*/\r
@XmlAccessorType(XmlAccessType.FIELD)\r
@Immutable\r
-public final class Alignment {\r
+public class Alignment {\r
\r
private AlignmentMetadata metadata;\r
private List<FastaSequence> sequences;\r
\r
- private Alignment() {\r
+ protected Alignment() {\r
// This has to has a default constructor for JaxB\r
}\r
\r
--- /dev/null
+/* Copyright (c) 2009 Peter Troshin\r
+ * Copyright (c) 2013 Alexander Sherstnev\r
+ * \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 1.0\r
+ * \r
+ * This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ * Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ * License for more details.\r
+ * \r
+ * A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+\r
+package compbio.data.sequence;\r
+\r
+import java.util.List;\r
+import java.util.ArrayList;\r
+\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+\r
+import compbio.util.annotation.Immutable;\r
+import compbio.data.sequence.Alignment;\r
+/**\r
+ * Multiple sequence alignment and Jpred prediction.\r
+ * \r
+ * Does not give any guarantees on the content of individual FastaSequece\r
+ * records. It does not guarantee neither the uniqueness of the names of\r
+ * sequences nor it guarantees the uniqueness of the sequences.\r
+ * \r
+ * @see FastaSequence\r
+ * @see AlignmentMetadata\r
+ * \r
+ * @author pvtroshin\r
+ * \r
+ * @version 1.0 September 2009\r
+ * \r
+ */\r
+@XmlAccessorType(XmlAccessType.FIELD)\r
+@Immutable\r
+public final class JpredAlignment extends Alignment{\r
+\r
+ private AlignmentMetadata metadata;\r
+ private List<FastaSequence> sequences;\r
+ \r
+ FastaSequence jnetpred;\r
+ FastaSequence JNETCONF;\r
+ FastaSequence JNETSOL25;\r
+ FastaSequence JNETSOL5;\r
+ FastaSequence JNETSOL0;\r
+ FastaSequence JNETHMM;\r
+ FastaSequence JNETPSSM;\r
+ FastaSequence JNETJURY;\r
+\r
+ private JpredAlignment() {\r
+ // This has to has a default constructor for JaxB\r
+ }\r
+\r
+ /**\r
+ * @param sequences\r
+ * @param program\r
+ * @param gapchar\r
+ */\r
+ public JpredAlignment(List<FastaSequence> sequences, Program program,\r
+ char gapchar) {\r
+ DecomposeInitalJpredSeq(sequences);\r
+ this.metadata = new AlignmentMetadata(Program.CLUSTAL, gapchar);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param sequences\r
+ * @param metadata\r
+ */\r
+ public JpredAlignment(List<FastaSequence> sequences, AlignmentMetadata metadata) {\r
+ DecomposeInitalJpredSeq(sequences);\r
+ this.metadata = metadata;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @param sequences\r
+ */\r
+ private void DecomposeInitalJpredSeq(List<FastaSequence> sequences) {\r
+ List<FastaSequence> realsequences = new ArrayList<FastaSequence>();\r
+ for (FastaSequence s : sequences) {\r
+ if (s.getId().equals("jnetpred")) {\r
+ this.jnetpred = s;\r
+ } else if (s.getId().equals("JNETCONF")) {\r
+ this.JNETCONF = s;\r
+ } else if (s.getId().equals("JNETSOL25")) {\r
+ this.JNETSOL25 = s;\r
+ } else if (s.getId().equals("JNETSOL5")) {\r
+ this.JNETSOL5 = s;\r
+ } else if (s.getId().equals("JNETSOL0")) {\r
+ this.JNETSOL0 = s;\r
+ } else if (s.getId().equals("JNETHMM")) {\r
+ this.JNETSOL0 = s;\r
+ } else if (s.getId().equals("JNETHMM")) {\r
+ this.JNETHMM = s;\r
+ } else if (s.getId().equals("JNETSOL0")) {\r
+ this.JNETPSSM = s;\r
+ } else if (s.getId().equals("JNETHMM")) {\r
+ this.JNETJURY = s;\r
+ } else {\r
+ realsequences.add(s);\r
+ }\r
+ }\r
