#####################################################################################################
# Key to database information and information for accessing them
+if (defined $jabaws) {
+ $db_path = "/data/UNIREFdb";
+ $db_entry = "cluster";
+}
+
my $database = {
## default database used by Jpred
## cluster-specific path for Jpred
cluster => {
- database => $db_path . "uniref90.filt",
- unfiltered => $db_path . "uniref90",
+ database => $db_path . "/uniref90.filt",
+ unfiltered => $db_path . "/uniref90",
},
## these other DBs are experimental ones used during development.
},
};
-pod2usage(' ERROR! Input file with a sequence should be provided with -sequence/-in') unless $infile;
-pod2usage(' ERROR! Unknown database at ' . $db_path . '. Use -dbpath and -dbname for configuring the database' ) unless exists $database->{$db_entry};
-pod2usage(' ERROR! UNIREF database doesn\'t exist. Use -dbpath and -dbname for configuring the database') unless -f $database->{$db_entry}{database};
+my $dp = $database->{$db_entry}{database};
+pod2usage("ERROR! Input file with a sequence should be provided with -sequence/-in") unless $infile;
+pod2usage("ERROR! Unknown database at $db_path. Use -dbpath and -dbname for configuring the database" ) unless exists $database->{$db_entry};
+pod2usage("ERROR! UNIREF database is not available at $dp. Use -dbpath and -dbname for configuring the database") unless -f $dp;
if ( defined $prefix ) {
unless (defined $outfile) {
*/\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
import compbio.runner.Util;\r
import compbio.runner.msa.ClustalO;\r
\r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "ClustalOWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalOWS")\r
public class ClustalOWS implements MsaWS<ClustalO> {\r
\r
private static Logger log = Logger.getLogger(ClustalOWS.class);\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.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
+ private static final PresetManager<Jpred> jpredPresets = Util.getPresets(Jpred.class);\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> confJpred = Configurator.configureExecutable(jpred, dataSet);\r
+ // Set the number of threads for the cluster execution from conf file\r
+ if (confJpred.getExecProvider() == Executable.ExecProvider.Cluster) {\r
+ int clusterCpuNum = SkeletalExecutable.getClusterCpuNum(jpred.getType());\r
+ if (clusterCpuNum != 0) {\r
+ jpred.setNCore(clusterCpuNum);\r
+ }\r
+ }\r
+ return confJpred;\r
+ }\r
+\r
+ @Override\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 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 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 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 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
\r
private static Logger log = Logger.getLogger(ProbconsWS.class);\r
\r
- private static final RunnerConfig<Probcons> probconsOptions = Util\r
- .getSupportedOptions(Probcons.class);\r
-\r
- private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util\r
- .getLimits(new Probcons().getType());\r
+ private static final RunnerConfig<Probcons> probconsOptions = Util.getSupportedOptions(Probcons.class);\r
+ private static final LimitsManager<Probcons> limitMan = compbio.engine.client.Util.getLimits(new Probcons().getType());\r
\r
@Override\r
public String align(List<FastaSequence> sequences)\r
throws JobSubmissionException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
- return WSUtil\r
- .align(sequences, confProbcons, log, "align", getLimit(""));\r
+ return WSUtil.align(sequences, confProbcons, log, "align", getLimit(""));\r
}\r
\r
ConfiguredExecutable<Probcons> init(List<FastaSequence> dataSet)\r
throws JobSubmissionException {\r
Probcons probcons = new Probcons();\r
- probcons.setInput(SkeletalExecutable.INPUT)\r
- .setOutput(SkeletalExecutable.OUTPUT)\r
- .setError(SkeletalExecutable.ERROR);\r
+ probcons.setInput(SkeletalExecutable.INPUT);\r
+ probcons.setOutput(SkeletalExecutable.OUTPUT);\r
+ probcons.setError(SkeletalExecutable.ERROR);\r
return Configurator.configureExecutable(probcons, dataSet);\r
}\r
\r
WrongParameterException {\r
WSUtil.validateFastaInput(sequences);\r
ConfiguredExecutable<Probcons> confProbcons = init(sequences);\r
- List<String> params = WSUtil.getCommands(options,\r
- Probcons.KEY_VALUE_SEPARATOR);\r
+ List<String> params = WSUtil.getCommands(options, Probcons.KEY_VALUE_SEPARATOR);\r
log.info("Setting parameters:" + params);\r
confProbcons.addParameters(params);\r
- return WSUtil.align(sequences, confProbcons, log, "customAlign",\r
- getLimit(""));\r
+ return WSUtil.align(sequences, confProbcons, log, "customAlign",getLimit(""));\r
}\r
\r
@Override\r
public Alignment getResult(String jobId) throws ResultNotAvailableException {\r
WSUtil.validateJobId(jobId);\r
AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
- ConfiguredExecutable<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine\r
- .getResults(jobId);\r
+ ConfiguredExecutable<Probcons> probcons = (ConfiguredExecutable<Probcons>) asyncEngine.getResults(jobId);\r
Alignment al = probcons.getResults();\r
// log(jobId, "getResults");\r
return al;\r
public ChunkHolder pullExecStatistics(String jobId, long position) {\r
WSUtil.validateJobId(jobId);\r
// TODO check if output is the one to return\r
- String file = Configurator.getWorkDirectory(jobId) + File.separator\r
- + new Probcons().getError();\r
+ String file = Configurator.getWorkDirectory(jobId) + File.separator + new Probcons().getError();\r
return WSUtil.pullFile(file, position);\r
}\r
\r
<message name="presetAnalizeResponse">
<part name="parameters" element="tns:presetAnalizeResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
- </message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
- </message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
</message>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="SequenceAnnotation">
<operation name="getAnnotation">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
