../../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">MsaWS</a></code></span></div>
415 <div class="block">Align a list of sequences with options.</div>
417 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
418 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#customAlign-java.util.List-java.util.List-">customAlign</a></code> in interface <code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></dd>
419 <dt><span class="paramLabel">Parameters:</span></dt>
420 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
421 any sequence validity checks. Nor does it checks whether the
422 sequences names are unique. It is responsibility of the caller
423 to validate this information</dd>
424 <dd><code>options</code> - A list of Options</dd>
425 <dt><span class="returnLabel">Returns:</span></dt>
426 <dd>jobId - unique identifier for the job</dd>
427 <dt><span class="throwsLabel">Throws:</span></dt>
428 <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
429 following reasons: 1) The number of sequences in the
430 submission or their average length is greater then defined by
431 the default Limit. 2) Any problems on the server side e.g. it
432 is misconfigured or malfunction, is reported via this
433 exception. In the first case the information on the limit
434 could be obtained from an exception.</dd>
435 <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
436 given web service, e.g. JABAWS is deployed on Windows and
437 Mafft service is called</dd>
438 <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
439 length exceeds what is defined by the limit</dd>
440 <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
441 supported, 2) The value of the option is defined outside the
442 boundaries. In both cases exception object contain the
443 information on the violating Option.</dd>
444 <dt><span class="seeLabel">See Also:</span></dt>
445 <dd><a href="../../../compbio/metadata/Option.html" title="class in compbio.metadata"><code>Default Limit is used to decide whether the calculation will be
446 permitted or denied</code></a></dd>
450 <a name="presetAlign-java.util.List-compbio.metadata.Preset-">
453 <ul class="blockList">
454 <li class="blockList">
456 <pre>public java.lang.String presetAlign(java.util.List<<a href="../../../compbio/data/sequence/FastaSequence.html" title="class in compbio.data.sequence">FastaSequence</a>> sequences,
457 <a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata">Preset</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> preset)
458 throws <a href="../../../compbio/metadata/JobSubmissionException.html" title="class in compbio.metadata">JobSubmissionException</a>,
459 <a href="../../../compbio/metadata/WrongParameterException.html" title="class in compbio.metadata">WrongParameterException</a></pre>
460 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">MsaWS</a></code></span></div>
461 <div class="block">Align a list of sequences with preset.
463 Limit for a presetName is used whether the calculation will be permitted
464 or denied. If no Limit was defined for a presetName, than default limit
467 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
468 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#presetAlign-java.util.List-compbio.metadata.Preset-">presetAlign</a></code> in interface <code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></dd>
469 <dt><span class="paramLabel">Parameters:</span></dt>
470 <dd><code>sequences</code> - List of FastaSequence objects. The programme does not perform
471 any sequence validity checks. Nor does it checks whether the
472 sequences names are unique. It is responsibility of the caller
473 to validate this information</dd>
474 <dd><code>preset</code> - A list of Options</dd>
475 <dt><span class="returnLabel">Returns:</span></dt>
476 <dd>String - jobId - unique identifier for the job</dd>
477 <dt><span class="throwsLabel">Throws:</span></dt>
478 <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
479 following reasons: 1) The number of sequences in the
480 submission or their average length is greater then defined by
481 the default Limit. 2) Any problems on the server side e.g. it
482 is misconfigured or malfunction, is reported via this
483 exception. In the first case the information on the limit
484 could be obtained from an exception.</dd>
485 <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
486 given web service, e.g. JABAWS is deployed on Windows and
487 Mafft service is called</dd>
488 <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
489 exceeds what is defined by the limit</dd>
490 <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
491 supported, 2) The value of the option is defined outside the
492 boundaries. In both cases exception object contain the
493 information on the violating Option.</dd>
494 <dt><span class="seeLabel">See Also:</span></dt>
495 <dd><a href="../../../compbio/metadata/Preset.html" title="class in compbio.metadata"><code>Preset</code></a></dd>
499 <a name="getResult-java.lang.String-">
502 <ul class="blockList">
503 <li class="blockList">
505 <pre>public <a href="../../../compbio/data/sequence/Alignment.html" title="class in compbio.data.sequence">Alignment</a> getResult(java.lang.String jobId)
506 throws <a href="../../../compbio/metadata/ResultNotAvailableException.html" title="class in compbio.metadata">ResultNotAvailableException</a></pre>
507 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">MsaWS</a></code></span></div>
508 <div class="block">Return the result of the job. This method waits for the job
509 <code>jobId</code> to complete before return.</div>
511 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
512 <dd><code><a href="../../../compbio/data/msa/MsaWS.html#getResult-java.lang.String-">getResult</a></code> in interface <code><a href="../../../compbio/data/msa/MsaWS.html" title="interface in compbio.data.msa">MsaWS</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></dd>
513 <dt><span class="paramLabel">Parameters:</span></dt>
514 <dd><code>jobId</code> - a unique job identifier</dd>
515 <dt><span class="returnLabel">Returns:</span></dt>
517 <dt><span class="throwsLabel">Throws:</span></dt>
518 <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
519 successful or the result of the execution could not be found.