+ this.sequences = realsequences;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return Jpred prediction \r
+ */\r
+ public String getJpredPrediction() {\r
+ return this.jnetpred.getSequence();\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return Jpred JNETSOL25 line\r
+ */\r
+ public String getJpredSOL25() {\r
+ return this.JNETSOL25.getSequence();\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return Jpred JNETSOL5 line\r
+ */\r
+ public String getJpredSOL5() {\r
+ return this.JNETSOL5.getSequence();\r
+ }\r
+ /**\r
+ * \r
+ * @return Jpred JNETSOL0 line\r
+ */\r
+ public String getJpredSOL0() {\r
+ return this.JNETSOL0.getSequence();\r
+ }\r
+ /**\r
+ * \r
+ * @return Jpred JNETCONF line\r
+ */\r
+ public String getJpredJNETCONF() {\r
+ return this.JNETCONF.getSequence();\r
+ }\r
+ /**\r
+ * \r
+ * @return list of FastaSequence records\r
+ */\r
+ public List<FastaSequence> getSequences() {\r
+ return sequences;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return a number of sequence in the alignment\r
+ */\r
+ public int getSize() {\r
+ return this.sequences.size();\r
+ }\r
+\r
+ /**\r
+ * \r
+ * @return AlignmentMetadata object\r
+ */\r
+ public AlignmentMetadata getMetadata() {\r
+ return metadata;\r
+ }\r
+\r
+ @Override\r
+ public String toString() {\r
+ String sseq = "";\r
+ for (FastaSequence fs : getSequences()) {\r
+ sseq += fs.toString() + "\n";\r
+ }\r
+ return sseq;\r
+ }\r
+\r
+ @Override\r
+ public int hashCode() {\r
+ final int prime = 31;\r
+ int result = 1;\r
+ result = prime * result\r
+ + ((metadata == null) ? 0 : metadata.hashCode());\r
+ result = prime * result\r
+ + ((sequences == null) ? 0 : sequences.hashCode());\r
+ return result;\r
+ }\r
+\r
+ /**\r
+ * Please note that this implementation does not take the order of sequences\r
+ * into account!\r
+ */\r
+ @Override\r
+ public boolean equals(Object obj) {\r
+ if (obj == null) {\r
+ return false;\r
+ }\r
+ if (!(obj instanceof Alignment)) {\r
+ return false;\r
+ }\r
+ Alignment al = (Alignment) obj;\r
+ if (this.getSize() != al.getSize()) {\r
+ return false;\r
+ }\r
+ if (!this.getMetadata().equals(al.getMetadata())) {\r
+ return false;\r
+ }\r
+ int outerCounter = 0;\r
+ int matchCounter = 0;\r
+ for (FastaSequence fs : getSequences()) {\r
+ outerCounter++;\r
+ for (FastaSequence fs1 : al.getSequences()) {\r
+ if (fs.equals(fs1)) {\r
+ matchCounter++;\r
+ continue;\r
+ }\r
+ }\r
+ // Match for at lease one element was not found!\r
+ if (outerCounter != matchCounter) {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ return true;\r
+ }\r
+\r
+}\r
\r
import org.apache.log4j.Logger;\r
\r
-import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.JpredAlignment;\r
import compbio.data.sequence.AlignmentMetadata;\r
import compbio.data.sequence.Program;\r
-import compbio.data.sequence.ScoreManager;\r
import compbio.data.sequence.SequenceUtil;\r
import compbio.engine.client.CommandBuilder;\r
import compbio.engine.client.Executable;\r
import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ResultNotAvailableException;\r
-import compbio.runner.Util;\r
\r
/**\r
* Command line\r
\r
public Jpred() {\r
addParameters(Arrays.asList("-logfile " + STAT_FILE));\r
+ addParameters(Arrays.asList("-jabaws"));\r
}\r
\r
// HashMap<Method, float[]>\r
+ @SuppressWarnings("unchecked")\r
@Override\r
- public Alignment getResults(String workDirectory)\r
+ public JpredAlignment getResults(String workDirectory)\r