- </operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="AAConWSPortBinding" type="tns:SequenceAnnotation">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
- <xs:complexType name="getPresets">
+ <xs:complexType name="getLimits">
<xs:sequence/>
</xs:complexType>
- <xs:complexType name="getPresetsResponse">
+ <xs:complexType name="getLimitsResponse">
<xs:sequence>
- <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetManager">
+ <xs:complexType name="limitsManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
+ <xs:complexType name="getPresets">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getPresetsResponse">
<xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimitResponse">
+ <xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
+ <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="ClustalWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
- </message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
- </message>
<message name="align">
<part name="parameters" element="tns:align"/>
</message>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="MsaWS">
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
- </operation>
<operation name="align">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="ClustalWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getResult">
- <soap:operation soapAction=""/>
- <input>
- <soap:body use="literal"/>
- </input>
- <output>
- <soap:body use="literal"/>
- </output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
- </operation>
<operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
<operation name="cancelJob">
<soap:operation soapAction=""/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getLimit">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="alignment" final="extension restriction">
+ <xs:complexType name="alignment">
<xs:sequence>
<xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
<xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimitsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
- <xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getLimitResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="cancelJob">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
<message name="presetAnalizeResponse">
<part name="parameters" element="tns:presetAnalizeResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
- </message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
- </message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
</message>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="SequenceAnnotation">
<operation name="getAnnotation">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
- </operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="DisemblWSPortBinding" type="tns:SequenceAnnotation">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
- <xs:complexType name="getPresets">
+ <xs:complexType name="getLimits">
<xs:sequence/>
</xs:complexType>
- <xs:complexType name="getPresetsResponse">
+ <xs:complexType name="getLimitsResponse">
<xs:sequence>
- <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetManager">
+ <xs:complexType name="limitsManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
+ <xs:complexType name="getPresets">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getPresetsResponse">
<xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimitResponse">
+ <xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
+ <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<message name="presetAnalizeResponse">
<part name="parameters" element="tns:presetAnalizeResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
- </message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
- </message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
</message>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="SequenceAnnotation">
<operation name="getAnnotation">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
- </operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="GlobPlotWSPortBinding" type="tns:SequenceAnnotation">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
- <xs:complexType name="getPresets">
+ <xs:complexType name="getLimits">
<xs:sequence/>
</xs:complexType>
- <xs:complexType name="getPresetsResponse">
+ <xs:complexType name="getLimitsResponse">
<xs:sequence>
- <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetManager">
+ <xs:complexType name="limitsManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
+ <xs:complexType name="getPresets">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getPresetsResponse">
<xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimitResponse">
+ <xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
+ <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<message name="presetAnalizeResponse">
<part name="parameters" element="tns:presetAnalizeResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
- </message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
- </message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
</message>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="SequenceAnnotation">
<operation name="getAnnotation">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
- </operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="IUPredWSPortBinding" type="tns:SequenceAnnotation">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimitsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
- <xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getLimitResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="cancelJob">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<!-- Generated by JAX-WS RI at http://jax-ws.dev.java.net. RI's version is Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
-<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="JpredWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:wsp1_2="http://schemas.xmlsoap.org/ws/2004/09/policy" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:wsam="http://www.w3.org/2007/05/addressing/metadata" xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd">
