Slight refactoring

git-svn-id: link to svn.lifesci.dundee.ac.uk/svn/barton/ptroshin/JABA2@4342 e3abac25-378b-4346-85de-24260fe3988d

diff --git a/testsrc/compbio/ws/client/TestAAConWS.java b/testsrc/compbio/ws/client/TestAAConWS.java
index 68b5987..19cd0b2 100644 (file)
--- a/testsrc/compbio/ws/client/TestAAConWS.java
+++ b/testsrc/compbio/ws/client/TestAAConWS.java
@@ -8,8 +8,11 @@ import java.io.File;
 import java.io.FileInputStream;\r
 import java.io.FileNotFoundException;\r
 import java.io.IOException;\r
+import java.net.ConnectException;\r
 import java.util.List;\r
 \r
+import javax.xml.ws.WebServiceException;\r
+\r
 import org.testng.annotations.BeforeTest;\r
 import org.testng.annotations.Test;\r
 \r
@@ -45,10 +48,17 @@ public class TestAAConWS {
                 * QName(namespace, "AAConWS"); Service serv = Service.create(url,\r
                 * qname); msaws = serv.getPort(new QName(namespace, "AAConWSPort"),\r
                 * Annotation.class);\r
-                */\r
-               JABAService client = Jws2Client.connect("http://localhost:8080/jabaws",\r
-                               Services.AAConWS);\r
-               msaws = (SequenceAnnotation<AACon>) client;\r
+                */try {\r
+                       JABAService client = Jws2Client.connect(\r
+                                       "http://localhost:8080/jabaws", Services.AAConWS);\r
+                       msaws = (SequenceAnnotation<AACon>) client;\r
+               } catch (ConnectException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (WebServiceException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               }\r
        }\r
 \r
        @Test(groups = {AllTestSuit.test_group_webservices})\r

diff --git a/testsrc/compbio/ws/client/WSTesterTester.java b/testsrc/compbio/ws/client/WSTesterTester.java
index 144c7b2..b8cf29d 100644 (file)
--- a/testsrc/compbio/ws/client/WSTesterTester.java
+++ b/testsrc/compbio/ws/client/WSTesterTester.java
@@ -1,8 +1,12 @@
 package compbio.ws.client;\r
 \r
 import static org.testng.Assert.assertTrue;\r
+import static org.testng.Assert.fail;\r
 \r
 import java.io.PrintWriter;\r
+import java.net.ConnectException;\r
+\r
+import javax.xml.ws.WebServiceException;\r
 \r
 import org.testng.annotations.Test;\r
 \r
@@ -12,15 +16,25 @@ public class WSTesterTester {
 \r
        public static final String SERVER = "http://localhost:8080/jabaws";\r
 \r
+       // public static final String SERVER =\r
+       // "http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba";\r
+\r
        @Test(groups = {AllTestSuit.test_group_webservices})\r
        public void testAllWindowsWS() {\r
                WSTester tester = new WSTester(SERVER,\r
                                new PrintWriter(System.out, true));\r
-\r
-               assertTrue(tester.checkService(Services.AAConWS));\r
-               assertTrue(tester.checkService(Services.JronnWS));\r
-               assertTrue(tester.checkService(Services.ClustalWS));\r
-               assertTrue(tester.checkService(Services.MuscleWS));\r
+               try {\r
+                       assertTrue(tester.checkService(Services.AAConWS));\r
+                       assertTrue(tester.checkService(Services.JronnWS));\r
+                       assertTrue(tester.checkService(Services.ClustalWS));\r
+                       assertTrue(tester.checkService(Services.MuscleWS));\r
+               } catch (ConnectException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (WebServiceException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               }\r
 \r
                // Will throw UnsupportedRuntimeException on windows\r
                // ws = Jws2Client.connect(SERVER, Services.MafftWS);\r
@@ -31,8 +45,16 @@ public class WSTesterTester {
        @Test(groups = {AllTestSuit.test_group_webservices})\r
        public void testAllWS() {\r
                WSTester tester = new WSTester(SERVER, new PrintWriter(System.out));\r
-               for (Services service : Services.values()) {\r
-                       assertTrue(tester.checkService(service));\r
+               try {\r
+                       for (Services service : Services.values()) {\r
+                               assertTrue(tester.checkService(service));\r
+                       }\r
+               } catch (ConnectException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
+               } catch (WebServiceException e) {\r
+                       e.printStackTrace();\r
+                       fail(e.getMessage());\r
                }\r
        }\r
 \r

diff --git a/webservices/compbio/data/msa/JABAService.java b/webservices/compbio/data/msa/JABAService.java
index 69d53f7..5f77d77 100644 (file)
--- a/webservices/compbio/data/msa/JABAService.java
+++ b/webservices/compbio/data/msa/JABAService.java
@@ -8,4 +8,9 @@ package compbio.data.msa;
  */\r
 public interface JABAService {\r
 \r
+       // JABAWS version 1.0 service name\r
+       static final String SERVICE_NAMESPACE = "http://msa.data.compbio/01/01/2010/";\r
+       // JABAWS version 2.0 service name\r
+       static final String V2_SERVICE_NAMESPACE = "http://msa.data.compbio/01/12/2010/";\r
+\r
 }\r

diff --git a/webservices/compbio/data/msa/RegistryWS.java b/webservices/compbio/data/msa/RegistryWS.java
index 9f55ff9..123546d 100644 (file)
--- a/webservices/compbio/data/msa/RegistryWS.java
+++ b/webservices/compbio/data/msa/RegistryWS.java
@@ -13,7 +13,7 @@ import compbio.ws.client.Services;
  * @author pvtroshin\r
  * @version 1.0 June 2011\r
  */\r
-@WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/")\r
+@WebService(targetNamespace = JABAService.V2_SERVICE_NAMESPACE)\r
 public interface RegistryWS extends JABAService {\r
 \r
        /**\r

diff --git a/webservices/compbio/data/msa/SequenceAnnotation.java b/webservices/compbio/data/msa/SequenceAnnotation.java
index c52c030..2d9d729 100644 (file)
--- a/webservices/compbio/data/msa/SequenceAnnotation.java
+++ b/webservices/compbio/data/msa/SequenceAnnotation.java
@@ -29,7 +29,7 @@ import compbio.metadata.WrongParameterException;
  * \r
  * @version 1.0 November 2010\r
  */\r
-@WebService(targetNamespace = "http://msa.data.compbio/01/12/2010/")\r
+@WebService(targetNamespace = JABAService.V2_SERVICE_NAMESPACE)\r
 public interface SequenceAnnotation<T>\r
                extends\r
                        JABAService,\r