throws ResultNotAvailableException {\r
- Alignment annotations = null;\r
+ JpredAlignment annotations = null;\r
try {\r
InputStream inStream = new FileInputStream(new File(workDirectory, getOutput()));\r
- annotations = new Alignment(SequenceUtil.readJpredFile(inStream), new AlignmentMetadata(Program.Jpred, '-'));\r
+ annotations = new JpredAlignment(SequenceUtil.readJpredFile(inStream), new AlignmentMetadata(Program.Jpred, '-'));\r
} catch (FileNotFoundException e) {\r
log.error(e.getMessage(), e.getCause());\r
throw new ResultNotAvailableException(e);\r
import org.testng.annotations.BeforeMethod;\r
import org.testng.annotations.Test;\r
\r
-import compbio.data.sequence.Alignment;\r
+import compbio.data.sequence.JpredAlignment;\r
import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.FilePuller;\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- Alignment annotations = confpred.getResults();\r
- assertNotNull(annotations);\r
- assertEquals(annotations.getSize(), 19);\r
- assertEquals(al1.getResults(), annotations);\r
+ JpredAlignment totalign = (JpredAlignment) confpred.getResults();\r
+ assertNotNull(totalign);\r
+ assertEquals(totalign.getSize(), 14);\r
+ assertEquals(al1.getResults(), totalign);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
}\r
}\r
\r
- @Test(groups = {AllTestSuit.test_group_runner})\r
+ @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
public void RunLocallyWithPreset() {\r
try {\r
ConfiguredExecutable<Jpred> confpred = Configurator.configureExecutable(pred, Executable.ExecProvider.Local);\r
lr.executeJob();\r
ConfiguredExecutable<?> al1 = lr.waitForResult();\r
assertNotNull(al1.getResults());\r
- Alignment annotations = confpred.getResults();\r
- assertNotNull(annotations);\r
- assertEquals(annotations.getSize(), 19);\r
- assertEquals(al1.getResults(), annotations);\r
+ JpredAlignment totalign = (JpredAlignment) confpred.getResults();\r
+ assertNotNull(totalign);\r
+ assertEquals(totalign.getSize(), 19);\r
+ assertEquals(al1.getResults(), totalign);\r
} catch (JobSubmissionException e) {\r
e.printStackTrace();\r
fail(e.getLocalizedMessage());\r
}\r
}\r
\r
- @Test(groups = {AllTestSuit.test_group_runner})\r
+ @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
public void readStatistics() {\r
try {\r
Jpred jpred = new Jpred();\r
}\r
}\r
\r
- @Test(groups = {AllTestSuit.test_group_runner})\r
+ @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
public void Persistance() {\r
try {\r
Jpred jpred = new Jpred();\r
}\r
}\r
\r
- @Test(groups = {AllTestSuit.test_group_runner})\r
+ @Test(enabled=false,groups = {AllTestSuit.test_group_runner})\r
public void ConfigurationLoading() {\r
try {\r
RunnerConfig<Jpred> jpredConfig = ConfExecutable.getRunnerOptions(Jpred.class);\r
Class<? extends JABAService> getServiceType() {\r
switch (this) {\r
case AAConWS :\r
- case JpredWS :\r
case JronnWS :\r
case DisemblWS :\r
case GlobPlotWS :\r
case IUPredWS :\r
return SequenceAnnotation.class;\r
+ case JpredWS :\r
case ClustalWS :\r
case ClustalOWS :\r
case MafftWS :\r
/* Copyright (c) 2011 Peter Troshin\r
+ * Copyright (c) 2013 Alexander Sherstnev\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0\r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
* \r
* @author pvtroshin\r
* \r
- * @version 1.0 February 2010\r
+ * @version 1.5 February 2013\r
*/\r
public class WSTester {\r
\r
/**\r
- * Sequences to be used as input for all WS\r