+<definitions targetNamespace="http://msa.data.compbio/01/01/2010/" name="JpredWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/01/2010/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:wsp1_2="http://schemas.xmlsoap.org/ws/2004/09/policy" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:wsam="http://www.w3.org/2007/05/addressing/metadata" xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd">
<types>
<xsd:schema>
- <xsd:import namespace="http://msa.data.compbio/01/12/2010/" schemaLocation="JpredWS_schema1.xsd"/>
+ <xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="JpredWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getAnnotation">
- <part name="parameters" element="tns:getAnnotation"/>
+ <message name="align">
+ <part name="parameters" element="tns:align"/>
</message>
- <message name="getAnnotationResponse">
- <part name="parameters" element="tns:getAnnotationResponse"/>
- </message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
- </message>
- <message name="analize">
- <part name="parameters" element="tns:analize"/>
- </message>
- <message name="analizeResponse">
- <part name="parameters" element="tns:analizeResponse"/>
+ <message name="alignResponse">
+ <part name="parameters" element="tns:alignResponse"/>
</message>
<message name="UnsupportedRuntimeException">
<part name="fault" element="tns:UnsupportedRuntimeException"/>
<message name="JobSubmissionException">
<part name="fault" element="tns:JobSubmissionException"/>
</message>
- <message name="customAnalize">
- <part name="parameters" element="tns:customAnalize"/>
+ <message name="presetAlign">
+ <part name="parameters" element="tns:presetAlign"/>
</message>
- <message name="customAnalizeResponse">
- <part name="parameters" element="tns:customAnalizeResponse"/>
+ <message name="presetAlignResponse">
+ <part name="parameters" element="tns:presetAlignResponse"/>
</message>
<message name="WrongParameterException">
<part name="fault" element="tns:WrongParameterException"/>
</message>
- <message name="presetAnalize">
- <part name="parameters" element="tns:presetAnalize"/>
+ <message name="customAlign">
+ <part name="parameters" element="tns:customAlign"/>
</message>
- <message name="presetAnalizeResponse">
- <part name="parameters" element="tns:presetAnalizeResponse"/>
+ <message name="customAlignResponse">
+ <part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
- <portType name="SequenceAnnotation">
- <operation name="getAnnotation">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationResponse" message="tns:getAnnotationResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotation/Fault/ResultNotAvailableException"/>
- </operation>
- <operation name="analize">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analizeRequest" message="tns:analize"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analizeResponse" message="tns:analizeResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/JobSubmissionException"/>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
+ <portType name="MsaWS">
+ <operation name="align">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
</operation>
- <operation name="customAnalize">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeRequest" message="tns:customAnalize"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeResponse" message="tns:customAnalizeResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/JobSubmissionException"/>
- <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/WrongParameterException"/>
+ <operation name="presetAlign">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignRequest" message="tns:presetAlign"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlignResponse" message="tns:presetAlignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/JobSubmissionException"/>
+ <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/presetAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="presetAnalize">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalizeRequest" message="tns:presetAnalize"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalizeResponse" message="tns:presetAnalizeResponse"/>
- <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/UnsupportedRuntimeException"/>
- <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/LimitExceededException"/>
- <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
- <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
+ <operation name="customAlign">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignRequest" message="tns:customAlign"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlignResponse" message="tns:customAlignResponse"/>
+ <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/UnsupportedRuntimeException"/>
+ <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/LimitExceededException"/>
+ <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
+ <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="cancelJob">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
</operation>
<operation name="getJobStatus">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsResponse" message="tns:getPresetsResponse"/>
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
</operation>
<operation name="getLimits">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+ </operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
</operation>
</portType>
- <binding name="JpredWSPortBinding" type="tns:SequenceAnnotation">
+ <binding name="JpredWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getAnnotation">
- <soap:operation soapAction=""/>
- <input>
- <soap:body use="literal"/>
- </input>
- <output>
- <soap:body use="literal"/>
- </output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
- </operation>
- <operation name="analize">
+ <operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="JobSubmissionException" use="literal"/>
</fault>
</operation>
- <operation name="customAnalize">
