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 (file)
--- a/webservices/compbio/data/msa/Category.java
+++ b/webservices/compbio/data/msa/Category.java
@@ -1,14 +1,3 @@
-package compbio.data.msa;\r
-\r
-import java.util.HashSet;\r
-import java.util.Set;\r
-import java.util.TreeSet;\r
-\r
-import javax.xml.bind.annotation.XmlAccessType;\r
-import javax.xml.bind.annotation.XmlAccessorType;\r
-\r
-import compbio.ws.client.Services;\r
-\r
 /**\r
  * Class that splits {@link Services} to categories. Services themselves have no\r
  * knowledge which category they belongs to.\r
@@ -21,6 +10,18 @@ import compbio.ws.client.Services;
  * @author pvtroshin\r
  * @version 1.0 September 2011\r
  */\r
+\r
+package compbio.data.msa;\r
+\r
+import java.util.HashSet;\r
+import java.util.Set;\r
+import java.util.TreeSet;\r
+\r
+import javax.xml.bind.annotation.XmlAccessType;\r
+import javax.xml.bind.annotation.XmlAccessorType;\r
+\r
+import compbio.ws.client.Services;\r
+\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
 public class Category {\r
        /*\r
@@ -34,7 +35,8 @@ public class Category {
        public static final String CATEGORY_ALIGNMENT = "Alignment";\r
        public static final String CATEGORY_DISORDER = "Protein Disorder";\r
        public static final String CATEGORY_CONSERVATION = "Conservation";\r
-\r
+       public static final String CATEGORY_PREDICTION = "Prediction";\r
+       \r
        public String name;\r
        Set<Services> services;\r
 \r
@@ -70,18 +72,21 @@ public class Category {
                disorder_services.add(Services.GlobPlotWS);\r
                disorder_services.add(Services.IUPredWS);\r
                disorder_services.add(Services.JronnWS);\r
-\r
                Category disorder = new Category(CATEGORY_DISORDER, disorder_services);\r
+\r
                Set<Services> conservation_services = new HashSet<Services>();\r
                conservation_services.add(Services.AAConWS);\r
+               Category conservation = new Category(CATEGORY_CONSERVATION, conservation_services);\r
 \r
-               Category conservation = new Category(CATEGORY_CONSERVATION,\r
-                               conservation_services);\r
+               Set<Services> prediction_services = new HashSet<Services>();\r
+               prediction_services.add(Services.JpredWS);\r
+               Category prediction = new Category(CATEGORY_PREDICTION, prediction_services);\r
 \r
                Set<Category> categories = new HashSet<Category>();\r
                categories.add(alignment);\r
                categories.add(disorder);\r
                categories.add(conservation);\r
+               categories.add(prediction);\r
 \r
                return categories;\r
        }\r

diff --git a/webservices/compbio/ws/client/Services.java b/webservices/compbio/ws/client/Services.java
index 2ffafb6..28bb5dd 100644 (file)
--- 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\r
         * part of minimal client package. Such things should go into ServicesUtil\r
         */\r
-       MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS;\r
+       MafftWS, MuscleWS, ClustalWS, ClustalOWS, TcoffeeWS, ProbconsWS, AAConWS, JronnWS, DisemblWS, GlobPlotWS, IUPredWS, JpredWS;\r
 \r
        public static Services getService(String servName) {\r
                servName = servName.trim().toLowerCase();\r
@@ -73,32 +73,31 @@ public enum Services {
                switch (this) {\r
                        // deliberate leaking\r
                        case AAConWS :\r
+                       case JpredWS :\r
                        case JronnWS :\r
                        case DisemblWS :\r
                        case GlobPlotWS :\r
                        case IUPredWS :\r
                                return SequenceAnnotation.class;\r
 \r
-                               // deliberate leaking\r
+                       // deliberate leaking\r
                        case ClustalWS :\r
                        case ClustalOWS :\r
                        case MafftWS :\r
                        case MuscleWS :\r
                        case ProbconsWS :\r
                        case TcoffeeWS :\r
-\r
                                return MsaWS.class;\r
+\r
                        default :\r
-                               throw new RuntimeException("Unrecognised Web Service Type "\r
-                                               + this + " - Should never happened!");\r
+                               throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
                }\r
        }\r
 \r
        JABAService getInterface(Service service) {\r
                assert service != null;\r
 \r
-               QName portName = new QName(service.getServiceName().getNamespaceURI(),\r
-                               this.toString() + "Port");\r
+               QName portName = new QName(service.getServiceName().getNamespaceURI(), this.toString() + "Port");\r
                return service.getPort(portName, this.getServiceType());\r
        }\r
 \r
@@ -106,6 +105,8 @@ public enum Services {
                switch (this) {\r
                        case AAConWS :\r
                                return AACON_INFO;\r
+                       case JpredWS :\r
+                               return JPRED_INFO;\r
                        case ClustalOWS :\r
                                return CLUSTAL_OMEGA_INFO;\r
                        case ClustalWS :\r
@@ -127,67 +128,77 @@ public enum Services {
                        case TcoffeeWS :\r
                                return TCOFFEE_INFO;\r
                        default :\r
-                               throw new RuntimeException("Unrecognised Web Service Type "\r
-                                               + this + " - Should never happened!");\r
+                               throw new RuntimeException("Unrecognised Web Service Type " + this + " - Should never happen!");\r
                }\r
        }\r
 \r
        public static final String AACON_INFO = new ServiceInfo(AAConWS,\r
-                       "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon")\r
-                       .toString();\r
-       public static final String CLUSTAL_INFO = new ServiceInfo(\r
-                       ClustalWS,\r
-                       "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"\r
-                                       + "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948. ",\r
+                       "in preparation", "1.0", "http://www.compbio.dundee.ac.uk/aacon").toString();\r
+\r
+       public static final String JPRED_INFO = new ServiceInfo(JpredWS,\r
+                       "Cole C, Barber JD, Barton GJ.reparation" + \r
+                       "The Jpred 3 secondary structure prediction server\n" +\r
+                       "Nucl. Acids Res. (2008) 36 (suppl 2): W197-W201., doi: 10.1093/nar/gkn238", \r
+                       "3.0", "http://www.compbio.dundee.ac.uk/www-jpred").toString();\r
+       \r
+       public static final String CLUSTAL_INFO = new ServiceInfo(ClustalWS,\r
+                       "Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, " + \r
+                       "Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG.\n" +\r
+                       "(2007). Clustal W and Clustal X version 2.0. Bioinformatics, 23, 2947-2948.",\r