diff --git a/webservices/compbio/data/msa/jaxws/GetConservation.java b/webservices/compbio/data/msa/jaxws/GetConservation.java
deleted file mode 100644 (file)
index cc3ba51..0000000
--- a/webservices/compbio/data/msa/jaxws/GetConservation.java
+++ /dev/null
@@ -1,36 +0,0 @@
-\r
-package compbio.data.msa.jaxws;\r
-\r
-import javax.xml.bind.annotation.XmlAccessType;\r
-import javax.xml.bind.annotation.XmlAccessorType;\r
-import javax.xml.bind.annotation.XmlElement;\r
-import javax.xml.bind.annotation.XmlRootElement;\r
-import javax.xml.bind.annotation.XmlType;\r
-\r
-@XmlRootElement(name = "getConservation", namespace = "http://msa.data.compbio/01/12/2010/")\r
-@XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getConservation", namespace = "http://msa.data.compbio/01/12/2010/")\r
-public class GetConservation {\r
-\r
-    @XmlElement(name = "jobId", namespace = "")\r
-    private String jobId;\r
-\r
-    /**\r
-     * \r
-     * @return\r
-     *     returns String\r
-     */\r
-    public String getJobId() {\r
-        return this.jobId;\r
-    }\r
-\r
-    /**\r
-     * \r
-     * @param jobId\r
-     *     the value for the jobId property\r
-     */\r
-    public void setJobId(String jobId) {\r
-        this.jobId = jobId;\r
-    }\r
-\r
-}\r

diff --git a/webservices/compbio/data/msa/jaxws/GetConservationResponse.java b/webservices/compbio/data/msa/jaxws/GetConservationResponse.java
deleted file mode 100644 (file)
index fe7fd58..0000000
--- a/webservices/compbio/data/msa/jaxws/GetConservationResponse.java
+++ /dev/null
@@ -1,37 +0,0 @@
-\r
-package compbio.data.msa.jaxws;\r
-\r
-import java.util.HashSet;\r
-import javax.xml.bind.annotation.XmlAccessType;\r
-import javax.xml.bind.annotation.XmlAccessorType;\r
-import javax.xml.bind.annotation.XmlElement;\r
-import javax.xml.bind.annotation.XmlRootElement;\r
-import javax.xml.bind.annotation.XmlType;\r
-\r
-@XmlRootElement(name = "getConservationResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
-@XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getConservationResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
-public class GetConservationResponse {\r
-\r
-    @XmlElement(name = "return", namespace = "")\r
-    private HashSet<compbio.data.sequence.Score> _return;\r
-\r
-    /**\r
-     * \r
-     * @return\r
-     *     returns HashSet<Score>\r
-     */\r
-    public HashSet<compbio.data.sequence.Score> getReturn() {\r
-        return this._return;\r
-    }\r
-\r
-    /**\r
-     * \r
-     * @param _return\r
-     *     the value for the _return property\r
-     */\r
-    public void setReturn(HashSet<compbio.data.sequence.Score> _return) {\r
-        this._return = _return;\r
-    }\r
-\r
-}\r

diff --git a/webservices/compbio/ws/client/Jws2Client.java b/webservices/compbio/ws/client/Jws2Client.java
index c18f100..e775727 100644 (file)
--- a/webservices/compbio/ws/client/Jws2Client.java
+++ b/webservices/compbio/ws/client/Jws2Client.java
@@ -28,6 +28,7 @@ import java.io.FileInputStream;
 import java.io.IOException;\r
 import java.io.PrintWriter;\r
 import java.io.Writer;\r
+import java.net.ConnectException;\r
 import java.net.MalformedURLException;\r
 import java.net.URL;\r
 import java.util.Arrays;\r
@@ -71,12 +72,6 @@ public class Jws2Client {
        private static final Logger log = Logger.getLogger(Jws2Client.class\r
                        .getCanonicalName());\r
 \r
-       // JABAWS version 1.0 service name\r
-       static final String QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/01/2010/";\r
-\r
-       // JABAWS version 2.0 service name\r
-       static final String V2_QUALIFIED_SERVICE_NAME = "http://msa.data.compbio/01/12/2010/";\r
-\r
        /**\r
         * Attempt to construct the URL object from the string\r
         * \r
@@ -199,6 +194,7 @@ public class Jws2Client {
                log.fine("Disconnected successfully!");\r
        }\r
 \r
+       // TODO make public?\r
        private void testService(String hostname, Services service)\r
                        throws IOException {\r
                RegistryWS registry = connectToRegistry(hostname);\r
@@ -210,6 +206,7 @@ public class Jws2Client {
                }\r
        }\r
 \r
+       // TODO make public?\r
        private void listServices(String hostname) throws IOException {\r
                RegistryWS registry = connectToRegistry(hostname);\r
                if (registry != null) {\r
@@ -320,17 +317,22 @@ public class Jws2Client {
                return analize(fastalist, wsproxy, preset, customOptions);\r
        }\r
        /**\r
-        * Connects to a web service by the host and the service name\r
+        * Connects to a web service by the host and the service name web service\r
+        * type\r
         * \r
-        * @param T\r
-        *            web service type\r
         * @param host\r
+        *            the fully qualified name of JABAWS server including JABAWS\r
+        *            context name e.g\r
+        *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
         * @param service\r
-        * @return MsaWS<T>\r
+        *            the name of the JABAWS service to connect to\r
+        * @return JABAService<T>\r
         * @throws WebServiceException\r
+        * @throws ConnectException\r
+        *             if fails to connect to the service on the host\r
         */\r
        public static JABAService connect(String host, Services service)\r
-                       throws WebServiceException {\r
+                       throws WebServiceException, ConnectException {\r
                URL url = null;\r
                log.log(Level.FINE, "Attempting to connect...");\r
                try {\r
@@ -341,17 +343,17 @@ public class Jws2Client {
                }\r
                Service serv = null;\r
                try {\r
-                       serv = service.getService(url, QUALIFIED_SERVICE_NAME);\r
+                       serv = service.getService(url, JABAService.SERVICE_NAMESPACE);\r
                } catch (WebServiceException wse) {\r
                        System.out.println("Connecting to JABAWS version 2 service");\r
                        if (isV2service(wse)) {\r
-                               serv = service.getService(url, V2_QUALIFIED_SERVICE_NAME);\r
+                               serv = service\r
+                                               .getService(url, JABAService.V2_SERVICE_NAMESPACE);\r
                        }\r
                }\r
                if (serv == null) {\r
-                       System.err.println("Could not connect to " + url\r
+                       throw new ConnectException("Could not connect to " + url\r
                                        + " the server is down?");\r
-                       // FIXME\r
                }\r
                JABAService serviceIF = service.getInterface(serv);\r
                log.log(Level.INFO, "Connected successfully!");\r
@@ -363,13 +365,25 @@ public class Jws2Client {
                String message = wse.getMessage();\r
                int idx = message.indexOf("not a valid service");\r
                if (idx > 0) {\r
-                       if (message.substring(idx).contains(V2_QUALIFIED_SERVICE_NAME)) {\r
+                       if (message.substring(idx).contains(\r
+                                       JABAService.V2_SERVICE_NAMESPACE)) {\r
                                return true;\r
                        }\r
                }\r
                return false;\r
        }\r
 \r
+       /**\r
+        * Get a connection of JABAWS registry\r
+        * \r
+        * @param host\r
+        *            the fully qualified name of JABAWS server including JABAWS\r
+        *            context name e.g\r
+        *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
+        * @return compbio.data.msa.RegistryWS - instance of a RegistryWS web\r
+        *         service\r
+        * @throws WebServiceException\r
+        */\r
        public static compbio.data.msa.RegistryWS connectToRegistry(String host)\r
                        throws WebServiceException {\r
                URL url = null;\r
@@ -382,7 +396,7 @@ public class Jws2Client {
                        e.printStackTrace();\r
                        // ignore as the host name is already verified\r
                }\r
-               QName qname = new QName(V2_QUALIFIED_SERVICE_NAME, service);\r
+               QName qname = new QName(JABAService.V2_SERVICE_NAMESPACE, service);\r
                Service serv = Service.create(url, qname);\r
 \r
                if (serv == null) {\r