+ <operation name="presetAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="presetAnalize">
+ <operation name="customAlign">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
<operation name="cancelJob">
<soap:operation soapAction=""/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getLimit">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
-<xs:schema version="1.0" targetNamespace="http://msa.data.compbio/01/12/2010/" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+<xs:schema version="1.0" targetNamespace="http://msa.data.compbio/01/01/2010/" xmlns:tns="http://msa.data.compbio/01/01/2010/" xmlns:xs="http://www.w3.org/2001/XMLSchema">
<xs:element name="JobSubmissionException" type="tns:JobSubmissionException"/>
<xs:element name="WrongParameterException" type="tns:WrongParameterException"/>
- <xs:element name="analize" type="tns:analize"/>
+ <xs:element name="align" type="tns:align"/>
- <xs:element name="analizeResponse" type="tns:analizeResponse"/>
+ <xs:element name="alignResponse" type="tns:alignResponse"/>
<xs:element name="cancelJob" type="tns:cancelJob"/>
<xs:element name="cancelJobResponse" type="tns:cancelJobResponse"/>
- <xs:element name="customAnalize" type="tns:customAnalize"/>
+ <xs:element name="customAlign" type="tns:customAlign"/>
- <xs:element name="customAnalizeResponse" type="tns:customAnalizeResponse"/>
-
- <xs:element name="getAnnotation" type="tns:getAnnotation"/>
-
- <xs:element name="getAnnotationResponse" type="tns:getAnnotationResponse"/>
+ <xs:element name="customAlignResponse" type="tns:customAlignResponse"/>
<xs:element name="getJobStatus" type="tns:getJobStatus"/>
<xs:element name="getPresetsResponse" type="tns:getPresetsResponse"/>
+ <xs:element name="getResult" type="tns:getResult"/>
+
+ <xs:element name="getResultResponse" type="tns:getResultResponse"/>
+
<xs:element name="getRunnerOptions" type="tns:getRunnerOptions"/>
<xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
<xs:element name="limits" type="tns:limitsManager"/>
- <xs:element name="presetAnalize" type="tns:presetAnalize"/>
+ <xs:element name="presetAlign" type="tns:presetAlign"/>
- <xs:element name="presetAnalizeResponse" type="tns:presetAnalizeResponse"/>
+ <xs:element name="presetAlignResponse" type="tns:presetAlignResponse"/>
<xs:element name="presets" type="tns:presetManager"/>
<xs:element name="runnerConfig" type="tns:runnerConfig"/>
- <xs:complexType name="customAnalize">
+ <xs:complexType name="align">
<xs:sequence>
<xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="options" type="tns:option" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="option">
- <xs:sequence>
- <xs:element name="description" type="xs:string"/>
- <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
- <xs:element name="name" type="xs:string"/>
- <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
- <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
- </xs:complexType>
-
- <xs:complexType name="customAnalizeResponse">
+ <xs:complexType name="alignResponse">
<xs:sequence>
<xs:element name="return" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="WrongParameterException">
+ <xs:complexType name="customAlign">
<xs:sequence>
- <xs:element name="message" type="xs:string" minOccurs="0"/>
+ <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="options" type="tns:option" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getRunnerOptions">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getRunnerOptionsResponse">
+ <xs:complexType name="option">
<xs:sequence>
- <xs:element name="return" type="tns:runnerConfig" minOccurs="0"/>
+ <xs:element name="description" type="xs:string"/>
+ <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
+ <xs:element name="name" type="xs:string"/>
+ <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
+ <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
</xs:sequence>
+ <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
</xs:complexType>
- <xs:complexType name="runnerConfig">
+ <xs:complexType name="customAlignResponse">
<xs:sequence>
- <xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
- <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="return" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="parameter">
- <xs:complexContent>
- <xs:extension base="tns:option">
- <xs:sequence>
- <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
- </xs:sequence>
- </xs:extension>
- </xs:complexContent>
- </xs:complexType>
-
- <xs:complexType name="valueConstrain">
+ <xs:complexType name="WrongParameterException">
<xs:sequence>
- <xs:element name="type" type="tns:type"/>
- <xs:element name="max" type="xs:string" minOccurs="0"/>
- <xs:element name="min" type="xs:string" minOccurs="0"/>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getJobStatus">
- <xs:sequence>
- <xs:element name="jobId" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getJobStatusResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:jobStatus" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="presetAnalize">
+ <xs:complexType name="presetAlign">
<xs:sequence>
<xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="preset" type="tns:preset" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetAnalizeResponse">
+ <xs:complexType name="presetAlignResponse">
<xs:sequence>
<xs:element name="return" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getAnnotation">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getAnnotationResponse">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="return" type="tns:scoreManager" minOccurs="0"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="scoreManager">
+ <xs:complexType name="limit">
<xs:sequence>
- <xs:element name="seqScores" type="tns:scoreHolder" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="preset" type="xs:string" minOccurs="0"/>
+ <xs:element name="seqNumber" type="xs:int"/>
+ <xs:element name="seqLength" type="xs:int"/>
</xs:sequence>
+ <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
</xs:complexType>