                        "2.0.12", "http://www.clustal.org/clustal2/").toString();\r
-       public static final String CLUSTAL_OMEGA_INFO = new ServiceInfo(\r
-                       ClustalOWS,\r
+\r
+       public static final String CLUSTAL_OMEGA_INFO = new ServiceInfo(ClustalOWS,\r
                        "Fast, scalable generation of high quality protein multiple sequence alignments using Clustal Omega\r\n"\r
-                                       + "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",\r
+                       + "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",\r
                        "1.0.2", "http://www.clustal.org/omega").toString();\r
-       public static final String DISEMBL_INFO = new ServiceInfo(\r
-                       DisemblWS,\r
+\r
+       public static final String DISEMBL_INFO = new ServiceInfo(DisemblWS,\r
                        "R. Linding, L.J. Jensen, F. Diella, P. Bork, T.J. Gibson and R.B. Russell\r\n"\r
-                                       + "Protein disorder prediction: implications for structural proteomics\r\n"\r
-                                       + "Structure Vol 11, Issue 11, 4 November 2003", "1.5",\r
+                       + "Protein disorder prediction: implications for structural proteomics\r\n"\r
+                       + "Structure Vol 11, Issue 11, 4 November 2003", "1.5",\r
                        "http://dis.embl.de/").toString();\r
-       public static final String GLOBPLOT_INFO = new ServiceInfo(\r
-                       GlobPlotWS,\r
-                       "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson "\r
-                                       + "'GlobPlot: exploring protein sequences for globularity and disorder.' Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n",\r
+\r
+       public static final String GLOBPLOT_INFO = new ServiceInfo(GlobPlotWS,\r
+                       "Rune Linding, Robert B. Russell, Victor Neduva and Toby J. Gibson " +\r
+                       "'GlobPlot: exploring protein sequences for globularity and disorder.' " + \r
+                       "Nucl. Acids Res. (2003) 31 (13): 3701-3708. doi: 10.1093/nar/gkg519\r\n",\r
                        "2.3", "http://globplot.embl.de/").toString();\r
-       public static final String IUPRED_INFO = new ServiceInfo(\r
-                       IUPredWS,\r
+\r
+       public static final String IUPRED_INFO = new ServiceInfo(IUPredWS,\r
                        "The Pairwise Energy Content Estimated from Amino Acid Composition Discriminates between Folded and Intrinsically Unstructured Proteins\r\n"\r
-                                       + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n"\r
-                                       + "J. Mol. Biol. (2005) 347, 827-839.", "1.0",\r
+                       + "Zsuzsanna Dosztányi, Veronika Csizmók, Péter Tompa and István Simon\r\n"\r
+                       + "J. Mol. Biol. (2005) 347, 827-839.", "1.0",\r
                        "http://iupred.enzim.hu/").toString();\r
+\r
        public static final String TCOFFEE_INFO = new ServiceInfo(TcoffeeWS,\r
                        "T-Coffee: A novel method for multiple sequence alignments  "\r
-                                       + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000",\r
-                       "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html")\r
-                       .toString();\r
+                       + "Notredame, Higgins, Heringa, JMB, 302 (205-217) 2000",\r
+                       "8.99", "http://tcoffee.crg.cat/apps/tcoffee/index.html").toString();\r
+\r
        public static final String MUSCLE_INFO = new ServiceInfo(\r
                        MuscleWS,\r
                        "Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.\r\n"\r
-                                       + "doi:10.1093/nar/gkh340", "3.8.31",\r
+                       + "doi:10.1093/nar/gkh340", "3.8.31",\r
                        "http://www.drive5.com/muscle/").toString();\r
+\r
        public static final String PROBCONS_INFO = new ServiceInfo(\r
                        ProbconsWS,\r
                        "Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: "\r
-                                       + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ",\r
-                       "1.12", "http://probcons.stanford.edu/").toString();;\r
+                       + "Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340. ",\r
+                       "1.12", "http://probcons.stanford.edu/").toString();\r
+\r
        public static final String JRONN_INFO = new ServiceInfo(\r
                        JronnWS,\r
                        "unpublished, original algorithm Yang,Z.R., Thomson,R., McMeil,P. and Esnouf,R.M. (2005) "\r
                                        + "RONN: the bio-basis function neural network technique applied to the "\r
                                        + "dectection of natively disordered regions in proteins Bioinformatics 21: 3369-3376\r\n",\r
-                       "1.0", "http://www.compbio.dundee.ac.uk/jabaws/").toString();;\r
+                       "1.0", "http://www.compbio.dundee.ac.uk/jabaws/").toString();\r
+\r
        public static final String MAFFT_INFO = new ServiceInfo(\r
                        MafftWS,\r
                        "Katoh, Toh 2010 (Bioinformatics 26:1899-1900)\r\n"\r
                                        + "Parallelization of the MAFFT multiple sequence alignment program. ",\r
-                       "6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString();;\r
+                       "6.8.57", "http://mafft.cbrc.jp/alignment/software/").toString();\r
 \r
        @XmlAccessorType(XmlAccessType.FIELD)\r
        static class ServiceInfo {\r
@@ -195,7 +206,7 @@ public enum Services {
                String reference;\r
                String version;\r
                String moreinfo;\r
-               final static String jabaws_version = "2.0";\r
+               final static String jabaws_version = "2.5";\r
                final static String line_delimiter = "\n";\r
 \r
                private ServiceInfo() {\r
@@ -211,8 +222,7 @@ public enum Services {
 \r
                @Override\r
                public String toString() {\r
-                       String value = "SERVICE: " + service + " version " + version\r
-                                       + line_delimiter;\r
+                       String value = "SERVICE: " + service + " version " + version + line_delimiter;\r
                        value += "JABAWS v. " + jabaws_version + line_delimiter;\r
                        value += "REFERENCES: " + reference + line_delimiter;\r
                        value += "MORE INFORMATION: " + moreinfo + line_delimiter;\r

diff --git a/webservices/compbio/ws/client/ServicesUtil.java b/webservices/compbio/ws/client/ServicesUtil.java
index 08b8131..26f1467 100644 (file)
--- 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;\r
 import compbio.engine.client.Executable;\r
 import compbio.runner.conservation.AACon;\r
+import compbio.runner.predictors.Jpred;\r
 import compbio.runner.disorder.Disembl;\r
 import compbio.runner.disorder.GlobPlot;\r
 import compbio.runner.disorder.IUPred;\r
@@ -33,6 +34,8 @@ public class ServicesUtil {
                switch (service) {\r
                        case AAConWS :\r
                                return AACon.class;\r