+ * Test sequences to be used as input for WS\r
*/\r
- public static final String fastaInput2records = ">Foo\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
- + "\n>Bar\n"\r
- + "ASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
- public static final String fastaInput1record = ">Foo\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV"\r
- + "\n";\r
-\r
- public static final String fastaAlignment = ">Foo\n"\r
- + "MTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
- + ">Bar\n"\r
- + "ASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n"\r
- + "";\r
-\r
- static final List<FastaSequence> seqs = loadSeqs(2);\r
+ public static final String fastaInput2records = \r
+ ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n"\r
+ + ">Bar\nASDAAPEHPGIALWLHALEDAGQAEAAAAYTRAHQLLPEEPYITAQLLNAVA\n";\r
+ public static final String fastaInput1record = \r
+ ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV\n";\r
+ public static final String fastaAlignment = \r
+ ">Foo\nMTADGPRELLQLRAAVRHRPQDFVAWLMLADAELGMGDTTAGEMAVQRGLALHPGHPEAV--------\n"\r
+ + ">Bar\nASDAAPEH------------PGIALWLHALE-DAGQAEAAA---AYTRAHQLLPEEPYITAQLLNAVA\n";\r
\r
+ /**\r
+ * Status strings\r
+ */\r
private static final String FAILED = "FAILED";\r
private static final String OK = "OK";\r
-\r
private static final String UNSUPPORTED = "UNSUPPORTED";\r
\r
/**\r
writer.print("Aligning with preset '" + preset.getName() + "'... ");\r
Alignment al = null;\r
try {\r
- String taskId = msaws.presetAlign(seqs, preset);\r
+ String taskId = msaws.presetAlign(loadSeqs(2), preset);\r
al = msaws.getResult(taskId);\r
if (al != null) {\r
writer.println(OK);\r
return succeed;\r
}\r
\r
- private <T> boolean testMsaWS(MsaWS<T> msaws) throws Exception {\r
+ private <T> boolean testMsaWS(MsaWS<T> msaws, Services service) throws Exception {\r
assert msaws != null;\r
\r
- boolean succeed = testDefaultAlignment(msaws);\r
+ boolean succeed = testDefaultAlignment(msaws, service);\r
// If exception above is thrown than the tests below is not run\r
\r
PresetManager<T> pmanager = msaws.getPresets();\r
}\r
\r
if (wservice instanceof MsaWS) {\r
- return testMsaWS((MsaWS<T>) wservice);\r
+ return testMsaWS((MsaWS<T>) wservice, service);\r
} else if (wservice instanceof SequenceAnnotation) {\r
return testSequenceAnnotationWS(\r
(SequenceAnnotation<T>) wservice, service);\r
if (service == Services.AAConWS) {\r
input = loadAlignment();\r
}\r
- if (service == Services.JpredWS) {\r
- input = loadSeqs(1);\r
- }\r
boolean success = testDefaultAnalyse(input, wservice, null, null);\r
\r
PresetManager<T> presetman = wservice.getPresets();\r
* @param msaws\r
* @throws UnsupportedRuntimeException\r
*/\r
- private <T> boolean testDefaultAlignment(MsaWS<T> msaws) throws Exception {\r
+ private <T> boolean testDefaultAlignment(MsaWS<T> msaws, Services service) throws Exception {\r
writer.print("Testing alignment with default parameters:");\r
Alignment al = null;\r
boolean succeed = false;\r
+ String taskId;\r
\r
- String taskId = msaws.align(seqs);\r
+ if (service == Services.JpredWS) {\r
+ taskId = msaws.align(loadSeqs(1));\r
+ } else {\r
+ taskId = msaws.align(loadSeqs(2));\r
+ }\r
writer.print("\nQuerying job status...");\r
JobStatus status = msaws.getJobStatus(taskId);\r
while (status != JobStatus.FINISHED) {\r
/* Copyright (c) 2011 Peter Troshin\r
- * Copyright (c) 2013 Alexander Sherstnev\r
* \r
- * JAva Bioinformatics Analysis Web Services (JABAWS)\r