- <xs:complexType name="scoreHolder">
+ <xs:complexType name="getLimitsResponse">
<xs:sequence>
- <xs:element name="id" type="xs:string" minOccurs="0"/>
- <xs:element name="scores" type="tns:score" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="score">
+ <xs:complexType name="limitsManager">
<xs:sequence>
- <xs:element name="method" type="xs:string" minOccurs="0"/>
- <xs:element name="ranges" type="tns:range" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="scores" type="xs:float" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="range">
+ <xs:complexType name="getPresets">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getPresetsResponse">
<xs:sequence>
- <xs:element name="from" type="xs:int"/>
- <xs:element name="to" type="xs:int"/>
+ <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="ResultNotAvailableException">
+ <xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="message" type="xs:string" minOccurs="0"/>
+ <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
+ <xs:complexType name="cancelJob">
+ <xs:sequence>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ </xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="cancelJobResponse">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="return" type="xs:boolean"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getRunnerOptions">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getRunnerOptionsResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:runnerConfig" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limit">
+ <xs:complexType name="runnerConfig">
<xs:sequence>
- <xs:element name="preset" type="xs:string" minOccurs="0"/>
- <xs:element name="seqNumber" type="xs:int"/>
- <xs:element name="seqLength" type="xs:int"/>
+ <xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
+ <xs:element name="runnerClassName" type="xs:string"/>
</xs:sequence>
- <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
- <xs:complexType name="getPresets">
- <xs:sequence/>
+ <xs:complexType name="parameter">
+ <xs:complexContent>
+ <xs:extension base="tns:option">
+ <xs:sequence>
+ <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
</xs:complexType>
- <xs:complexType name="getPresetsResponse">
+ <xs:complexType name="valueConstrain">
<xs:sequence>
- <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+ <xs:element name="type" type="tns:type"/>
+ <xs:element name="max" type="xs:string" minOccurs="0"/>
+ <xs:element name="min" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetManager">
+ <xs:complexType name="getResult">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
+ <xs:complexType name="getResultResponse">
<xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="tns:alignment" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimitResponse">
+ <xs:complexType name="alignment">
<xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
+ <xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
+ <xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJob">
+ <xs:complexType name="alignmentMetadata">
<xs:sequence>
- <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+ <xs:element name="program" type="tns:program" minOccurs="0"/>
+ <xs:element name="gapchar" type="xs:unsignedShort"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="cancelJobResponse">
+ <xs:complexType name="ResultNotAvailableException">
<xs:sequence>
- <xs:element name="return" type="xs:boolean"/>
+ <xs:element name="message" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="analize">
+ <xs:complexType name="getJobStatus">
<xs:sequence>
- <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="analizeResponse">
+ <xs:complexType name="getJobStatusResponse">
<xs:sequence>
- <xs:element name="return" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="tns:jobStatus" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
</xs:restriction>
</xs:simpleType>
+ <xs:simpleType name="program">
+ <xs:restriction base="xs:string">
+ <xs:enumeration value="CLUSTAL"/>
+ <xs:enumeration value="MAFFT"/>
+ <xs:enumeration value="MUSCLE"/>
+ <xs:enumeration value="Tcoffee"/>
+ <xs:enumeration value="Probcons"/>
+ <xs:enumeration value="Jpred"/>
+ </xs:restriction>
+ </xs:simpleType>
+
<xs:simpleType name="jobStatus">
<xs:restriction base="xs:string">
<xs:enumeration value="PENDING"/>
<message name="presetAnalizeResponse">
<part name="parameters" element="tns:presetAnalizeResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
- </message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
- </message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
</message>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="SequenceAnnotation">
<operation name="getAnnotation">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
- </operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="JronnWSPortBinding" type="tns:SequenceAnnotation">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="cancelJob">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="cancelJob">
+ <operation name="getJobStatus">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getJobStatus">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimit">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
- <xs:complexType name="getPresets">
+ <xs:complexType name="getLimits">
<xs:sequence/>
</xs:complexType>
- <xs:complexType name="getPresetsResponse">
+ <xs:complexType name="getLimitsResponse">
<xs:sequence>
- <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="presetManager">
+ <xs:complexType name="limitsManager">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string"/>
- <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
+ <xs:complexType name="getPresets">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getPresetsResponse">
<xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+ <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimitResponse">
+ <xs:complexType name="presetManager">
<xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
+ <xs:element name="runnerClassName" type="xs:string"/>