+                       case JpredWS :\r
+                               return Jpred.class;\r
                        case ClustalOWS :\r
                                return ClustalO.class;\r
                        case ClustalWS :\r
@@ -54,14 +57,11 @@ public class ServicesUtil {
                        case IUPredWS :\r
                                return IUPred.class;\r
                        default :\r
-                               throw new RuntimeException(\r
-                                               "Unknown web service implementation class for service: "\r
-                                                               + service);\r
+                               throw new RuntimeException("Unknown web service implementation class for service: " + service);\r
                }\r
        }\r
 \r
-       public static Class<? extends Executable<?>> getRunnerByJobDirectory(\r
-                       File jobdir) {\r
+       public static Class<? extends Executable<?>> getRunnerByJobDirectory(File jobdir) {\r
                Services service = getServiceByRunnerName(getRunnerNameByJobDirectory(jobdir));\r
                return getServiceImpl(service);\r
        }\r
@@ -82,8 +82,7 @@ public class ServicesUtil {
 \r
        private static Services getServiceByRunnerName(String name) {\r
                for (Services service : Services.values()) {\r
-                       String runnerName = getServiceImpl(service).getSimpleName()\r
-                                       .toLowerCase();\r
+                       String runnerName = getServiceImpl(service).getSimpleName().toLowerCase();\r
                        name = name.trim().toLowerCase();\r
                        if (name.startsWith(runnerName)) {\r
                                return service;\r

diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java
index c6eaf76..e9a349c 100644 (file)
--- 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\r
                                + pseparator + "serviceName>");\r
                System.out.println();\r
-               System.out\r
-                               .println(hostkey\r
+               System.out.println(hostkey\r
                                                + pseparator\r
                                                + "<host_and_context> - a full URL to the JABAWS web server including context path e.g. http://10.31.1.159:8080/ws");\r
-               System.out\r
-                               .println(servicekey\r
+               System.out.println(servicekey\r
                                                + pseparator\r
                                                + "<ServiceName> - optional if unspecified all services are tested otherwise one of "\r
                                                + Arrays.toString(Services.values()));\r
@@ -221,8 +219,7 @@ public class WSTester {
        private <T> boolean checkService(JABAService wservice, Services service) {\r
                try {\r
                        if (wservice == null) {\r
-                               throw new NullPointerException(\r
-                                               "JABAService instance must be provided!");\r
+                               throw new NullPointerException("JABAService instance must be provided!");\r
                        }\r
 \r
                        if (wservice instanceof MsaWS) {\r
@@ -231,8 +228,7 @@ public class WSTester {
                                return testSequenceAnnotationWS(\r
                                                (SequenceAnnotation<T>) wservice, service);\r
                        } else {\r
-                               throw new UnsupportedOperationException("The service: "\r
-                                               + wservice.getClass() + " is not supported! ");\r
+                               throw new UnsupportedOperationException("The service: " + wservice.getClass() + " is not supported! ");\r
                        }\r
                } catch (Exception e) {\r
                        reportException(e);\r
@@ -382,8 +378,7 @@ public class WSTester {
                String host = CmdHelper.getHost(args);\r
                String serviceName = CmdHelper.getServiceName(args);\r
                if (!Jws2Client.validURL(host)) {\r
-                       System.err\r
-                                       .println("<host_and_context> parameter is not provided or is incorrect!");\r
+                       System.err.println("<host_and_context> parameter is not provided or is incorrect!");\r
                        System.exit(1);\r
                }\r
                WSTester tester = new WSTester(host, new PrintWriter(System.out, true));\r
@@ -391,8 +386,7 @@ public class WSTester {
                if (serviceName != null) {\r
                        Services service = Services.getService(serviceName);\r
                        if (service == null) {\r
-                               tester.writer.println("Service '" + serviceName\r
-                                               + "' is not supported. Valid values are: "\r
+                               tester.writer.println("Service '" + serviceName + "' is not supported. Valid values are: "\r
                                                + Arrays.toString(Services.values()));\r
                                tester.writer.println();\r
                                printUsage();\r
@@ -402,8 +396,7 @@ public class WSTester {
                        System.exit(0);\r
                }\r
 \r
-               tester.writer\r
-                               .println("<ServiceName> is not provided checking all known services...");\r
+               tester.writer.println("<ServiceName> is not provided checking all known services...");\r
 \r
                for (Services serv : Services.values()) {\r
                        tester.writer.println();\r
@@ -425,8 +418,8 @@ public class WSTester {
                        WebServiceException {\r
                JABAService ws = Jws2Client.connect(hostname, service);\r
                if (ws == null) {\r
-                       writer.println("Cannot estabilish the connection to host "\r
-                                       + hostname + " with service " + service.toString());\r
+                       String line = "Cannot estabilish the connection to host " + hostname + " with service ";\r
+                       writer.println(line + service.toString());\r
                        return false;\r
                }\r
                boolean succeed = false;\r
@@ -442,11 +435,9 @@ public class WSTester {
 \r
        private void reportResults(Services serv, boolean succeed) {\r
                if (succeed) {\r
-                       writer.println("Check is completed. The Service " + serv\r
-                                       + " IS WORKING\n");\r
+                       writer.println("Check is completed. The Service " + serv + " IS WORKING\n");\r
                } else {\r
-                       writer.println("Check is aborted. The Service " + serv\r
-                                       + " HAS SOME PROBLEMS\n");\r
+                       writer.println("Check is aborted. The Service " + serv + " HAS SOME PROBLEMS\n");\r
                }\r
        }\r
 }\r

diff --git a/webservices/compbio/ws/server/JpredWS.java b/webservices/compbio/ws/server/JpredWS.java