diff --git a/webservices/compbio/ws/client/WSTester.java b/webservices/compbio/ws/client/WSTester.java
index 4f721fe..def8efe 100644 (file)
--- a/webservices/compbio/ws/client/WSTester.java
+++ b/webservices/compbio/ws/client/WSTester.java
@@ -26,9 +26,12 @@ import java.io.ByteArrayInputStream;
 import java.io.Closeable;\r
 import java.io.IOException;\r
 import java.io.PrintWriter;\r
+import java.net.ConnectException;\r
 import java.util.Arrays;\r
 import java.util.List;\r
 \r
+import javax.xml.ws.WebServiceException;\r
+\r
 import org.apache.log4j.Logger;\r
 \r
 import compbio.data.msa.JABAService;\r
@@ -116,6 +119,15 @@ public class WSTester {
        private final PrintWriter writer;\r
        private final String hostname;\r
 \r
+       /**\r
+        * Construct an instance of JABAWS tester\r
+        * \r
+        * @param hostname\r
+        *            - fully qualified host and context name of JABAWS e.g.\r
+        *            http://nanna.cluster.lifesci.dundee.ac.uk:8080/jaba\r
+        * @param writer\r
+        *            a PrintWriter instance to writer test log to.\r
+        */\r
        public WSTester(String hostname, PrintWriter writer) {\r
                if (Util.isEmpty(hostname)) {\r
                        throw new NullPointerException("Hostname must be provided!");\r
@@ -403,7 +415,17 @@ public class WSTester {
 \r
        }\r
 \r
-       public boolean checkService(Services service) {\r
+       /**\r
+        * Test JABA web service\r
+        * \r
+        * @param service\r
+        *            the service to test\r
+        * @return true if the service works as expected, false otherwise\r
+        * @throws WebServiceException\r
+        * @throws ConnectException\r
+        */\r
+       public boolean checkService(Services service) throws ConnectException,\r
+                       WebServiceException {\r
                JABAService ws = Jws2Client.connect(hostname, service);\r
                if (ws == null) {\r
                        writer.println("Cannot estabilish the connection to host "\r

diff --git a/webservices/compbio/ws/server/AAConWS.java b/webservices/compbio/ws/server/AAConWS.java
index d9fd54f..1318beb 100644 (file)
--- a/webservices/compbio/ws/server/AAConWS.java
+++ b/webservices/compbio/ws/server/AAConWS.java
@@ -8,6 +8,7 @@ import javax.jws.WebService;
 \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
@@ -18,7 +19,7 @@ import compbio.metadata.LimitExceededException;
 import compbio.metadata.UnsupportedRuntimeException;\r
 import compbio.runner.conservation.AACon;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "AAConWS")\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "AAConWS")\r
 public class AAConWS extends SequenceAnnotationService<AACon>\r
                implements\r
                        SequenceAnnotation<AACon> {\r

diff --git a/webservices/compbio/ws/server/ClustalWS.java b/webservices/compbio/ws/server/ClustalWS.java
index 61944de..75683c3 100644 (file)
--- a/webservices/compbio/ws/server/ClustalWS.java
+++ b/webservices/compbio/ws/server/ClustalWS.java
@@ -25,6 +25,7 @@ import javax.jws.WebService;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.msa.JABAService;\r
 import compbio.data.msa.MsaWS;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
@@ -46,7 +47,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;\r
 import compbio.runner.msa.ClustalW;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ClustalWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ClustalWS")\r
 public class ClustalWS implements MsaWS<ClustalW> {\r
 \r
        private static Logger log = Logger.getLogger(ClustalWS.class);\r

diff --git a/webservices/compbio/ws/server/DisemblWS.java b/webservices/compbio/ws/server/DisemblWS.java
index f609143..5410879 100644 (file)
--- a/webservices/compbio/ws/server/DisemblWS.java
+++ b/webservices/compbio/ws/server/DisemblWS.java
@@ -6,6 +6,7 @@ import javax.jws.WebService;
 \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.metadata.JobSubmissionException;\r
@@ -16,7 +17,7 @@ import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;\r
 import compbio.runner.disorder.Disembl;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "DisemblWS")\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "DisemblWS")\r
 public class DisemblWS extends SequenceAnnotationService<Disembl>\r
                implements\r
                        SequenceAnnotation<Disembl> {\r

diff --git a/webservices/compbio/ws/server/GlobPlotWS.java b/webservices/compbio/ws/server/GlobPlotWS.java
index 5ed6331..bfbecb7 100644 (file)
--- a/webservices/compbio/ws/server/GlobPlotWS.java
+++ b/webservices/compbio/ws/server/GlobPlotWS.java
@@ -6,6 +6,7 @@ import javax.jws.WebService;
 \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.metadata.JobSubmissionException;\r
@@ -16,7 +17,7 @@ import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;\r
 import compbio.runner.disorder.GlobPlot;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "GlobPlotWS")\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "GlobPlotWS")\r
 public class GlobPlotWS extends SequenceAnnotationService<GlobPlot>\r
                implements\r
                        SequenceAnnotation<GlobPlot> {\r