+ <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="MafftWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
- </message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
- </message>
<message name="align">
<part name="parameters" element="tns:align"/>
</message>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="MsaWS">
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
- </operation>
<operation name="align">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="MafftWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getResult">
- <soap:operation soapAction=""/>
- <input>
- <soap:body use="literal"/>
- </input>
- <output>
- <soap:body use="literal"/>
- </output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
- </operation>
<operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
<operation name="cancelJob">
<soap:operation soapAction=""/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getLimit">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="alignment" final="extension restriction">
+ <xs:complexType name="alignment">
<xs:sequence>
<xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
<xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimitsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
- <xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getLimitResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="cancelJob">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="MuscleWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
- </message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
- </message>
<message name="align">
<part name="parameters" element="tns:align"/>
</message>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="MsaWS">
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
- </operation>
<operation name="align">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="MuscleWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getResult">
- <soap:operation soapAction=""/>
- <input>
- <soap:body use="literal"/>
- </input>
- <output>
- <soap:body use="literal"/>
- </output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
- </operation>
<operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
<operation name="cancelJob">
<soap:operation soapAction=""/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getLimit">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimitsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
- <xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getLimitResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="cancelJob">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="alignment" final="extension restriction">
+ <xs:complexType name="alignment">
<xs:sequence>
<xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
<xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
<xsd:import namespace="http://msa.data.compbio/01/01/2010/" schemaLocation="TcoffeeWS_schema1.xsd"/>
</xsd:schema>
</types>
- <message name="getResult">
- <part name="parameters" element="tns:getResult"/>
- </message>
- <message name="getResultResponse">
- <part name="parameters" element="tns:getResultResponse"/>
- </message>
- <message name="ResultNotAvailableException">
- <part name="fault" element="tns:ResultNotAvailableException"/>
- </message>
<message name="align">
<part name="parameters" element="tns:align"/>
</message>
<message name="customAlignResponse">
<part name="parameters" element="tns:customAlignResponse"/>
</message>
- <message name="pullExecStatistics">
- <part name="parameters" element="tns:pullExecStatistics"/>
+ <message name="getResult">
+ <part name="parameters" element="tns:getResult"/>
</message>
- <message name="pullExecStatisticsResponse">
- <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+ <message name="getResultResponse">
+ <part name="parameters" element="tns:getResultResponse"/>
+ </message>
+ <message name="ResultNotAvailableException">
+ <part name="fault" element="tns:ResultNotAvailableException"/>
</message>
<message name="cancelJob">
<part name="parameters" element="tns:cancelJob"/>
<message name="getJobStatusResponse">
<part name="parameters" element="tns:getJobStatusResponse"/>
</message>
- <message name="getLimit">
- <part name="parameters" element="tns:getLimit"/>
- </message>
- <message name="getLimitResponse">
- <part name="parameters" element="tns:getLimitResponse"/>
- </message>
- <message name="getRunnerOptions">
- <part name="parameters" element="tns:getRunnerOptions"/>
+ <message name="pullExecStatistics">
+ <part name="parameters" element="tns:pullExecStatistics"/>
</message>
- <message name="getRunnerOptionsResponse">
- <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ <message name="pullExecStatisticsResponse">
+ <part name="parameters" element="tns:pullExecStatisticsResponse"/>
</message>
<message name="getPresets">
<part name="parameters" element="tns:getPresets"/>
<message name="getLimitsResponse">
<part name="parameters" element="tns:getLimitsResponse"/>
</message>
+ <message name="getLimit">
+ <part name="parameters" element="tns:getLimit"/>
+ </message>
+ <message name="getLimitResponse">
+ <part name="parameters" element="tns:getLimitResponse"/>
+ </message>
+ <message name="getRunnerOptions">
+ <part name="parameters" element="tns:getRunnerOptions"/>
+ </message>
+ <message name="getRunnerOptionsResponse">
+ <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+ </message>
<portType name="MsaWS">
- <operation name="getResult">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
- <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
- </operation>
<operation name="align">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignRequest" message="tns:align"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/alignResponse" message="tns:alignResponse"/>
<fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/JobSubmissionException"/>
<fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/customAlign/Fault/WrongParameterException"/>