new file mode 100644 (file)
index 0000000..61ec773
--- /dev/null
+++ b/webservices/compbio/ws/server/JpredWS.java
@@ -0,0 +1,88 @@
+/* Copyright (c) 2011 Peter Troshin\r
+ * Copyright (c) 2013 Alexander Sherstnev\r
+ *  \r
+ *  JAva Bioinformatics Analysis Web Services (JABAWS)\r
+ *  @version: 2.5     \r
+ * \r
+ *  This library is free software; you can redistribute it and/or modify it under the terms of the\r
+ *  Apache License version 2 as published by the Apache Software Foundation\r
+ * \r
+ *  This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without\r
+ *  even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache \r
+ *  License for more details.\r
+ * \r
+ *  A copy of the license is in apache_license.txt. It is also available here:\r
+ * @see: http://www.apache.org/licenses/LICENSE-2.0.txt\r
+ * \r
+ * Any republication or derived work distributed in source code form\r
+ * must include this copyright and license notice.\r
+ */\r
+package compbio.ws.server;\r
+\r
+import java.io.File;\r
+import java.util.Arrays;\r
+import java.util.List;\r
+\r
+import javax.jws.WebService;\r
+\r
+import org.apache.log4j.Logger;\r
+\r
+import compbio.data.msa.JABAService;\r
+import compbio.data.msa.SequenceAnnotation;\r
+import compbio.data.sequence.FastaSequence;\r
+import compbio.engine.Configurator;\r
+import compbio.engine.client.ConfiguredExecutable;\r
+import compbio.metadata.ChunkHolder;\r
+import compbio.metadata.JobSubmissionException;\r
+import compbio.metadata.LimitExceededException;\r
+import compbio.metadata.Option;\r
+import compbio.metadata.Preset;\r
+import compbio.metadata.UnsupportedRuntimeException;\r
+import compbio.metadata.WrongParameterException;\r
+import compbio.runner.predictors.Jpred;\r
+\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JpredWS")\r
+public class JpredWS extends SequenceAnnotationService<Jpred>\r
+               implements SequenceAnnotation<Jpred> {\r
+\r
+       private static Logger log = Logger.getLogger(JpredWS.class);\r
+\r
+       public JpredWS() {\r
+               super(new Jpred(), log);\r
+       }\r
+\r
+       @Override\r
+       public String analize(List<FastaSequence> sequences)\r
+                       throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException {\r
+               WSUtil.validateJpredInput(sequences);\r
+               ConfiguredExecutable<Jpred> confpred = init(sequences);\r
+\r
+               // set default conservation method to fastest - SHENKIN\r
+               // TODO: This violates encapsulation, should be moved to the runners\r
+               // level.\r
+               //confpred.addParameters(Arrays.asList("-m=SHENKIN"));\r
+               return WSUtil.analize(sequences, confpred, log, "JpredWS analize", getLimit(""));\r
+       }\r
+\r
+       @Override\r
+       public String customAnalize(List<FastaSequence> sequences, List<Option<Jpred>> options) \r
+                                       throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {\r
+               WSUtil.validateJpredInput(sequences);\r
+               return super.customAnalize(sequences, options);\r
+       }\r
+\r
+       @Override\r
+       public String presetAnalize(List<FastaSequence> sequences, Preset<Jpred> preset)\r
+                       throws UnsupportedRuntimeException, LimitExceededException, JobSubmissionException, WrongParameterException {\r
+               WSUtil.validateJpredInput(sequences);\r
+               return super.presetAnalize(sequences, preset);\r
+       }\r
+\r
+       @Override\r
+       public ChunkHolder pullExecStatistics(String jobId, long position) {\r
+               WSUtil.validateJobId(jobId);\r
+               String file = Configurator.getWorkDirectory(jobId) + File.separator + Jpred.getStatFile();\r
+               return WSUtil.pullFile(file, position);\r
+       }\r
+\r
+}\r

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index 7341989..ebf4b3e 100644 (file)
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -159,10 +159,29 @@ public final class WSUtil {
                        }\r
                        if (fs.getLength() != len) {\r
                                throw new JobSubmissionException(\r
-                                               "All sequences must be of the same length. Please align "\r
-                                                               + "the sequences prior to submission! The first sequence length is : "\r
-                                                               + len + " but the sequence '" + fs.getId()\r
-                                                               + "' length is " + fs.getLength());\r
+                                               "All sequences must be of the same length. Please align the sequences " + \r
+                                               " prior to submission! The first sequence length is : " + len + \r
+                                               " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
+                       }\r
+               }\r
+       }\r
+\r
+       public static void validateJpredInput(List<FastaSequence> sequences)\r
+                       throws JobSubmissionException {\r
+               validateFastaInput(sequences);\r
+               int len = 0;\r
+               for (FastaSequence fs : sequences) {\r
+                       if (len == 0) {\r
+                               len = fs.getLength();\r
+                               System.out.println("1st FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());\r
+                               continue;\r
+                       }\r
+                       if (fs.getLength() != len) {\r
+                               System.out.println("FASTA rec: id = " + fs.getId() + ": seq = " + fs.getSequence());\r
+                               throw new JobSubmissionException(\r
+                                               "All sequences must be of the same length. Please align the sequences " + \r
+                                               " prior to submission! The first sequence length is : " + len + \r
+                                               " but the sequence '" + fs.getId() + "' length is " + fs.getLength());\r
                        }\r
                }\r
        }\r
@@ -171,8 +190,7 @@ public final class WSUtil {
                        throws ResultNotAvailableException {\r
                WSUtil.validateJobId(jobId);\r
                AsyncExecutor asyncEngine = Configurator.getAsyncEngine(jobId);\r
-               ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine\r
-                               .getResults(jobId);\r
+               ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine.getResults(jobId);\r
                ScoreManager mas = aacon.getResults();\r
                log.trace(jobId + " getConservation : " + mas);\r
                return mas;\r

diff --git a/webservices/compbio/ws/server/resource/JpredWS.wsdl b/webservices/compbio/ws/server/resource/JpredWS.wsdl
new file mode 100644 (file)
index 0000000..976aee1
--- /dev/null
+++ b/webservices/compbio/ws/server/resource/JpredWS.wsdl
@@ -0,0 +1,292 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<!-- Generated by JAX-WS RI at http://jax-ws.dev.java.net. RI's version is Metro/2.1 (branches/2.1-6728; 2011-02-03T14:14:58+0000) JAXWS-RI/2.2.3 JAXWS/2.2. -->