diff --git a/webservices/compbio/ws/server/IUPredWS.java b/webservices/compbio/ws/server/IUPredWS.java
index bcc5faa..58ab01e 100644 (file)
--- a/webservices/compbio/ws/server/IUPredWS.java
+++ b/webservices/compbio/ws/server/IUPredWS.java
@@ -6,6 +6,7 @@ import javax.jws.WebService;
 \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.metadata.JobSubmissionException;\r
@@ -15,7 +16,7 @@ import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;\r
 import compbio.runner.disorder.IUPred;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "IUPredWS")\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "IUPredWS")\r
 public class IUPredWS extends SequenceAnnotationService<IUPred>\r
                implements\r
                        SequenceAnnotation<IUPred> {\r

diff --git a/webservices/compbio/ws/server/JronnWS.java b/webservices/compbio/ws/server/JronnWS.java
index c3fe1f4..3dd493e 100644 (file)
--- a/webservices/compbio/ws/server/JronnWS.java
+++ b/webservices/compbio/ws/server/JronnWS.java
@@ -6,13 +6,14 @@ import javax.jws.WebService;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.msa.JABAService;\r
 import compbio.data.msa.SequenceAnnotation;\r
 import compbio.engine.Configurator;\r
 import compbio.metadata.ChunkHolder;\r
 import compbio.runner.conservation.AACon;\r
 import compbio.runner.disorder.Jronn;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "JronnWS")\r
+@WebService(endpointInterface = "compbio.data.msa.SequenceAnnotation", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "JronnWS")\r
 public class JronnWS extends SequenceAnnotationService<Jronn>\r
                implements\r
                        SequenceAnnotation<Jronn> {\r

diff --git a/webservices/compbio/ws/server/MafftWS.java b/webservices/compbio/ws/server/MafftWS.java
index 12805af..6a0d39e 100644 (file)
--- a/webservices/compbio/ws/server/MafftWS.java
+++ b/webservices/compbio/ws/server/MafftWS.java
@@ -25,6 +25,7 @@ import javax.jws.WebService;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.msa.JABAService;\r
 import compbio.data.msa.MsaWS;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
@@ -46,7 +47,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;\r
 import compbio.runner.msa.Mafft;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MafftWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MafftWS")\r
 public class MafftWS implements MsaWS<Mafft> {\r
 \r
        private static Logger log = Logger.getLogger(MafftWS.class);\r

diff --git a/webservices/compbio/ws/server/MuscleWS.java b/webservices/compbio/ws/server/MuscleWS.java
index 0e5d3ef..fa9bdbc 100644 (file)
--- a/webservices/compbio/ws/server/MuscleWS.java
+++ b/webservices/compbio/ws/server/MuscleWS.java
@@ -25,6 +25,7 @@ import javax.jws.WebService;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.msa.JABAService;\r
 import compbio.data.msa.MsaWS;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
@@ -46,7 +47,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;\r
 import compbio.runner.msa.Muscle;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "MuscleWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "MuscleWS")\r
 public class MuscleWS implements MsaWS<Muscle> {\r
 \r
        private static Logger log = Logger.getLogger(MuscleWS.class);\r

diff --git a/webservices/compbio/ws/server/ProbconsWS.java b/webservices/compbio/ws/server/ProbconsWS.java
index 4ab7a34..5b93355 100644 (file)
--- a/webservices/compbio/ws/server/ProbconsWS.java
+++ b/webservices/compbio/ws/server/ProbconsWS.java
@@ -25,6 +25,7 @@ import javax.jws.WebService;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.msa.JABAService;\r
 import compbio.data.msa.MsaWS;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
@@ -46,7 +47,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;\r
 import compbio.runner.msa.Probcons;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "ProbconsWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "ProbconsWS")\r
 public class ProbconsWS implements MsaWS<Probcons> {\r
 \r
        private static Logger log = Logger.getLogger(ProbconsWS.class);\r

diff --git a/webservices/compbio/ws/server/RegistryWS.java b/webservices/compbio/ws/server/RegistryWS.java
index 0ff4294..ae56e5b 100644 (file)
--- a/webservices/compbio/ws/server/RegistryWS.java
+++ b/webservices/compbio/ws/server/RegistryWS.java
@@ -26,7 +26,7 @@ import compbio.ws.client.WSTester;
  * @author pvtroshin\r
  * \r
  */\r
-@WebService(endpointInterface = "compbio.data.msa.RegistryWS", targetNamespace = "http://msa.data.compbio/01/12/2010/", serviceName = "RegistryWS")\r
+@WebService(endpointInterface = "compbio.data.msa.RegistryWS", targetNamespace = JABAService.V2_SERVICE_NAMESPACE, serviceName = "RegistryWS")\r
 public class RegistryWS implements compbio.data.msa.RegistryWS, JABAService {\r
 \r
        // Ask for resource injection\r
@@ -123,8 +123,16 @@ public class RegistryWS implements compbio.data.msa.RegistryWS, JABAService {
                // the server\r
                synchronized (operating) {\r
                        for (Services service : Services.values()) {\r
-                               if (tester.checkService(service)) {\r
-                                       operating.put(service, new Date());\r
+                               try {\r
+                                       if (tester.checkService(service)) {\r
+                                               operating.put(service, new Date());\r
+                                       }\r
+                               } catch (Exception e) {\r
+                                       log.info(e, e.getCause());\r
+                                       writer.println("Fails to connect to a web service: "\r
+                                                       + service + " With " + e.getLocalizedMessage()\r
+                                                       + "\nDetails: ");\r
+                                       e.printStackTrace(writer);\r
                                }\r
                        }\r
                }\r
@@ -156,12 +164,16 @@ public class RegistryWS implements compbio.data.msa.RegistryWS, JABAService {
                                        operating.put(service, new Date());\r
                                }\r
                        }\r
+               } catch (Exception e) {\r
+                       log.info(e, e.getCause());\r
+                       writer.println("Fails to connect to a web service: " + service\r
+                                       + " With " + e.getLocalizedMessage() + "\nDetails: ");\r
+                       e.printStackTrace(writer);\r
                } finally {\r
                        writer.close();\r
                }\r
                return testlog.toString();\r
        }\r
-\r
        @Override\r
        public boolean isOperating(Services service) {\r
                init();\r