</operation>
- <operation name="pullExecStatistics">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+ <operation name="getResult">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultRequest" message="tns:getResult"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResultResponse" message="tns:getResultResponse"/>
+ <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getResult/Fault/ResultNotAvailableException"/>
</operation>
<operation name="cancelJob">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
</operation>
- <operation name="getLimit">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
- </operation>
- <operation name="getRunnerOptions">
- <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
- <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ <operation name="pullExecStatistics">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
</operation>
<operation name="getPresets">
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
<input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
<output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
</operation>
+ <operation name="getLimit">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
+ </operation>
+ <operation name="getRunnerOptions">
+ <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+ <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+ </operation>
</portType>
<binding name="TcoffeeWSPortBinding" type="tns:MsaWS">
<soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
- <operation name="getResult">
- <soap:operation soapAction=""/>
- <input>
- <soap:body use="literal"/>
- </input>
- <output>
- <soap:body use="literal"/>
- </output>
- <fault name="ResultNotAvailableException">
- <soap:fault name="ResultNotAvailableException" use="literal"/>
- </fault>
- </operation>
<operation name="align">
<soap:operation soapAction=""/>
<input>
<soap:fault name="WrongParameterException" use="literal"/>
</fault>
</operation>
- <operation name="pullExecStatistics">
+ <operation name="getResult">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<output>
<soap:body use="literal"/>
</output>
+ <fault name="ResultNotAvailableException">
+ <soap:fault name="ResultNotAvailableException" use="literal"/>
+ </fault>
</operation>
<operation name="cancelJob">
<soap:operation soapAction=""/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimit">
+ <operation name="pullExecStatistics">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getRunnerOptions">
+ <operation name="getPresets">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getPresets">
+ <operation name="getLimits">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
<soap:body use="literal"/>
</output>
</operation>
- <operation name="getLimits">
+ <operation name="getLimit">
+ <soap:operation soapAction=""/>
+ <input>
+ <soap:body use="literal"/>
+ </input>
+ <output>
+ <soap:body use="literal"/>
+ </output>
+ </operation>
+ <operation name="getRunnerOptions">
<soap:operation soapAction=""/>
<input>
<soap:body use="literal"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimits">
- <xs:sequence/>
- </xs:complexType>
-
- <xs:complexType name="getLimitsResponse">
+ <xs:complexType name="getLimit">
<xs:sequence>
- <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ <xs:element name="presetName" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="limitsManager">
+ <xs:complexType name="getLimitResponse">
<xs:sequence>
- <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
- <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="return" type="tns:limit" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
<xs:attribute name="isDefault" type="xs:boolean" use="required"/>
</xs:complexType>
+ <xs:complexType name="getLimits">
+ <xs:sequence/>
+ </xs:complexType>
+
+ <xs:complexType name="getLimitsResponse">
+ <xs:sequence>
+ <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+ </xs:sequence>
+ </xs:complexType>
+
+ <xs:complexType name="limitsManager">
+ <xs:sequence>
+ <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+ <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+ </xs:sequence>
+ </xs:complexType>
+
<xs:complexType name="getPresets">
<xs:sequence/>
</xs:complexType>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="getLimit">
- <xs:sequence>
- <xs:element name="presetName" type="xs:string" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
- <xs:complexType name="getLimitResponse">
- <xs:sequence>
- <xs:element name="return" type="tns:limit" minOccurs="0"/>
- </xs:sequence>
- </xs:complexType>
-
<xs:complexType name="cancelJob">
<xs:sequence>
<xs:element name="jobId" type="xs:string" minOccurs="0"/>
</xs:sequence>
</xs:complexType>
- <xs:complexType name="alignment" final="extension restriction">
+ <xs:complexType name="alignment">
<xs:sequence>
<xs:element name="metadata" type="tns:alignmentMetadata" minOccurs="0"/>
<xs:element name="sequences" type="tns:fastaSequence" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/IUPredWS.wsdl
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JpredWS.wsdl
+ [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JronnWS.wsdl
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MafftWS.wsdl
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RegistryWS.wsdl
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/RegistryWS_schema1.xsd
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/SequenceAnnotation.wsdl
- [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/SequenceAnnotation_schema1.xsd
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
[delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