+<definitions targetNamespace="http://msa.data.compbio/01/12/2010/" name="JpredWS" xmlns="http://schemas.xmlsoap.org/wsdl/" xmlns:wsp="http://www.w3.org/ns/ws-policy" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:wsp1_2="http://schemas.xmlsoap.org/ws/2004/09/policy" xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/" xmlns:wsam="http://www.w3.org/2007/05/addressing/metadata" xmlns:wsu="http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd">
+  <types>
+    <xsd:schema>
+      <xsd:import namespace="http://msa.data.compbio/01/12/2010/" schemaLocation="JpredWS_schema1.xsd"/>
+    </xsd:schema>
+  </types>
+  <message name="getAnnotation">
+    <part name="parameters" element="tns:getAnnotation"/>
+  </message>
+  <message name="getAnnotationResponse">
+    <part name="parameters" element="tns:getAnnotationResponse"/>
+  </message>
+  <message name="ResultNotAvailableException">
+    <part name="fault" element="tns:ResultNotAvailableException"/>
+  </message>
+  <message name="analize">
+    <part name="parameters" element="tns:analize"/>
+  </message>
+  <message name="analizeResponse">
+    <part name="parameters" element="tns:analizeResponse"/>
+  </message>
+  <message name="UnsupportedRuntimeException">
+    <part name="fault" element="tns:UnsupportedRuntimeException"/>
+  </message>
+  <message name="LimitExceededException">
+    <part name="fault" element="tns:LimitExceededException"/>
+  </message>
+  <message name="JobSubmissionException">
+    <part name="fault" element="tns:JobSubmissionException"/>
+  </message>
+  <message name="customAnalize">
+    <part name="parameters" element="tns:customAnalize"/>
+  </message>
+  <message name="customAnalizeResponse">
+    <part name="parameters" element="tns:customAnalizeResponse"/>
+  </message>
+  <message name="WrongParameterException">
+    <part name="fault" element="tns:WrongParameterException"/>
+  </message>
+  <message name="presetAnalize">
+    <part name="parameters" element="tns:presetAnalize"/>
+  </message>
+  <message name="presetAnalizeResponse">
+    <part name="parameters" element="tns:presetAnalizeResponse"/>
+  </message>
+  <message name="pullExecStatistics">
+    <part name="parameters" element="tns:pullExecStatistics"/>
+  </message>
+  <message name="pullExecStatisticsResponse">
+    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+  </message>
+  <message name="cancelJob">
+    <part name="parameters" element="tns:cancelJob"/>
+  </message>
+  <message name="cancelJobResponse">
+    <part name="parameters" element="tns:cancelJobResponse"/>
+  </message>
+  <message name="getJobStatus">
+    <part name="parameters" element="tns:getJobStatus"/>
+  </message>
+  <message name="getJobStatusResponse">
+    <part name="parameters" element="tns:getJobStatusResponse"/>
+  </message>
+  <message name="getLimit">
+    <part name="parameters" element="tns:getLimit"/>
+  </message>
+  <message name="getLimitResponse">
+    <part name="parameters" element="tns:getLimitResponse"/>
+  </message>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
+  </message>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  </message>
+  <message name="getPresets">
+    <part name="parameters" element="tns:getPresets"/>
+  </message>
+  <message name="getPresetsResponse">
+    <part name="parameters" element="tns:getPresetsResponse"/>
+  </message>
+  <message name="getLimits">
+    <part name="parameters" element="tns:getLimits"/>
+  </message>
+  <message name="getLimitsResponse">
+    <part name="parameters" element="tns:getLimitsResponse"/>
+  </message>
+  <portType name="SequenceAnnotation">
+    <operation name="getAnnotation">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationRequest" message="tns:getAnnotation"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotationResponse" message="tns:getAnnotationResponse"/>
+      <fault message="tns:ResultNotAvailableException" name="ResultNotAvailableException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getAnnotation/Fault/ResultNotAvailableException"/>
+    </operation>
+    <operation name="analize">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analizeRequest" message="tns:analize"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analizeResponse" message="tns:analizeResponse"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/UnsupportedRuntimeException"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/LimitExceededException"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/analize/Fault/JobSubmissionException"/>
+    </operation>
+    <operation name="customAnalize">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeRequest" message="tns:customAnalize"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeResponse" message="tns:customAnalizeResponse"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/UnsupportedRuntimeException"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/LimitExceededException"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/JobSubmissionException"/>
+      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalize/Fault/WrongParameterException"/>
+    </operation>
+    <operation name="presetAnalize">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalizeRequest" message="tns:presetAnalize"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalizeResponse" message="tns:presetAnalizeResponse"/>
+      <fault message="tns:UnsupportedRuntimeException" name="UnsupportedRuntimeException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/UnsupportedRuntimeException"/>
+      <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/LimitExceededException"/>
+      <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/JobSubmissionException"/>
+      <fault message="tns:WrongParameterException" name="WrongParameterException" wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/presetAnalize/Fault/WrongParameterException"/>
+    </operation>
+    <operation name="pullExecStatistics">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+    </operation>
+    <operation name="cancelJob">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobRequest" message="tns:cancelJob"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/cancelJobResponse" message="tns:cancelJobResponse"/>
+    </operation>
+    <operation name="getJobStatus">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusRequest" message="tns:getJobStatus"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getJobStatusResponse" message="tns:getJobStatusResponse"/>
+    </operation>
+    <operation name="getLimit">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
+    </operation>
+    <operation name="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    </operation>
+    <operation name="getPresets">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsRequest" message="tns:getPresets"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getPresetsResponse" message="tns:getPresetsResponse"/>
+    </operation>
+    <operation name="getLimits">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
+    </operation>
+  </portType>
+  <binding name="JpredWSPortBinding" type="tns:SequenceAnnotation">
+    <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
+    <operation name="getAnnotation">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+      <fault name="ResultNotAvailableException">
+        <soap:fault name="ResultNotAvailableException" use="literal"/>