diff --git a/webservices/compbio/ws/server/TcoffeeWS.java b/webservices/compbio/ws/server/TcoffeeWS.java
index 59b4c19..3083b11 100644 (file)
--- a/webservices/compbio/ws/server/TcoffeeWS.java
+++ b/webservices/compbio/ws/server/TcoffeeWS.java
@@ -25,6 +25,7 @@ import javax.jws.WebService;
 \r
 import org.apache.log4j.Logger;\r
 \r
+import compbio.data.msa.JABAService;\r
 import compbio.data.msa.MsaWS;\r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
@@ -47,7 +48,7 @@ import compbio.metadata.WrongParameterException;
 import compbio.runner.Util;\r
 import compbio.runner.msa.Tcoffee;\r
 \r
-@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = "http://msa.data.compbio/01/01/2010/", serviceName = "TcoffeeWS")\r
+@WebService(endpointInterface = "compbio.data.msa.MsaWS", targetNamespace = JABAService.SERVICE_NAMESPACE, serviceName = "TcoffeeWS")\r
 public class TcoffeeWS implements MsaWS<Tcoffee> {\r
 \r
        private static Logger log = Logger.getLogger(TcoffeeWS.class);\r

diff --git a/webservices/compbio/ws/server/resource/AAConWS.wsdl b/webservices/compbio/ws/server/resource/AAConWS.wsdl
index 8ff9829..772fca7 100644 (file)
--- a/webservices/compbio/ws/server/resource/AAConWS.wsdl
+++ b/webservices/compbio/ws/server/resource/AAConWS.wsdl
@@ -45,18 +45,18 @@
   <message name="ResultNotAvailableException">
     <part name="fault" element="tns:ResultNotAvailableException"/>
   </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="pullExecStatistics">
+    <part name="parameters" element="tns:pullExecStatistics"/>
+  </message>
+  <message name="pullExecStatisticsResponse">
+    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+  </message>
   <message name="getJobStatus">
     <part name="parameters" element="tns:getJobStatus"/>
   </message>
@@ -69,11 +69,11 @@
   <message name="getLimitResponse">
     <part name="parameters" element="tns:getLimitResponse"/>
   </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
+  <message name="getLimits">
+    <part name="parameters" element="tns:getLimits"/>
   </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  <message name="getLimitsResponse">
+    <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
   <message name="getPresets">
     <part name="parameters" element="tns:getPresets"/>
@@ -81,11 +81,11 @@
   <message name="getPresetsResponse">
     <part name="parameters" element="tns:getPresetsResponse"/>
   </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
   </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
   </message>
   <portType name="SequenceAnnotation">
     <operation name="analize">
@@ -116,14 +116,14 @@
       <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="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="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="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"/>
@@ -132,17 +132,17 @@
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitRequest" message="tns:getLimit"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitResponse" message="tns:getLimitResponse"/>
     </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    <operation name="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>
     <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 name="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
     </operation>
   </portType>
   <binding name="AAConWSPortBinding" type="tns:SequenceAnnotation">
@@ -219,7 +219,7 @@
         <soap:fault name="ResultNotAvailableException" use="literal"/>
       </fault>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="cancelJob">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="cancelJob">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd b/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
index 99b9b4d..6f34ece 100644 (file)
--- a/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/AAConWS_schema1.xsd
@@ -255,6 +255,23 @@
     </xs:sequence>
   </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="getLimits">
     <xs:sequence/>
   </xs:complexType>
@@ -281,23 +298,6 @@
     <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"/>

diff --git a/webservices/compbio/ws/server/resource/ClustalWS.wsdl b/webservices/compbio/ws/server/resource/ClustalWS.wsdl
index d317bac..7ea9514 100644 (file)
--- a/webservices/compbio/ws/server/resource/ClustalWS.wsdl
+++ b/webservices/compbio/ws/server/resource/ClustalWS.wsdl
@@ -45,18 +45,18 @@
   <message name="alignResponse">
     <part name="parameters" element="tns:alignResponse"/>
   </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="pullExecStatistics">
+    <part name="parameters" element="tns:pullExecStatistics"/>
+  </message>
+  <message name="pullExecStatisticsResponse">
+    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+  </message>
   <message name="getJobStatus">
     <part name="parameters" element="tns:getJobStatus"/>
   </message>
@@ -69,11 +69,11 @@
   <message name="getLimitResponse">
     <part name="parameters" element="tns:getLimitResponse"/>
   </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
+  <message name="getLimits">
+    <part name="parameters" element="tns:getLimits"/>
   </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  <message name="getLimitsResponse">
+    <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
   <message name="getPresets">
     <part name="parameters" element="tns:getPresets"/>
@@ -81,11 +81,11 @@
   <message name="getPresetsResponse">
     <part name="parameters" element="tns:getPresetsResponse"/>
   </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
   </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
   </message>
   <portType name="MsaWS">
     <operation name="getResult">
@@ -116,14 +116,14 @@
       <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
       <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
     </operation>
-    <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
-    </operation>
     <operation name="cancelJob">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
     </operation>
+    <operation name="pullExecStatistics">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+    </operation>
     <operation name="getJobStatus">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
@@ -132,17 +132,17 @@
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
     </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    <operation name="getLimits">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
     <operation name="getPresets">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
     </operation>
-    <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+    <operation name="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
     </operation>
   </portType>
   <binding name="ClustalWSPortBinding" type="tns:MsaWS">
@@ -219,7 +219,7 @@
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="cancelJob">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="cancelJob">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
index 05f2a89..c432550 100644 (file)
--- a/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/ClustalWS_schema1.xsd
@@ -161,32 +161,6 @@
     </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>
@@ -218,6 +192,32 @@
     </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="getLimit">
     <xs:sequence>
       <xs:element name="presetName" type="xs:string" minOccurs="0"/>