- * @version: 2.5 \r
+ * JAva Bioinformatics Analysis Web Services (JABAWS) @version: 2.0 \r
* \r
* This library is free software; you can redistribute it and/or modify it under the terms of the\r
* Apache License version 2 as published by the Apache Software Foundation\r
* Any republication or derived work distributed in source code form\r
* must include this copyright and license notice.\r
*/\r
+\r
package compbio.ws.server;\r
\r
import java.io.File;\r
import org.apache.log4j.Logger;\r
\r
import compbio.data.msa.JABAService;\r
-import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.msa.MsaWS;\r
+import compbio.data.sequence.Alignment;\r
import compbio.data.sequence.FastaSequence;\r
+import compbio.engine.AsyncExecutor;\r
import compbio.engine.Configurator;\r
import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.engine.client.Executable;\r
+import compbio.engine.client.SkeletalExecutable;\r
import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobStatus;\r
import compbio.metadata.JobSubmissionException;\r
-import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.Limit;\r
+import compbio.metadata.LimitsManager;\r
import compbio.metadata.Option;\r
import compbio.metadata.Preset;\r
-import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.PresetManager;\r
+import compbio.metadata.ResultNotAvailableException;\r
+import compbio.metadata.RunnerConfig;\r
import compbio.metadata.WrongParameterException;\r
+import compbio.runner.Util;\r
import compbio.runner.predictors.Jpred;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS")\r
-public class JpredWS extends SequenceAnnotationService<Jpred>\r
- implements SequenceAnnotation<Jpred> {\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS")\r
+public class JpredWS implements MsaWS<Jpred> {\r
\r
private static Logger log = Logger.getLogger(JpredWS.class);\r
\r
- public JpredWS() {\r
- super(new Jpred(), log);\r
+ private static final RunnerConfig<Jpred> jpredOptions = Util.getSupportedOptions(Jpred.class);\r
+\r
+ private static final PresetManager<Jpred> jpredPresets = Util.getPresets(Jpred.class);\r
+\r
+ private static final LimitsManager<Jpred> limitMan = compbio.engine.client.Util.getLimits(new Jpred().getType());\r
+\r
+ @Override\r
+ public String align(List<FastaSequence> sequences)\r
+ throws JobSubmissionException {\r
+\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<Jpred> confClust = init(sequences);\r
+ return WSUtil.align(sequences, confClust, log, "align", getLimit(""));\r
+ }\r
+\r
+ ConfiguredExecutable<Jpred> init(List<FastaSequence> dataSet)\r
+ throws JobSubmissionException {\r
+ Jpred jpred = new Jpred();\r
+ jpred.setInput(SkeletalExecutable.INPUT);\r
+ jpred.setOutput(SkeletalExecutable.OUTPUT);\r
+ jpred.setError(SkeletalExecutable.ERROR);\r
+ ConfiguredExecutable<Jpred> confClust = Configurator.configureExecutable(jpred, dataSet);\r
+ // Set the number of threads for the cluster execution from conf file\r
+ if (confClust.getExecProvider() == Executable.ExecProvider.Cluster) {\r
+ int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(jpred.getType());\r
+ if (clusterCpuNum != 0) {\r
+ jpred.setNCore(clusterCpuNum);\r
+ }\r
+ }\r
+ return confClust;\r
}\r
\r
@Override\r
- public String analize(List<FastaSequence> sequences)\r
- throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException {\r
- WSUtil.validateJpredInput(sequences);\r
