From: Sasha Sherstnev Date: Fri, 9 Aug 2013 09:13:33 +0000 (+0100) Subject: JpredWS code and codes which provide support for JpredWS X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c46caed03164e4396eb55dc30e7db3558a7b06cc;p=jabaws.git JpredWS code and codes which provide support for JpredWS --- diff --git a/webservices/compbio/data/msa/Category.java b/webservices/compbio/data/msa/Category.java index 56bf1de..59bcf30 100644 --- a/webservices/compbio/data/msa/Category.java +++ b/webservices/compbio/data/msa/Category.java @@ -1,14 +1,3 @@ -package compbio.data.msa; - -import java.util.HashSet; -import java.util.Set; -import java.util.TreeSet; - -import javax.xml.bind.annotation.XmlAccessType; -import javax.xml.bind.annotation.XmlAccessorType; - -import compbio.ws.client.Services; - /** * Class that splits {@link Services} to categories. Services themselves have no * knowledge which category they belongs to. @@ -21,6 +10,18 @@ import compbio.ws.client.Services; * @author pvtroshin * @version 1.0 September 2011 */ + +package compbio.data.msa; + +import java.util.HashSet; +import java.util.Set; +import java.util.TreeSet; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; + +import compbio.ws.client.Services; + @XmlAccessorType(XmlAccessType.FIELD) public class Category { /* @@ -34,7 +35,8 @@ public class Category { public static final String CATEGORY_ALIGNMENT = "Alignment"; public static final String CATEGORY_DISORDER = "Protein Disorder"; public static final String CATEGORY_CONSERVATION = "Conservation"; - + public static final String CATEGORY_PREDICTION = "Prediction"; + public String name; Set services; @@ -70,18 +72,21 @@ public class Category { disorder_services.add(Services.GlobPlotWS); disorder_services.add(Services.IUPredWS); disorder_services.add(Services.JronnWS); - Category disorder = new Category(CATEGORY_DISORDER, disorder_services); + Set conservation_services = new HashSet(); conservation_services.add(Services.AAConWS); + Category conservation = new Category(CATEGORY_CONSERVATION, conservation_services); - Category conservation = new Category(CATEGORY_CONSERVATION, - conservation_services); + Set prediction_services = new HashSet(); + prediction_services.add(Services.JpredWS); + Category prediction = new Category(CATEGORY_PREDICTION, prediction_services); Set categories = new HashSet(); categories.add(alignment); categories.add(disorder); categories.add(conservation); + categories.add(prediction); return categories; } diff --git a/webservices/compbio/ws/client/Services.java b/webservices/compbio/ws/client/Services.java index 2ffafb6..28bb5dd 100644 --- a/webservices/compbio/ws/client/Services.java +++ b/webservices/compbio/ws/client/Services.java @@ -39,7 +39,7 @@ public enum Services { * Make sure this class has NO references to runners or engines as it is a * part of minimal client package. Such things should go into ServicesUtil */ - MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS; + MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS; public static Services getService(String servName) { servName = servName.trim().toLowerCase(); @@ -73,32 +73,31 @@ public enum Services { switch (this) { // deliberate leaking case AAConWS : + case JpredWS : case JronnWS : case DisemblWS : case GlobPlotWS : case IUPredWS : return SequenceAnnotation.class; - // deliberate leaking + // deliberate leaking case ClustalWS : case ClustalOWS : case MafftWS : case MuscleWS : case ProbconsWS : case TcoffeeWS : - return MsaWS.class; + default : - throw new RuntimeException("Unrecognised Web Service Type " - + this + " - Should never happened!"); + throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!"); } } JABAService getInterface(Service service) { assert service != null; - QName portName = new QName(service.getServiceName().getNamespaceURI(), - this.toString() + "Port"); + QName portName = new QName(service.getServiceName().getNamespaceURI(), this.toString() + "Port"); return service.getPort(portName, this.getServiceType()); } @@ -106,6 +105,8 @@ public enum Services { switch (this) { case AAConWS : return AACON_INFO; + case JpredWS : + return JPRED_INFO; case ClustalOWS : return CLUSTAL_OMEGA_INFO; case ClustalWS : @@ -127,67 +128,77 @@ public enum Services { case TcoffeeWS : return TCOFFEE_INFO; default : - throw new RuntimeException("Unrecognised Web Service Type " - + this + " - Should never happened!"); + throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!"); } } public static final String AACON_INFO = new ServiceInfo(AAConWS, - "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon") - .toString(); - public static final String CLUSTAL_INFO = new ServiceInfo( - ClustalWS, - "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.\r\n" - + "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. ", + "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon").toString(); + + public static final String JPRED_INFO = new ServiceInfo(JpredWS, + "Cole C, Barber JD, Barton GJ.reparation" + + "The Jpred 3 secondary structure prediction server\n" + + "Nucl. Acids Res. (2008) 36 (suppl 2): W197-W201., doi: 10.1093/nar/gkn238", + "3.0", "http://www.compbio.dundee.ac.uk/www-jpred").toString(); + + public static final String CLUSTAL_INFO = new ServiceInfo(ClustalWS, + "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, " + + "Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.\n" + + "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.", "2.0.12", "http://www.clustal.org/clustal2/").toString(); - public static final String CLUSTAL_OMEGA_INFO = new ServiceInfo( - ClustalOWS, + + public static final String CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS, "Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n" - + "Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D. Thompson, Desmond G. Higgins", + + "Fabian Sievers, Andreas Wilm, David Dineen, Toby J. Gibson, Kevin Karplus, Weizhong Li, Rodrigo Lopez, Hamish McWilliam, Michael Remmert, Johannes Söding, Julie D. Thompson, Desmond G. Higgins", "1.0.2", "http://www.clustal.org/omega").toString(); - public static final String DISEMBL_INFO = new ServiceInfo( - DisemblWS, + + public static final String DISEMBL_INFO = new ServiceInfo(DisemblWS, "R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n" - + "Protein disorder prediction: implications for structural proteomics\r\n" - + "Structure Vol 11, Issue 11, 4 November 2003", "1.5", + + "Protein disorder prediction: implications for structural proteomics\r\n" + + "Structure Vol 11, Issue 11, 4 November 2003", "1.5", "http://dis.embl.de/").toString(); - public static final String GLOBPLOT_INFO = new ServiceInfo( - GlobPlotWS, - "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " - + "'GlobPlot: exploring protein sequences for globularity and disorder.' Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n", + + public static final String GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS, + "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " + + "'GlobPlot: exploring protein sequences for globularity and disorder.' " + + "Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n", "2.3", "http://globplot.embl.de/").toString(); - public static final String IUPRED_INFO = new ServiceInfo( - IUPredWS, + + public static final String IUPRED_INFO = new ServiceInfo(IUPredWS, "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n" - + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n" - + "J. Mol. Biol. (2005) 347, 827-839.", "1.0", + + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n" + + "J. Mol. Biol. (2005) 347, 827-839.", "1.0", "http://iupred.enzim.hu/").toString(); + public static final String TCOFFEE_INFO = new ServiceInfo(TcoffeeWS, "T-Coffee: A novel method for multiple sequence alignments " - + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000", - "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html") - .toString(); + + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000", + "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html").toString(); + public static final String MUSCLE_INFO = new ServiceInfo( MuscleWS, "Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n" - + "doi:10.1093/nar/gkh340", "3.8.31", + + "doi:10.1093/nar/gkh340", "3.8.31", "http://www.drive5.com/muscle/").toString(); + public static final String PROBCONS_INFO = new ServiceInfo( ProbconsWS, "Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: " - + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ", - "1.12", "http://probcons.stanford.edu/").toString();; + + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ", + "1.12", "http://probcons.stanford.edu/").toString(); + public static final String JRONN_INFO = new ServiceInfo( JronnWS, "unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) " + "RONN: the bio-basis function neural network technique applied to the " + "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n", - "1.0", "http://www.compbio.dundee.ac.uk/jabaws/").toString();; + "1.0", "http://www.compbio.dundee.ac.uk/jabaws/").toString(); + public static final String MAFFT_INFO = new ServiceInfo( MafftWS, "Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n" + "Parallelization of the MAFFT multiple sequence alignment program. ", - "6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString();; + "6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString(); @XmlAccessorType(XmlAccessType.FIELD) static class ServiceInfo { @@ -195,7 +206,7 @@ public enum Services { String reference; String version; String moreinfo; - final static String jabaws_version = "2.0"; + final static String jabaws_version = "2.5"; final static String line_delimiter = "\n"; private ServiceInfo() { @@ -211,8 +222,7 @@ public enum Services { @Override public String toString() { - String value = "SERVICE: " + service + " version " + version - + line_delimiter; + String value = "SERVICE: " + service + " version " + version + line_delimiter; value += "JABAWS v. " + jabaws_version + line_delimiter; value += "REFERENCES: " + reference + line_delimiter; value += "MORE INFORMATION: " + moreinfo + line_delimiter; diff --git a/webservices/compbio/ws/client/ServicesUtil.java b/webservices/compbio/ws/client/ServicesUtil.java index 08b8131..26f1467 100644 --- a/webservices/compbio/ws/client/ServicesUtil.java +++ b/webservices/compbio/ws/client/ServicesUtil.java @@ -5,6 +5,7 @@ import java.io.File; import compbio.engine.client.ConfExecutable; import compbio.engine.client.Executable; import compbio.runner.conservation.AACon; +import compbio.runner.predictors.Jpred; import compbio.runner.disorder.Disembl; import compbio.runner.disorder.GlobPlot; import compbio.runner.disorder.IUPred; @@ -33,6 +34,8 @@ public class ServicesUtil { switch (service) { case AAConWS : return AACon.class; + case JpredWS : + return Jpred.class; case ClustalOWS : return ClustalO.class; case ClustalWS : @@ -54,14 +57,11 @@ public class ServicesUtil { case IUPredWS : return IUPred.class; default : - throw new RuntimeException( - "Unknown web service implementation class for service: " - + service); + throw new RuntimeException("Unknown web service implementation class for service: " + service); } } - public static Class> getRunnerByJobDirectory( - File jobdir) { + public static Class> getRunnerByJobDirectory(File jobdir) { Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir)); return getServiceImpl(service); } @@ -82,8 +82,7 @@ public class ServicesUtil { private static Services getServiceByRunnerName(String name) { for (Services service : Services.values()) { - String runnerName = getServiceImpl(service).getSimpleName() - .toLowerCase(); + String runnerName = getServiceImpl(service).getSimpleName().toLowerCase(); name = name.trim().toLowerCase(); if (name.startsWith(runnerName)) { return service; diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java index c6eaf76..e9a349c 100644 --- a/webservices/compbio/ws/client/WSTester.java +++ b/webservices/compbio/ws/client/WSTester.java @@ -141,12 +141,10 @@ public class WSTester { + pseparator + "host_and_context " + "<" + servicekey + pseparator + "serviceName>"); System.out.println(); - System.out - .println(hostkey + System.out.println(hostkey + pseparator + " - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws"); - System.out - .println(servicekey + System.out.println(servicekey + pseparator + " - optional if unspecified all services are tested otherwise one of " + Arrays.toString(Services.values())); @@ -221,8 +219,7 @@ public class WSTester { private boolean checkService(JABAService wservice, Services service) { try { if (wservice == null) { - throw new NullPointerException( - "JABAService instance must be provided!"); + throw new NullPointerException("JABAService instance must be provided!"); } if (wservice instanceof MsaWS) { @@ -231,8 +228,7 @@ public class WSTester { return testSequenceAnnotationWS( (SequenceAnnotation) wservice, service); } else { - throw new UnsupportedOperationException("The service: " - + wservice.getClass() + " is not supported! "); + throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! "); } } catch (Exception e) { reportException(e); @@ -382,8 +378,7 @@ public class WSTester { String host = CmdHelper.getHost(args); String serviceName = CmdHelper.getServiceName(args); if (!Jws2Client.validURL(host)) { - System.err - .println(" parameter is not provided or is incorrect!"); + System.err.println(" parameter is not provided or is incorrect!"); System.exit(1); } WSTester tester = new WSTester(host, new PrintWriter(System.out, true)); @@ -391,8 +386,7 @@ public class WSTester { if (serviceName != null) { Services service = Services.getService(serviceName); if (service == null) { - tester.writer.println("Service '" + serviceName - + "' is not supported. Valid values are: " + tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: " + Arrays.toString(Services.values())); tester.writer.println(); printUsage(); @@ -402,8 +396,7 @@ public class WSTester { System.exit(0); } - tester.writer - .println(" is not provided checking all known services..."); + tester.writer.println(" is not provided checking all known services..."); for (Services serv : Services.values()) { tester.writer.println(); @@ -425,8 +418,8 @@ public class WSTester { WebServiceException { JABAService ws = Jws2Client.connect(hostname, service); if (ws == null) { - writer.println("Cannot estabilish the connection to host " - + hostname + " with service " + service.toString()); + String line = "Cannot estabilish the connection to host " + hostname + " with service "; + writer.println(line + service.toString()); return false; } boolean succeed = false; @@ -442,11 +435,9 @@ public class WSTester { private void reportResults(Services serv, boolean succeed) { if (succeed) { - writer.println("Check is completed. The Service " + serv - + " IS WORKING\n"); + writer.println("Check is completed. The Service " + serv + " IS WORKING\n"); } else { - writer.println("Check is aborted. The Service " + serv - + " HAS SOME PROBLEMS\n"); + writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n"); } } } diff --git a/webservices/compbio/ws/server/JpredWS.java b/webservices/compbio/ws/server/JpredWS.java new file mode 100644 index 0000000..61ec773 --- /dev/null +++ b/webservices/compbio/ws/server/JpredWS.java @@ -0,0 +1,88 @@ +/* Copyright (c) 2011 Peter Troshin + * Copyright (c) 2013 Alexander Sherstnev + * + * JAva Bioinformatics Analysis Web Services (JABAWS) + * @version: 2.5 + * + * This library is free software; you can redistribute it and/or modify it under the terms of the + * Apache License version 2 as published by the Apache Software Foundation + * + * This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without + * even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache + * License for more details. + * + * A copy of the license is in apache_license.txt. It is also available here: + * @see: http://www.apache.org/licenses/LICENSE-2.0.txt + * + * Any republication or derived work distributed in source code form + * must include this copyright and license notice. + */ +package compbio.ws.server; + +import java.io.File; +import java.util.Arrays; +import java.util.List; + +import javax.jws.WebService; + +import org.apache.log4j.Logger; + +import compbio.data.msa.JABAService; +import compbio.data.msa.SequenceAnnotation; +import compbio.data.sequence.FastaSequence; +import compbio.engine.Configurator; +import compbio.engine.client.ConfiguredExecutable; +import compbio.metadata.ChunkHolder; +import compbio.metadata.JobSubmissionException; +import compbio.metadata.LimitExceededException; +import compbio.metadata.Option; +import compbio.metadata.Preset; +import compbio.metadata.UnsupportedRuntimeException; +import compbio.metadata.WrongParameterException; +import compbio.runner.predictors.Jpred; + +@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS") +public class JpredWS extends SequenceAnnotationService + implements SequenceAnnotation { + + private static Logger log = Logger.getLogger(JpredWS.class); + + public JpredWS() { + super(new Jpred(), log); + } + + @Override + public String analize(List sequences) + throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException { + WSUtil.validateJpredInput(sequences); + ConfiguredExecutable confpred = init(sequences); + + // set default conservation method to fastest - SHENKIN + // TODO: This violates encapsulation, should be moved to the runners + // level. + //confpred.addParameters(Arrays.asList("-m=SHENKIN")); + return WSUtil.analize(sequences, confpred, log, "JpredWS analize", getLimit("")); + } + + @Override + public String customAnalize(List sequences, List> options) + throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException { + WSUtil.validateJpredInput(sequences); + return super.customAnalize(sequences, options); + } + + @Override + public String presetAnalize(List sequences, Preset preset) + throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException { + WSUtil.validateJpredInput(sequences); + return super.presetAnalize(sequences, preset); + } + + @Override + public ChunkHolder pullExecStatistics(String jobId, long position) { + WSUtil.validateJobId(jobId); + String file = Configurator.getWorkDirectory(jobId) + File.separator + Jpred.getStatFile(); + return WSUtil.pullFile(file, position); + } + +} diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java index 7341989..ebf4b3e 100644 --- a/webservices/compbio/ws/server/WSUtil.java +++ b/webservices/compbio/ws/server/WSUtil.java @@ -159,10 +159,29 @@ public final class WSUtil { } if (fs.getLength() != len) { throw new JobSubmissionException( - "All sequences must be of the same length. Please align " - + "the sequences prior to submission! The first sequence length is : " - + len + " but the sequence '" + fs.getId() - + "' length is " + fs.getLength()); + "All sequences must be of the same length. Please align the sequences " + + " prior to submission! The first sequence length is : " + len + + " but the sequence '" + fs.getId() + "' length is " + fs.getLength()); + } + } + } + + public static void validateJpredInput(List sequences) + throws JobSubmissionException { + validateFastaInput(sequences); + int len = 0; + for (FastaSequence fs : sequences) { + if (len == 0) { + len = fs.getLength(); + System.out.println("1st FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence()); + continue; + } + if (fs.getLength() != len) { + System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence()); + throw new JobSubmissionException( + "All sequences must be of the same length. Please align the sequences " + + " prior to submission! The first sequence length is : " + len + + " but the sequence '" + fs.getId() + "' length is " + fs.getLength()); } } } @@ -171,8 +190,7 @@ public final class WSUtil { throws ResultNotAvailableException { WSUtil.validateJobId(jobId); AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId); - ConfiguredExecutable aacon = (ConfiguredExecutable) asyncEngine - .getResults(jobId); + ConfiguredExecutable aacon = (ConfiguredExecutable) asyncEngine.getResults(jobId); ScoreManager mas = aacon.getResults(); log.trace(jobId + " getConservation : " + mas); return mas; diff --git a/webservices/compbio/ws/server/resource/JpredWS.wsdl b/webservices/compbio/ws/server/resource/JpredWS.wsdl new file mode 100644 index 0000000..976aee1 --- /dev/null +++ b/webservices/compbio/ws/server/resource/JpredWS.wsdl @@ -0,0 +1,292 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd new file mode 100644 index 0000000..f62aefc --- /dev/null +++ b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd @@ -0,0 +1,366 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/wsbuild.log b/wsbuild.log new file mode 100644 index 0000000..3303f31 --- /dev/null +++ b/wsbuild.log @@ -0,0 +1,1214 @@ + +build-server: + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/AAConWS.wsdl + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/ClustalWS.wsdl + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/DisemblWS.wsdl + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd + [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/MafftWS_schema1.xsd + [delete] Deleting /home/asherstnev/Projects/Java.projects/jabaws/secure-git/develop/webservices/compbio/ws/server/resource/MuscleWS.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/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] + [wsgen] [should process method: analize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: analize(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize] + [wsgen] [should process method: customAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: customAnalize(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize] + [wsgen] [should process method: presetAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: presetAnalize(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize] + [wsgen] [should process method: getAnnotation 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] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement] + [wsgen] [should process method: cancelJob hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [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/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/GetJobStatus.java + [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimit.java + [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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/PullExecStatistics.java + [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java + [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.AAConWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.SequenceAnnotation] + [wsgen] [should process method: analize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: analize(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize] + [wsgen] [should process method: customAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: customAnalize(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize] + [wsgen] [should process method: presetAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: presetAnalize(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize] + [wsgen] [should process method: getAnnotation 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] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement] + [wsgen] [should process method: cancelJob hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [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/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/GetJobStatus.java + [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimit.java + [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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/PullExecStatistics.java + [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java + [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.ClustalWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS] + [wsgen] [should process method: align hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: align(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: customAlign(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: presetAlign(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: getResult(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits] + [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/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/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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 + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.MuscleWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS] + [wsgen] [should process method: align hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: align(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: customAlign(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: presetAlign(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: getResult(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits] + [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/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/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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 + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.MafftWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS] + [wsgen] [should process method: align hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: align(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: customAlign(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: presetAlign(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: getResult(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits] + [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/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/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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 + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.TcoffeeWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.MsaWS] + [wsgen] [should process method: align hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: align(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: customAlign(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: presetAlign(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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: getResult(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS] + [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] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits] + [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/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/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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 + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.DisemblWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.SequenceAnnotation] + [wsgen] [should process method: analize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: analize(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize] + [wsgen] [should process method: customAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: customAnalize(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize] + [wsgen] [should process method: presetAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: presetAnalize(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize] + [wsgen] [should process method: getAnnotation 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] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement] + [wsgen] [should process method: cancelJob hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [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/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/GetJobStatus.java + [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimit.java + [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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/PullExecStatistics.java + [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java + [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.GlobPlotWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.SequenceAnnotation] + [wsgen] [should process method: analize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: analize(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize] + [wsgen] [should process method: customAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: customAnalize(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize] + [wsgen] [should process method: presetAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: presetAnalize(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize] + [wsgen] [should process method: getAnnotation 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] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement] + [wsgen] [should process method: cancelJob hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [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/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/GetJobStatus.java + [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimit.java + [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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/PullExecStatistics.java + [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java + [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.JronnWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.SequenceAnnotation] + [wsgen] [should process method: analize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: analize(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize] + [wsgen] [should process method: customAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: customAnalize(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize] + [wsgen] [should process method: presetAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: presetAnalize(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize] + [wsgen] [should process method: getAnnotation 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] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement] + [wsgen] [should process method: cancelJob hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [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/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/GetJobStatus.java + [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimit.java + [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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/PullExecStatistics.java + [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java + [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.IUPredWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.SequenceAnnotation] + [wsgen] [should