diff --git a/webservices/compbio/ws/server/resource/DisemblWS.wsdl b/webservices/compbio/ws/server/resource/DisemblWS.wsdl
index 324f199..ad062c4 100644 (file)
--- a/webservices/compbio/ws/server/resource/DisemblWS.wsdl
+++ b/webservices/compbio/ws/server/resource/DisemblWS.wsdl
@@ -24,18 +24,18 @@
   <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="analize">
     <part name="parameters" element="tns:analize"/>
   </message>
   <message name="analizeResponse">
     <part name="parameters" element="tns:analizeResponse"/>
   </message>
+  <message name="presetAnalize">
+    <part name="parameters" element="tns:presetAnalize"/>
+  </message>
+  <message name="presetAnalizeResponse">
+    <part name="parameters" element="tns:presetAnalizeResponse"/>
+  </message>
   <message name="getAnnotation">
     <part name="parameters" element="tns:getAnnotation"/>
   </message>
@@ -51,29 +51,17 @@
   <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="pullExecStatistics">
     <part name="parameters" element="tns:pullExecStatistics"/>
   </message>
   <message name="pullExecStatisticsResponse">
     <part name="parameters" element="tns:pullExecStatisticsResponse"/>
   </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 name="getJobStatus">
+    <part name="parameters" element="tns:getJobStatus"/>
   </message>
-  <message name="getPresetsResponse">
-    <part name="parameters" element="tns:getPresetsResponse"/>
+  <message name="getJobStatusResponse">
+    <part name="parameters" element="tns:getJobStatusResponse"/>
   </message>
   <message name="getLimit">
     <part name="parameters" element="tns:getLimit"/>
@@ -87,6 +75,18 @@
   <message name="getLimitsResponse">
     <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
+  <message name="getPresets">
+    <part name="parameters" element="tns:getPresets"/>
+  </message>
+  <message name="getPresetsResponse">
+    <part name="parameters" element="tns:getPresetsResponse"/>
+  </message>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
+  </message>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  </message>
   <portType name="SequenceAnnotation">
     <operation name="customAnalize">
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeRequest" message="tns:customAnalize"/>
@@ -96,6 +96,13 @@
       <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="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="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"/>
@@ -104,13 +111,6 @@
       <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="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="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"/>
@@ -120,21 +120,13 @@
       <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="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="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 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"/>
@@ -144,6 +136,14 @@
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
+    <operation name="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="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    </operation>
   </portType>
   <binding name="DisemblWSPortBinding" type="tns:SequenceAnnotation">
     <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
@@ -168,7 +168,7 @@
         <soap:fault name="WrongParameterException" use="literal"/>
       </fault>
     </operation>
-    <operation name="presetAnalize">
+    <operation name="analize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -185,11 +185,8 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
-      <fault name="WrongParameterException">
-        <soap:fault name="WrongParameterException" use="literal"/>
-      </fault>
     </operation>
-    <operation name="analize">
+    <operation name="presetAnalize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -206,6 +203,9 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
+      <fault name="WrongParameterException">
+        <soap:fault name="WrongParameterException" use="literal"/>
+      </fault>
     </operation>
     <operation name="getAnnotation">
       <soap:operation soapAction=""/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getJobStatus">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -237,7 +237,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="getJobStatus">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -246,7 +246,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimit">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getPresets">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -264,7 +264,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimit">
+    <operation name="getPresets">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd b/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
index 321cfdd..a03987f 100644 (file)
--- a/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/DisemblWS_schema1.xsd
@@ -262,6 +262,23 @@
     </xs:sequence>
   </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="getLimits">
     <xs:sequence/>
   </xs:complexType>
@@ -300,23 +317,6 @@
     </xs:sequence>
   </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="cancelJob">
     <xs:sequence>
       <xs:element name="jobId" type="xs:string" minOccurs="0"/>

diff --git a/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl b/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
index 9577bb8..67f9169 100644 (file)
--- a/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
+++ b/webservices/compbio/ws/server/resource/GlobPlotWS.wsdl
@@ -24,18 +24,18 @@
   <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="analize">
     <part name="parameters" element="tns:analize"/>
   </message>
   <message name="analizeResponse">
     <part name="parameters" element="tns:analizeResponse"/>
   </message>
+  <message name="presetAnalize">
+    <part name="parameters" element="tns:presetAnalize"/>
+  </message>
+  <message name="presetAnalizeResponse">
+    <part name="parameters" element="tns:presetAnalizeResponse"/>
+  </message>
   <message name="getAnnotation">
     <part name="parameters" element="tns:getAnnotation"/>
   </message>
@@ -51,29 +51,17 @@
   <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="pullExecStatistics">
     <part name="parameters" element="tns:pullExecStatistics"/>
   </message>
   <message name="pullExecStatisticsResponse">
     <part name="parameters" element="tns:pullExecStatisticsResponse"/>
   </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 name="getJobStatus">
+    <part name="parameters" element="tns:getJobStatus"/>
   </message>
-  <message name="getPresetsResponse">
-    <part name="parameters" element="tns:getPresetsResponse"/>
+  <message name="getJobStatusResponse">
+    <part name="parameters" element="tns:getJobStatusResponse"/>
   </message>
   <message name="getLimit">
     <part name="parameters" element="tns:getLimit"/>
@@ -87,6 +75,18 @@
   <message name="getLimitsResponse">
     <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
+  <message name="getPresets">
+    <part name="parameters" element="tns:getPresets"/>
+  </message>
+  <message name="getPresetsResponse">
+    <part name="parameters" element="tns:getPresetsResponse"/>
+  </message>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
+  </message>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  </message>
   <portType name="SequenceAnnotation">
     <operation name="customAnalize">
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeRequest" message="tns:customAnalize"/>
@@ -96,6 +96,13 @@
       <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="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="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"/>
@@ -104,13 +111,6 @@
       <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="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="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"/>
@@ -120,21 +120,13 @@
       <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="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="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 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"/>
@@ -144,6 +136,14 @@
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
+    <operation name="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="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    </operation>
   </portType>
   <binding name="GlobPlotWSPortBinding" type="tns:SequenceAnnotation">
     <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
@@ -168,7 +168,7 @@
         <soap:fault name="WrongParameterException" use="literal"/>
       </fault>
     </operation>
-    <operation name="presetAnalize">
+    <operation name="analize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -185,11 +185,8 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
-      <fault name="WrongParameterException">
-        <soap:fault name="WrongParameterException" use="literal"/>
-      </fault>
     </operation>
-    <operation name="analize">
+    <operation name="presetAnalize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -206,6 +203,9 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
+      <fault name="WrongParameterException">
+        <soap:fault name="WrongParameterException" use="literal"/>
+      </fault>
     </operation>
     <operation name="getAnnotation">
       <soap:operation soapAction=""/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getJobStatus">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -237,7 +237,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="getJobStatus">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -246,7 +246,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimit">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getPresets">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -264,7 +264,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimit">
+    <operation name="getPresets">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd b/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
index 72ac6ff..d44ec86 100644 (file)
--- a/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/GlobPlotWS_schema1.xsd
@@ -275,6 +275,23 @@
     </xs:sequence>
   </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="getLimits">
     <xs:sequence/>
   </xs:complexType>
@@ -313,23 +330,6 @@
     </xs:sequence>
   </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="cancelJob">
     <xs:sequence>
       <xs:element name="jobId" type="xs:string" minOccurs="0"/>