- ConfiguredExecutable<Jpred> confpred = init(sequences);\r
-\r
- // set default conservation method to fastest - SHENKIN\r
- // TODO: This violates encapsulation, should be moved to the runners\r
- // level.\r
- //confpred.addParameters(Arrays.asList("-m=SHENKIN"));\r
- return WSUtil.analize(sequences, confpred, log, "JpredWS analize", getLimit(""));\r
+ public String presetAlign(List<FastaSequence> sequences,\r
+ Preset<Jpred> preset) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ if (preset == null) {\r
+ throw new WrongParameterException("Preset must be provided!");\r
+ }\r
+ Limit<Jpred> limit = getLimit(preset.getName());\r
+ ConfiguredExecutable<Jpred> confClust = init(sequences);\r
+ confClust.addParameters(preset.getOptions());\r
+ return WSUtil.align(sequences, confClust, log, "presetAlign", limit);\r
}\r
\r
@Override\r
- public String customAnalize(List<FastaSequence> sequences, List<Option<Jpred>> options) \r
- throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {\r
- WSUtil.validateJpredInput(sequences);\r
- return super.customAnalize(sequences, options);\r
+ public String customAlign(List<FastaSequence> sequences,\r
+ List<Option<Jpred>> options) throws JobSubmissionException,\r
+ WrongParameterException {\r
+ WSUtil.validateFastaInput(sequences);\r
+ ConfiguredExecutable<Jpred> confClust = init(sequences);\r
+ List<String> params = WSUtil.getCommands(options, Jpred.KEY_VALUE_SEPARATOR);\r
+ confClust.addParameters(params);\r
+ log.info("Setting parameters: " + params);\r
+ return WSUtil.align(sequences, confClust, log, "customAlign", getLimit(""));\r
+ }\r
+\r
+ @Override\r
+ public RunnerConfig<Jpred> getRunnerOptions() {\r
+ return jpredOptions;\r
+ }\r
+\r
+ @SuppressWarnings("unchecked")\r
+ @Override\r
+ public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
+ WSUtil.validateJobId(jobId);\r
+ AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
+ ConfiguredExecutable<Jpred> jpred = (ConfiguredExecutable<Jpred>) asyncEngine.getResults(jobId);\r
+ return jpred.getResults();\r
+ }\r
+\r
+ @Override\r
+ public Limit<Jpred> getLimit(String presetName) {\r
+ if (limitMan == null) {\r
+ // No limit is configured\r
+ return null;\r
+ }\r
+ Limit<Jpred> limit = limitMan.getLimitByName(presetName);\r
+ return limit;\r
+ }\r
+\r
+ @Override\r
+ public LimitsManager<Jpred> getLimits() {\r
+ return limitMan;\r
+ }\r
+\r
+ @Override\r
+ public boolean cancelJob(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ boolean result = WSUtil.cancelJob(jobId);\r
+ return result;\r
+ }\r
+\r
+ @Override\r
+ public JobStatus getJobStatus(String jobId) {\r
+ WSUtil.validateJobId(jobId);\r
+ JobStatus status = WSUtil.getJobStatus(jobId);\r
+ return status;\r
}\r
\r
@Override\r
- public String presetAnalize(List<FastaSequence> sequences, Preset<Jpred> preset)\r
- throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {\r
- WSUtil.validateJpredInput(sequences);\r
- return super.presetAnalize(sequences, preset);\r
+ public PresetManager<Jpred> getPresets() {\r
+ return jpredPresets;\r
}\r
\r
@Override\r
public ChunkHolder pullExecStatistics(String jobId, long position) {\r
WSUtil.validateJobId(jobId);\r
String file = Configurator.getWorkDirectory(jobId) + File.separator + Jpred.getStatFile();\r
- return WSUtil.pullFile(file, position);\r
+ ChunkHolder cholder = WSUtil.pullFile(file, position);\r
+ return cholder;\r
}\r
\r
}\r
git://source.jalview.org / jabaws.git / commitdiff