+      </fault>
+    </operation>
+    <operation name="analize">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+      <fault name="UnsupportedRuntimeException">
+        <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+      </fault>
+      <fault name="LimitExceededException">
+        <soap:fault name="LimitExceededException" use="literal"/>
+      </fault>
+      <fault name="JobSubmissionException">
+        <soap:fault name="JobSubmissionException" use="literal"/>
+      </fault>
+    </operation>
+    <operation name="customAnalize">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+      <fault name="UnsupportedRuntimeException">
+        <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+      </fault>
+      <fault name="LimitExceededException">
+        <soap:fault name="LimitExceededException" use="literal"/>
+      </fault>
+      <fault name="JobSubmissionException">
+        <soap:fault name="JobSubmissionException" use="literal"/>
+      </fault>
+      <fault name="WrongParameterException">
+        <soap:fault name="WrongParameterException" use="literal"/>
+      </fault>
+    </operation>
+    <operation name="presetAnalize">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+      <fault name="UnsupportedRuntimeException">
+        <soap:fault name="UnsupportedRuntimeException" use="literal"/>
+      </fault>
+      <fault name="LimitExceededException">
+        <soap:fault name="LimitExceededException" use="literal"/>
+      </fault>
+      <fault name="JobSubmissionException">
+        <soap:fault name="JobSubmissionException" use="literal"/>
+      </fault>
+      <fault name="WrongParameterException">
+        <soap:fault name="WrongParameterException" use="literal"/>
+      </fault>
+    </operation>
+    <operation name="pullExecStatistics">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+    </operation>
+    <operation name="cancelJob">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+    </operation>
+    <operation name="getJobStatus">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+    </operation>
+    <operation name="getLimit">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+    </operation>
+    <operation name="getRunnerOptions">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+    </operation>
+    <operation name="getPresets">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+    </operation>
+    <operation name="getLimits">
+      <soap:operation soapAction=""/>
+      <input>
+        <soap:body use="literal"/>
+      </input>
+      <output>
+        <soap:body use="literal"/>
+      </output>
+    </operation>
+  </binding>
+  <service name="JpredWS">
+    <port name="JpredWSPort" binding="tns:JpredWSPortBinding">
+      <soap:address location="REPLACE_WITH_ACTUAL_URL"/>
+    </port>
+  </service>
+</definitions>
+

diff --git a/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
new file mode 100644 (file)
index 0000000..f62aefc
--- /dev/null
+++ b/webservices/compbio/ws/server/resource/JpredWS_schema1.xsd
@@ -0,0 +1,366 @@
+<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
+<xs:schema version="1.0" targetNamespace="http://msa.data.compbio/01/12/2010/" xmlns:tns="http://msa.data.compbio/01/12/2010/" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+
+  <xs:element name="JobSubmissionException" type="tns:JobSubmissionException"/>
+
+  <xs:element name="LimitExceededException" type="tns:LimitExceededException"/>
+
+  <xs:element name="ResultNotAvailableException" type="tns:ResultNotAvailableException"/>
+
+  <xs:element name="UnsupportedRuntimeException" type="tns:UnsupportedRuntimeException"/>
+
+  <xs:element name="WrongParameterException" type="tns:WrongParameterException"/>
+
+  <xs:element name="analize" type="tns:analize"/>
+
+  <xs:element name="analizeResponse" type="tns:analizeResponse"/>
+
+  <xs:element name="cancelJob" type="tns:cancelJob"/>
+
+  <xs:element name="cancelJobResponse" type="tns:cancelJobResponse"/>
+
+  <xs:element name="customAnalize" type="tns:customAnalize"/>
+
+  <xs:element name="customAnalizeResponse" type="tns:customAnalizeResponse"/>
+
+  <xs:element name="getAnnotation" type="tns:getAnnotation"/>
+
+  <xs:element name="getAnnotationResponse" type="tns:getAnnotationResponse"/>
+
+  <xs:element name="getJobStatus" type="tns:getJobStatus"/>
+
+  <xs:element name="getJobStatusResponse" type="tns:getJobStatusResponse"/>
+
+  <xs:element name="getLimit" type="tns:getLimit"/>
+
+  <xs:element name="getLimitResponse" type="tns:getLimitResponse"/>
+
+  <xs:element name="getLimits" type="tns:getLimits"/>
+
+  <xs:element name="getLimitsResponse" type="tns:getLimitsResponse"/>
+
+  <xs:element name="getPresets" type="tns:getPresets"/>
+
+  <xs:element name="getPresetsResponse" type="tns:getPresetsResponse"/>
+
+  <xs:element name="getRunnerOptions" type="tns:getRunnerOptions"/>
+
+  <xs:element name="getRunnerOptionsResponse" type="tns:getRunnerOptionsResponse"/>
+
+  <xs:element name="limits" type="tns:limitsManager"/>
+
+  <xs:element name="presetAnalize" type="tns:presetAnalize"/>
+
+  <xs:element name="presetAnalizeResponse" type="tns:presetAnalizeResponse"/>
+
+  <xs:element name="presets" type="tns:presetManager"/>
+
+  <xs:element name="pullExecStatistics" type="tns:pullExecStatistics"/>
+
+  <xs:element name="pullExecStatisticsResponse" type="tns:pullExecStatisticsResponse"/>
+
+  <xs:element name="runnerConfig" type="tns:runnerConfig"/>
+
+  <xs:complexType name="customAnalize">
+    <xs:sequence>
+      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="options" type="tns:option" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="fastaSequence">
+    <xs:sequence>
+      <xs:element name="id" type="xs:string" minOccurs="0"/>
+      <xs:element name="sequence" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="option">
+    <xs:sequence>
+      <xs:element name="description" type="xs:string"/>
+      <xs:element name="optionNames" type="xs:string" maxOccurs="unbounded"/>
+      <xs:element name="name" type="xs:string"/>
+      <xs:element name="furtherDetails" type="xs:anyURI" minOccurs="0"/>
+      <xs:element name="defaultValue" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+    <xs:attribute name="isRequired" type="xs:boolean" use="required"/>
+  </xs:complexType>
+
+  <xs:complexType name="customAnalizeResponse">
+    <xs:sequence>
+      <xs:element name="return" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="UnsupportedRuntimeException">
+    <xs:sequence>
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="LimitExceededException">
+    <xs:sequence>
+      <xs:element name="actualNumberofSequences" type="xs:int"/>
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
+      <xs:element name="numberOfSequencesAllowed" type="xs:int"/>
+      <xs:element name="sequenceLenghtActual" type="xs:int"/>
+      <xs:element name="sequenceLenghtAllowed" type="xs:int"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="JobSubmissionException">
+    <xs:sequence>
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="WrongParameterException">
+    <xs:sequence>
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getRunnerOptions">
+    <xs:sequence/>
+  </xs:complexType>
+
+  <xs:complexType name="getRunnerOptionsResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:runnerConfig" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="runnerConfig">