diff --git a/webservices/compbio/ws/server/resource/IUPredWS.wsdl b/webservices/compbio/ws/server/resource/IUPredWS.wsdl
index f10eb02..4627adb 100644 (file)
--- a/webservices/compbio/ws/server/resource/IUPredWS.wsdl
+++ b/webservices/compbio/ws/server/resource/IUPredWS.wsdl
@@ -24,18 +24,18 @@
   <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="analize">
     <part name="parameters" element="tns:analize"/>
   </message>
   <message name="analizeResponse">
     <part name="parameters" element="tns:analizeResponse"/>
   </message>
+  <message name="presetAnalize">
+    <part name="parameters" element="tns:presetAnalize"/>
+  </message>
+  <message name="presetAnalizeResponse">
+    <part name="parameters" element="tns:presetAnalizeResponse"/>
+  </message>
   <message name="getAnnotation">
     <part name="parameters" element="tns:getAnnotation"/>
   </message>
@@ -51,29 +51,17 @@
   <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="pullExecStatistics">
     <part name="parameters" element="tns:pullExecStatistics"/>
   </message>
   <message name="pullExecStatisticsResponse">
     <part name="parameters" element="tns:pullExecStatisticsResponse"/>
   </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 name="getJobStatus">
+    <part name="parameters" element="tns:getJobStatus"/>
   </message>
-  <message name="getPresetsResponse">
-    <part name="parameters" element="tns:getPresetsResponse"/>
+  <message name="getJobStatusResponse">
+    <part name="parameters" element="tns:getJobStatusResponse"/>
   </message>
   <message name="getLimit">
     <part name="parameters" element="tns:getLimit"/>
@@ -87,6 +75,18 @@
   <message name="getLimitsResponse">
     <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
+  <message name="getPresets">
+    <part name="parameters" element="tns:getPresets"/>
+  </message>
+  <message name="getPresetsResponse">
+    <part name="parameters" element="tns:getPresetsResponse"/>
+  </message>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
+  </message>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  </message>
   <portType name="SequenceAnnotation">
     <operation name="customAnalize">
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeRequest" message="tns:customAnalize"/>
@@ -96,6 +96,13 @@
       <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="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="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"/>
@@ -104,13 +111,6 @@
       <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="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="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"/>
@@ -120,21 +120,13 @@
       <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="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="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 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"/>
@@ -144,6 +136,14 @@
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
+    <operation name="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="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    </operation>
   </portType>
   <binding name="IUPredWSPortBinding" type="tns:SequenceAnnotation">
     <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
@@ -168,7 +168,7 @@
         <soap:fault name="WrongParameterException" use="literal"/>
       </fault>
     </operation>
-    <operation name="presetAnalize">
+    <operation name="analize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -185,11 +185,8 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
-      <fault name="WrongParameterException">
-        <soap:fault name="WrongParameterException" use="literal"/>
-      </fault>
     </operation>
-    <operation name="analize">
+    <operation name="presetAnalize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -206,6 +203,9 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
+      <fault name="WrongParameterException">
+        <soap:fault name="WrongParameterException" use="literal"/>
+      </fault>
     </operation>
     <operation name="getAnnotation">
       <soap:operation soapAction=""/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getJobStatus">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -237,7 +237,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="getJobStatus">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -246,7 +246,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimit">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getPresets">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -264,7 +264,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimit">
+    <operation name="getPresets">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd b/webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
index 9c46d87..73e9d98 100644 (file)
--- a/webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/IUPredWS_schema1.xsd
@@ -248,6 +248,37 @@
     </xs:sequence>
   </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="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="getLimits">
     <xs:sequence/>
   </xs:complexType>
@@ -286,37 +317,6 @@
     </xs:sequence>
   </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="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="cancelJob">
     <xs:sequence>
       <xs:element name="jobId" type="xs:string" minOccurs="0"/>

diff --git a/webservices/compbio/ws/server/resource/JronnWS.wsdl b/webservices/compbio/ws/server/resource/JronnWS.wsdl
index baca048..f8caa2c 100644 (file)
--- a/webservices/compbio/ws/server/resource/JronnWS.wsdl
+++ b/webservices/compbio/ws/server/resource/JronnWS.wsdl
@@ -24,18 +24,18 @@
   <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="analize">
     <part name="parameters" element="tns:analize"/>
   </message>
   <message name="analizeResponse">
     <part name="parameters" element="tns:analizeResponse"/>
   </message>
+  <message name="presetAnalize">
+    <part name="parameters" element="tns:presetAnalize"/>
+  </message>
+  <message name="presetAnalizeResponse">
+    <part name="parameters" element="tns:presetAnalizeResponse"/>
+  </message>
   <message name="getAnnotation">
     <part name="parameters" element="tns:getAnnotation"/>
   </message>
@@ -51,29 +51,17 @@
   <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="pullExecStatistics">
     <part name="parameters" element="tns:pullExecStatistics"/>
   </message>
   <message name="pullExecStatisticsResponse">
     <part name="parameters" element="tns:pullExecStatisticsResponse"/>
   </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 name="getJobStatus">
+    <part name="parameters" element="tns:getJobStatus"/>
   </message>
-  <message name="getPresetsResponse">
-    <part name="parameters" element="tns:getPresetsResponse"/>
+  <message name="getJobStatusResponse">
+    <part name="parameters" element="tns:getJobStatusResponse"/>
   </message>
   <message name="getLimit">
     <part name="parameters" element="tns:getLimit"/>
@@ -87,6 +75,18 @@
   <message name="getLimitsResponse">
     <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
+  <message name="getPresets">
+    <part name="parameters" element="tns:getPresets"/>
+  </message>
+  <message name="getPresetsResponse">
+    <part name="parameters" element="tns:getPresetsResponse"/>
+  </message>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
+  </message>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  </message>
   <portType name="SequenceAnnotation">
     <operation name="customAnalize">
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/customAnalizeRequest" message="tns:customAnalize"/>
@@ -96,6 +96,13 @@
       <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="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="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"/>
@@ -104,13 +111,6 @@
       <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="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="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"/>
@@ -120,21 +120,13 @@
       <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="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="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 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"/>
@@ -144,6 +136,14 @@
       <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsRequest" message="tns:getLimits"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
+    <operation name="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="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/SequenceAnnotation/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    </operation>
   </portType>
   <binding name="JronnWSPortBinding" type="tns:SequenceAnnotation">
     <soap:binding transport="http://schemas.xmlsoap.org/soap/http" style="document"/>
@@ -168,7 +168,7 @@
         <soap:fault name="WrongParameterException" use="literal"/>
       </fault>
     </operation>
-    <operation name="presetAnalize">
+    <operation name="analize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -185,11 +185,8 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
-      <fault name="WrongParameterException">
-        <soap:fault name="WrongParameterException" use="literal"/>
-      </fault>
     </operation>
-    <operation name="analize">
+    <operation name="presetAnalize">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -206,6 +203,9 @@
       <fault name="JobSubmissionException">
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
+      <fault name="WrongParameterException">
+        <soap:fault name="WrongParameterException" use="literal"/>
+      </fault>
     </operation>
     <operation name="getAnnotation">
       <soap:operation soapAction=""/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getJobStatus">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -237,7 +237,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="getJobStatus">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -246,7 +246,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimit">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getPresets">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -264,7 +264,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimit">
+    <operation name="getPresets">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd b/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
index 1da2262..6f34ece 100644 (file)
--- a/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/JronnWS_schema1.xsd
@@ -255,6 +255,23 @@
     </xs:sequence>
   </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="getLimits">
     <xs:sequence/>
   </xs:complexType>
@@ -293,23 +310,6 @@
     </xs:sequence>
   </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="cancelJob">
     <xs:sequence>
       <xs:element name="jobId" type="xs:string" minOccurs="0"/>