[wsgen] command line: wsgen -classpath /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-beanutils-1.7.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-collections-3.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-lang-2.3.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/commons-logging-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-annotations-1.0.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-ga-1.1.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/compbio-util-1.4.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/derby-10.8.2.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/displaytag-export-poi-1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/drmaa.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/itext-1.4.7.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/jstl-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/log4j-1.2.15.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/poi-3.2-FINAL-20081019.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/standard-1.1.2.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-api.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-rt.jar:/home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/lib/webservices-tools.jar -d /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/WEB-INF/classes -Xendorsed -keep -wsdl -r /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource -s /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices -verbose compbio.ws.server.JpredWS
[wsgen] Note: ap round: 1
- [wsgen] [ProcessedMethods Interface: compbio.data.msa.SequenceAnnotation<T>]
- [wsgen] [should process method: analize hasWebMethods: false ]
+ [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS<T>]
+ [wsgen] [should process method: align hasWebMethods: false ]
[wsgen] [endpointReferencesInterface: true]
[wsgen] [declaring class has WebSevice: true]
[wsgen] [returning: true]
- [wsgen] [WrapperGen - method: analize(java.util.List<compbio.data.sequence.FastaSequence>)]
- [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
- [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize]
- [wsgen] [should process method: customAnalize hasWebMethods: false ]
+ [wsgen] [WrapperGen - method: align(java.util.List<compbio.data.sequence.FastaSequence>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.Align]
+ [wsgen] [should process method: customAlign hasWebMethods: false ]
[wsgen] [endpointReferencesInterface: true]
[wsgen] [declaring class has WebSevice: true]
[wsgen] [returning: true]
- [wsgen] [WrapperGen - method: customAnalize(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
- [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
- [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize]
- [wsgen] [should process method: presetAnalize hasWebMethods: false ]
+ [wsgen] [WrapperGen - method: customAlign(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAlign]
+ [wsgen] [should process method: presetAlign hasWebMethods: false ]
[wsgen] [endpointReferencesInterface: true]
[wsgen] [declaring class has WebSevice: true]
[wsgen] [returning: true]
- [wsgen] [WrapperGen - method: presetAnalize(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
- [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
- [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize]
- [wsgen] [should process method: getAnnotation hasWebMethods: false ]
+ [wsgen] [WrapperGen - method: presetAlign(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAlign]
+ [wsgen] [should process method: getResult hasWebMethods: false ]
[wsgen] [endpointReferencesInterface: true]
[wsgen] [declaring class has WebSevice: true]
[wsgen] [returning: true]
- [wsgen] [WrapperGen - method: getAnnotation(java.lang.String)]
- [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
- [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation]
+ [wsgen] [WrapperGen - method: getResult(java.lang.String)]
+ [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+ [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetResult]
[wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService]
[wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement]
[wsgen] [should process method: cancelJob hasWebMethods: false ]
[wsgen] [WrapperGen - method: getLimits()]
[wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata<T>]
[wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
- [wsgen] compbio/data/msa/jaxws/Analize.java
- [wsgen] compbio/data/msa/jaxws/AnalizeResponse.java
+ [wsgen] compbio/data/msa/jaxws/Align.java
+ [wsgen] compbio/data/msa/jaxws/AlignResponse.java
[wsgen] compbio/data/msa/jaxws/CancelJob.java
[wsgen] compbio/data/msa/jaxws/CancelJobResponse.java
- [wsgen] compbio/data/msa/jaxws/CustomAnalize.java
- [wsgen] compbio/data/msa/jaxws/CustomAnalizeResponse.java
- [wsgen] compbio/data/msa/jaxws/GetAnnotation.java
- [wsgen] compbio/data/msa/jaxws/GetAnnotationResponse.java
+ [wsgen] compbio/data/msa/jaxws/CustomAlign.java
+ [wsgen] compbio/data/msa/jaxws/CustomAlignResponse.java
[wsgen] compbio/data/msa/jaxws/GetJobStatus.java
[wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java
[wsgen] compbio/data/msa/jaxws/GetLimit.java
[wsgen] compbio/data/msa/jaxws/GetLimitsResponse.java
[wsgen] compbio/data/msa/jaxws/GetPresets.java
[wsgen] compbio/data/msa/jaxws/GetPresetsResponse.java
+ [wsgen] compbio/data/msa/jaxws/GetResult.java
+ [wsgen] compbio/data/msa/jaxws/GetResultResponse.java
[wsgen] compbio/data/msa/jaxws/GetRunnerOptions.java
[wsgen] compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
[wsgen] compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
[wsgen] compbio/data/msa/jaxws/LimitExceededExceptionBean.java
- [wsgen] compbio/data/msa/jaxws/PresetAnalize.java
- [wsgen] compbio/data/msa/jaxws/PresetAnalizeResponse.java
+ [wsgen] compbio/data/msa/jaxws/PresetAlign.java
+ [wsgen] compbio/data/msa/jaxws/PresetAlignResponse.java
[wsgen] compbio/data/msa/jaxws/PullExecStatistics.java
[wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java
[wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
destdir="${classes}" \r
resourcedestdir="${wsdl.dir}" \r
keep="true" genwsdl="true" \r
- extension="false" \r
- xendorsed="true" \r
+ extension="false"\r
+ xendorsed="true"\r
verbose="true">\r
<classpath refid="classes.path" />\r
<classpath refid="project.classpath" />\r
git://source.jalview.org / jabaws.git / commitdiff