+    <xs:sequence>
+      <xs:element name="options" type="tns:option" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="parameters" type="tns:parameter" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="prmSeparator" type="xs:string" minOccurs="0"/>
+      <xs:element name="runnerClassName" type="xs:string"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="parameter">
+    <xs:complexContent>
+      <xs:extension base="tns:option">
+        <xs:sequence>
+          <xs:element name="possibleValues" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>
+          <xs:element name="validValue" type="tns:valueConstrain" minOccurs="0"/>
+        </xs:sequence>
+      </xs:extension>
+    </xs:complexContent>
+  </xs:complexType>
+
+  <xs:complexType name="valueConstrain">
+    <xs:sequence>
+      <xs:element name="type" type="tns:type"/>
+      <xs:element name="max" type="xs:string" minOccurs="0"/>
+      <xs:element name="min" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="pullExecStatistics">
+    <xs:sequence>
+      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+      <xs:element name="position" type="xs:long"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="pullExecStatisticsResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:chunkHolder" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="chunkHolder">
+    <xs:sequence>
+      <xs:element name="chunk" type="xs:string" minOccurs="0"/>
+      <xs:element name="position" type="xs:long"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getJobStatus">
+    <xs:sequence>
+      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getJobStatusResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:jobStatus" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="presetAnalize">
+    <xs:sequence>
+      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="preset" type="tns:preset" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="preset">
+    <xs:sequence>
+      <xs:element name="name" type="xs:string"/>
+      <xs:element name="description" type="xs:string" minOccurs="0"/>
+      <xs:element name="optlist" minOccurs="0">
+        <xs:complexType>
+          <xs:sequence>
+            <xs:element name="option" type="xs:string" maxOccurs="unbounded"/>
+          </xs:sequence>
+        </xs:complexType>
+      </xs:element>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="presetAnalizeResponse">
+    <xs:sequence>
+      <xs:element name="return" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getAnnotation">
+    <xs:sequence>
+      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getAnnotationResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:scoreManager" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="scoreManager">
+    <xs:sequence>
+      <xs:element name="seqScores" type="tns:scoreHolder" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="scoreHolder">
+    <xs:sequence>
+      <xs:element name="id" type="xs:string" minOccurs="0"/>
+      <xs:element name="scores" type="tns:score" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="score">
+    <xs:sequence>
+      <xs:element name="method" type="xs:string" minOccurs="0"/>
+      <xs:element name="ranges" type="tns:range" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+      <xs:element name="scores" type="xs:float" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="range">
+    <xs:sequence>
+      <xs:element name="from" type="xs:int"/>
+      <xs:element name="to" type="xs:int"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="ResultNotAvailableException">
+    <xs:sequence>
+      <xs:element name="message" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getLimits">
+    <xs:sequence/>
+  </xs:complexType>
+
+  <xs:complexType name="getLimitsResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:limitsManager" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="limitsManager">
+    <xs:sequence>
+      <xs:element name="runnerClassName" type="xs:string" minOccurs="0"/>
+      <xs:element name="limit" type="tns:limit" nillable="true" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="limit">
+    <xs:sequence>
+      <xs:element name="preset" type="xs:string" minOccurs="0"/>
+      <xs:element name="seqNumber" type="xs:int"/>
+      <xs:element name="seqLength" type="xs:int"/>
+    </xs:sequence>
+    <xs:attribute name="isDefault" type="xs:boolean" use="required"/>
+  </xs:complexType>
+
+  <xs:complexType name="getPresets">
+    <xs:sequence/>
+  </xs:complexType>
+
+  <xs:complexType name="getPresetsResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:presetManager" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="presetManager">
+    <xs:sequence>
+      <xs:element name="runnerClassName" type="xs:string"/>
+      <xs:element name="preset" type="tns:preset" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getLimit">
+    <xs:sequence>
+      <xs:element name="presetName" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="getLimitResponse">
+    <xs:sequence>
+      <xs:element name="return" type="tns:limit" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="cancelJob">
+    <xs:sequence>
+      <xs:element name="jobId" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="cancelJobResponse">
+    <xs:sequence>
+      <xs:element name="return" type="xs:boolean"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="analize">
+    <xs:sequence>
+      <xs:element name="fastaSequences" type="tns:fastaSequence" minOccurs="0" maxOccurs="unbounded"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:complexType name="analizeResponse">
+    <xs:sequence>
+      <xs:element name="return" type="xs:string" minOccurs="0"/>
+    </xs:sequence>
+  </xs:complexType>
+
+  <xs:simpleType name="type">
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="Integer"/>
+      <xs:enumeration value="Float"/>
+    </xs:restriction>
+  </xs:simpleType>
+
+  <xs:simpleType name="jobStatus">
+    <xs:restriction base="xs:string">
+      <xs:enumeration value="PENDING"/>
+      <xs:enumeration value="RUNNING"/>
+      <xs:enumeration value="CANCELLED"/>
+      <xs:enumeration value="FINISHED"/>
+      <xs:enumeration value="FAILED"/>
+      <xs:enumeration value="UNDEFINED"/>
+      <xs:enumeration value="STARTED"/>
+      <xs:enumeration value="SUBMITTED"/>
+      <xs:enumeration value="COLLECTED"/>
+    </xs:restriction>
+  </xs:simpleType>
+</xs:schema>
+

diff --git a/wsbuild.log b/wsbuild.log
new file mode 100644 (file)
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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize]
+    [wsgen] [should process method: customAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAnalize(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize]
+    [wsgen] [should process method: presetAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAnalize(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize]
+    [wsgen] [should process method: getAnnotation hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getAnnotation(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+    [wsgen] compbio/data/msa/jaxws/Analize.java
+    [wsgen] compbio/data/msa/jaxws/AnalizeResponse.java
+    [wsgen] compbio/data/msa/jaxws/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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize]