520 (e.g. removed). Exception could also be thrown due to the
521 lower level problems on the server i.e. IOException,
522 FileNotFoundException problems as well as
523 UnknownFileFormatException.</dd>
527 <a name="getLimit-java.lang.String-">
530 <ul class="blockList">
531 <li class="blockList">
533 <pre>public <a href="../../../compbio/metadata/Limit.html" title="class in compbio.metadata">Limit</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> getLimit(java.lang.String presetName)</pre>
534 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">Metadata</a></code></span></div>
535 <div class="block">Get a Limit for a preset.</div>
537 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
538 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getLimit-java.lang.String-">getLimit</a></code> in interface <code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></dd>
539 <dt><span class="paramLabel">Parameters:</span></dt>
540 <dd><code>presetName</code> - the name of the preset. if no name is provided, then the
541 default preset is returned. If no limit for a particular
542 preset is defined then the default preset is returned</dd>
543 <dt><span class="returnLabel">Returns:</span></dt>
548 <a name="getLimits--">
551 <ul class="blockList">
552 <li class="blockList">
554 <pre>public <a href="../../../compbio/metadata/LimitsManager.html" title="class in compbio.metadata">LimitsManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> getLimits()</pre>
555 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/Metadata.html#getLimits--">Metadata</a></code></span></div>
556 <div class="block">List Limits supported by a web service.</div>
558 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
559 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getLimits--">getLimits</a></code> in interface <code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></dd>
560 <dt><span class="returnLabel">Returns:</span></dt>
561 <dd>LimitManager</dd>
565 <a name="pullExecStatistics-java.lang.String-long-">
568 <ul class="blockList">
569 <li class="blockList">
570 <h4>pullExecStatistics</h4>
571 <pre>public <a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata">ChunkHolder</a> pullExecStatistics(java.lang.String jobId,
572 long position)</pre>
573 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">JManagement</a></code></span></div>
574 <div class="block">Reads 1kb chunk from the statistics file which is specific to a given web
575 service from the <code>position</code>. If in time of a request less then
576 1kb data is available from the position to the end of the file, then it
577 returns all the data available from the position to the end of the file.</div>
579 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
580 <dd><code><a href="../../../compbio/data/msa/JManagement.html#pullExecStatistics-java.lang.String-long-">pullExecStatistics</a></code> in interface <code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
581 <dt><span class="paramLabel">Parameters:</span></dt>
582 <dd><code>jobId</code> - - unique job identifier</dd>
583 <dd><code>position</code> - - next position within the file to read</dd>
584 <dt><span class="returnLabel">Returns:</span></dt>
585 <dd>ChunkHolder - which contains a chunk of data and a next position
586 within the file from which no data has been read</dd>
587 <dt><span class="seeLabel">See Also:</span></dt>
588 <dd><a href="../../../compbio/metadata/ChunkHolder.html" title="class in compbio.metadata"><code>ChunkHolder</code></a></dd>
592 <a name="cancelJob-java.lang.String-">
595 <ul class="blockList">
596 <li class="blockList">
598 <pre>public boolean cancelJob(java.lang.String jobId)</pre>
599 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">JManagement</a></code></span></div>
600 <div class="block">Stop running the job <code>jobId</code> but leave its output untouched</div>
602 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
603 <dd><code><a href="../../../compbio/data/msa/JManagement.html#cancelJob-java.lang.String-">cancelJob</a></code> in interface <code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
604 <dt><span class="returnLabel">Returns:</span></dt>
605 <dd>true if job was cancelled successfully, false otherwise</dd>
609 <a name="getJobStatus-java.lang.String-">
612 <ul class="blockList">
613 <li class="blockList">
614 <h4>getJobStatus</h4>
615 <pre>public <a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata">JobStatus</a> getJobStatus(java.lang.String jobId)</pre>
616 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">JManagement</a></code></span></div>
617 <div class="block">Return the status of the job.</div>
619 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
620 <dd><code><a href="../../../compbio/data/msa/JManagement.html#getJobStatus-java.lang.String-">getJobStatus</a></code> in interface <code><a href="../../../compbio/data/msa/JManagement.html" title="interface in compbio.data.msa">JManagement</a></code></dd>
621 <dt><span class="paramLabel">Parameters:</span></dt>
622 <dd><code>jobId</code> - - unique job identifier</dd>
623 <dt><span class="returnLabel">Returns:</span></dt>
624 <dd>JobStatus - status of the job</dd>
625 <dt><span class="seeLabel">See Also:</span></dt>
626 <dd><a href="../../../compbio/metadata/JobStatus.html" title="enum in compbio.metadata"><code>JobStatus</code></a></dd>
630 <a name="getPresets--">
633 <ul class="blockList">
634 <li class="blockList">
636 <pre>public <a href="../../../compbio/metadata/PresetManager.html" title="class in compbio.metadata">PresetManager</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> getPresets()</pre>
637 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/Metadata.html#getPresets--">Metadata</a></code></span></div>
638 <div class="block">Get presets supported by a web service</div>
640 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
641 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getPresets--">getPresets</a></code> in interface <code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></dd>
642 <dt><span class="returnLabel">Returns:</span></dt>
643 <dd>PresetManager the object contains information about presets
644 supported by a web service</dd>
648 <a name="getRunnerOptions--">
651 <ul class="blockListLast">
652 <li class="blockList">
653 <h4>getRunnerOptions</h4>
654 <pre>public <a href="../../../compbio/metadata/RunnerConfig.html" title="class in compbio.metadata">RunnerConfig</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>> getRunnerOptions()</pre>
655 <div class="block"><span class="descfrmTypeLabel">Description copied from interface: <code><a href="../../../compbio/data/msa/Metadata.html#getRunnerOptions--">Metadata</a></code></span></div>
656 <div class="block">Get options supported by a web service</div>
658 <dt><span class="overrideSpecifyLabel">Specified by:</span></dt>
659 <dd><code><a href="../../../compbio/data/msa/Metadata.html#getRunnerOptions--">getRunnerOptions</a></code> in interface <code><a href="../../../compbio/data/msa/Metadata.html" title="interface in compbio.data.msa">Metadata</a><<a href="../../../compbio/runner/msa/Mafft.html" title="class in compbio.runner.msa">Mafft</a>></code></dd>
660 <dt><span class="returnLabel">Returns:</span></dt>
661 <dd>RunnerConfig the list of options and parameters supported by a
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