process method: analize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: analize(java.util.List)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize] + [wsgen] [should process method: customAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: customAnalize(java.util.List,java.util.List>)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize] + [wsgen] [should process method: presetAnalize hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: presetAnalize(java.util.List,compbio.metadata.Preset)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize] + [wsgen] [should process method: getAnnotation 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] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement] + [wsgen] [should process method: cancelJob hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: cancelJob(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.CancelJob] + [wsgen] [should process method: getJobStatus hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getJobStatus(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetJobStatus] + [wsgen] [should process method: pullExecStatistics hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: pullExecStatistics(java.lang.String,long)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.JManagement] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.PullExecStatistics] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.Metadata] + [wsgen] [should process method: getRunnerOptions hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getRunnerOptions()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetRunnerOptions] + [wsgen] [should process method: getPresets hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getPresets()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetPresets] + [wsgen] [should process method: getLimit hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimit(java.lang.String)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimit] + [wsgen] [should process method: getLimits hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: false] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLimits()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.Metadata] + [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/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/GetJobStatus.java + [wsgen] compbio/data/msa/jaxws/GetJobStatusResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimit.java + [wsgen] compbio/data/msa/jaxws/GetLimitResponse.java + [wsgen] compbio/data/msa/jaxws/GetLimits.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/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/PullExecStatistics.java + [wsgen] compbio/data/msa/jaxws/PullExecStatisticsResponse.java + [wsgen] compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java + [wsgen] compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java + [wsgen] compbio/data/msa/jaxws/WrongParameterExceptionBean.java + [wsgen] Note: ap round: 2 + [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.RegistryWS + [wsgen] Note: ap round: 1 + [wsgen] [ProcessedMethods Interface: compbio.data.msa.RegistryWS] + [wsgen] [should process method: getSupportedServices hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getSupportedServices()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetSupportedServices] + [wsgen] [should process method: getLastTested hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLastTested(compbio.ws.client.Services)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLastTested] + [wsgen] [should process method: getLastTestedOn hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getLastTestedOn(compbio.ws.client.Services)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLastTestedOn] + [wsgen] [should process method: testAllServices hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: testAllServices()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.TestAllServices] + [wsgen] [should process method: testService hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: testService(compbio.ws.client.Services)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.TestService] + [wsgen] [should process method: isOperating hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: isOperating(compbio.ws.client.Services)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.IsOperating] + [wsgen] [should process method: getServiceDescription hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getServiceDescription(compbio.ws.client.Services)] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetServiceDescription] + [wsgen] [should process method: getServiceCategories hasWebMethods: false ] + [wsgen] [endpointReferencesInterface: true] + [wsgen] [declaring class has WebSevice: true] + [wsgen] [returning: true] + [wsgen] [WrapperGen - method: getServiceCategories()] + [wsgen] [method.getDeclaringType(): compbio.data.msa.RegistryWS] + [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetServiceCategories] + [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService] + [wsgen] compbio/data/msa/jaxws/GetLastTested.java + [wsgen] compbio/data/msa/jaxws/GetLastTestedOn.java + [wsgen] compbio/data/msa/jaxws/GetLastTestedOnResponse.java + [wsgen] compbio/data/msa/jaxws/GetLastTestedResponse.java + [wsgen] compbio/data/msa/jaxws/GetServiceCategories.java + [wsgen] compbio/data/msa/jaxws/GetServiceCategoriesResponse.java + [wsgen] compbio/data/msa/jaxws/GetServiceDescription.java + [wsgen] compbio/data/msa/jaxws/GetServiceDescriptionResponse.java + [wsgen] compbio/data/msa/jaxws/GetSupportedServices.java + [wsgen] compbio/data/msa/jaxws/GetSupportedServicesResponse.java + [wsgen] compbio/data/msa/jaxws/IsOperating.java + [wsgen] compbio/data/msa/jaxws/IsOperatingResponse.java + [wsgen] compbio/data/msa/jaxws/TestAllServices.java + [wsgen] compbio/data/msa/jaxws/TestAllServicesResponse.java + [wsgen] compbio/data/msa/jaxws/TestService.java + [wsgen] compbio/data/msa/jaxws/TestServiceResponse.java + [wsgen] Note: ap round: 2 + +BUILD SUCCESSFUL +Total time: 8 seconds