+    [wsgen] [should process method: customAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAnalize(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize]
+    [wsgen] [should process method: presetAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAnalize(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize]
+    [wsgen] [should process method: getAnnotation hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getAnnotation(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+    [wsgen] compbio/data/msa/jaxws/Analize.java
+    [wsgen] compbio/data/msa/jaxws/AnalizeResponse.java
+    [wsgen] compbio/data/msa/jaxws/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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Align]
+    [wsgen] [should process method: customAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAlign(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAlign]
+    [wsgen] [should process method: presetAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAlign(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAlign]
+    [wsgen] [should process method: getResult hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getResult(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetResult]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement]
+    [wsgen] [should process method: cancelJob hasWebMethods: false ]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Align]
+    [wsgen] [should process method: customAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAlign(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAlign]
+    [wsgen] [should process method: presetAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAlign(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAlign]
+    [wsgen] [should process method: getResult hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getResult(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetResult]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement]
+    [wsgen] [should process method: cancelJob hasWebMethods: false ]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Align]
+    [wsgen] [should process method: customAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAlign(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAlign]
+    [wsgen] [should process method: presetAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAlign(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAlign]
+    [wsgen] [should process method: getResult hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getResult(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetResult]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement]
+    [wsgen] [should process method: cancelJob hasWebMethods: false ]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Align]
+    [wsgen] [should process method: customAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAlign(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAlign]
+    [wsgen] [should process method: presetAlign hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAlign(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAlign]
+    [wsgen] [should process method: getResult hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getResult(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.MsaWS<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetResult]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JABAService]
+    [wsgen] [ProcessedMethods Interface: compbio.data.msa.JManagement]
+    [wsgen] [should process method: cancelJob hasWebMethods: false ]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize]
+    [wsgen] [should process method: customAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAnalize(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize]
+    [wsgen] [should process method: presetAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAnalize(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize]
+    [wsgen] [should process method: getAnnotation hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getAnnotation(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+    [wsgen] compbio/data/msa/jaxws/Analize.java
+    [wsgen] compbio/data/msa/jaxws/AnalizeResponse.java
+    [wsgen] compbio/data/msa/jaxws/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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize]
+    [wsgen] [should process method: customAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAnalize(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize]
+    [wsgen] [should process method: presetAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAnalize(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize]
+    [wsgen] [should process method: getAnnotation hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getAnnotation(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+    [wsgen] compbio/data/msa/jaxws/Analize.java
+    [wsgen] compbio/data/msa/jaxws/AnalizeResponse.java
+    [wsgen] compbio/data/msa/jaxws/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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize]
+    [wsgen] [should process method: customAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAnalize(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize]
+    [wsgen] [should process method: presetAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAnalize(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize]
+    [wsgen] [should process method: getAnnotation hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getAnnotation(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+    [wsgen] compbio/data/msa/jaxws/Analize.java
+    [wsgen] compbio/data/msa/jaxws/AnalizeResponse.java
+    [wsgen] compbio/data/msa/jaxws/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<T>]
+    [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<compbio.data.sequence.FastaSequence>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.Analize]
+    [wsgen] [should process method: customAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: customAnalize(java.util.List<compbio.data.sequence.FastaSequence>,java.util.List<compbio.metadata.Option<T>>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.CustomAnalize]
+    [wsgen] [should process method: presetAnalize hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: presetAnalize(java.util.List<compbio.data.sequence.FastaSequence>,compbio.metadata.Preset<T>)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.PresetAnalize]
+    [wsgen] [should process method: getAnnotation hasWebMethods: false ]
+    [wsgen] [endpointReferencesInterface: true]
+    [wsgen] [declaring class has WebSevice: true]
+    [wsgen] [returning: true]
+    [wsgen] [WrapperGen - method: getAnnotation(java.lang.String)]
+    [wsgen] [method.getDeclaringType(): compbio.data.msa.SequenceAnnotation<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetAnnotation]
+    [wsgen] [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [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<T>]
+    [wsgen] [requestWrapper: compbio.data.msa.jaxws.GetLimits]
+    [wsgen] compbio/data/msa/jaxws/Analize.java
+    [wsgen] compbio/data/msa/jaxws/AnalizeResponse.java
+    [wsgen] compbio/data/msa/jaxws/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