diff --git a/webservices/compbio/ws/server/resource/MafftWS.wsdl b/webservices/compbio/ws/server/resource/MafftWS.wsdl
index c7bfe2e..c4fcf1c 100644 (file)
--- a/webservices/compbio/ws/server/resource/MafftWS.wsdl
+++ b/webservices/compbio/ws/server/resource/MafftWS.wsdl
@@ -45,18 +45,18 @@
   <message name="alignResponse">
     <part name="parameters" element="tns:alignResponse"/>
   </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="pullExecStatistics">
+    <part name="parameters" element="tns:pullExecStatistics"/>
+  </message>
+  <message name="pullExecStatisticsResponse">
+    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+  </message>
   <message name="getJobStatus">
     <part name="parameters" element="tns:getJobStatus"/>
   </message>
@@ -69,11 +69,11 @@
   <message name="getLimitResponse">
     <part name="parameters" element="tns:getLimitResponse"/>
   </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
+  <message name="getLimits">
+    <part name="parameters" element="tns:getLimits"/>
   </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  <message name="getLimitsResponse">
+    <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
   <message name="getPresets">
     <part name="parameters" element="tns:getPresets"/>
@@ -81,11 +81,11 @@
   <message name="getPresetsResponse">
     <part name="parameters" element="tns:getPresetsResponse"/>
   </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
   </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
   </message>
   <portType name="MsaWS">
     <operation name="getResult">
@@ -116,14 +116,14 @@
       <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
       <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
     </operation>
-    <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
-    </operation>
     <operation name="cancelJob">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
     </operation>
+    <operation name="pullExecStatistics">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+    </operation>
     <operation name="getJobStatus">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
@@ -132,17 +132,17 @@
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
     </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    <operation name="getLimits">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
     <operation name="getPresets">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
     </operation>
-    <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+    <operation name="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
     </operation>
   </portType>
   <binding name="MafftWSPortBinding" type="tns:MsaWS">
@@ -219,7 +219,7 @@
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="cancelJob">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="cancelJob">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
index 05f2a89..c432550 100644 (file)
--- a/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/MafftWS_schema1.xsd
@@ -161,32 +161,6 @@
     </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>
@@ -218,6 +192,32 @@
     </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="getLimit">
     <xs:sequence>
       <xs:element name="presetName" type="xs:string" minOccurs="0"/>

diff --git a/webservices/compbio/ws/server/resource/MuscleWS.wsdl b/webservices/compbio/ws/server/resource/MuscleWS.wsdl
index 867020c..da4ed97 100644 (file)
--- a/webservices/compbio/ws/server/resource/MuscleWS.wsdl
+++ b/webservices/compbio/ws/server/resource/MuscleWS.wsdl
@@ -45,18 +45,18 @@
   <message name="alignResponse">
     <part name="parameters" element="tns:alignResponse"/>
   </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="pullExecStatistics">
+    <part name="parameters" element="tns:pullExecStatistics"/>
+  </message>
+  <message name="pullExecStatisticsResponse">
+    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+  </message>
   <message name="getJobStatus">
     <part name="parameters" element="tns:getJobStatus"/>
   </message>
@@ -69,11 +69,11 @@
   <message name="getLimitResponse">
     <part name="parameters" element="tns:getLimitResponse"/>
   </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
+  <message name="getLimits">
+    <part name="parameters" element="tns:getLimits"/>
   </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  <message name="getLimitsResponse">
+    <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
   <message name="getPresets">
     <part name="parameters" element="tns:getPresets"/>
@@ -81,11 +81,11 @@
   <message name="getPresetsResponse">
     <part name="parameters" element="tns:getPresetsResponse"/>
   </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
   </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
   </message>
   <portType name="MsaWS">
     <operation name="getResult">
@@ -116,14 +116,14 @@
       <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
       <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
     </operation>
-    <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
-    </operation>
     <operation name="cancelJob">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
     </operation>
+    <operation name="pullExecStatistics">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+    </operation>
     <operation name="getJobStatus">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
@@ -132,17 +132,17 @@
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
     </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    <operation name="getLimits">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
     <operation name="getPresets">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
     </operation>
-    <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+    <operation name="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
     </operation>
   </portType>
   <binding name="MuscleWSPortBinding" type="tns:MsaWS">
@@ -219,7 +219,7 @@
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="cancelJob">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="cancelJob">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
index e6c3574..0895916 100644 (file)
--- a/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/MuscleWS_schema1.xsd
@@ -152,32 +152,6 @@
     </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>
@@ -209,6 +183,32 @@
     </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="getLimit">
     <xs:sequence>
       <xs:element name="presetName" type="xs:string" minOccurs="0"/>

diff --git a/webservices/compbio/ws/server/resource/RegistryWS.wsdl b/webservices/compbio/ws/server/resource/RegistryWS.wsdl
index 8d7ec01..6760f66 100644 (file)
--- a/webservices/compbio/ws/server/resource/RegistryWS.wsdl
+++ b/webservices/compbio/ws/server/resource/RegistryWS.wsdl
@@ -12,6 +12,12 @@
   <message name="getSupportedServicesResponse">
     <part name="parameters" element="tns:getSupportedServicesResponse"/>
   </message>
+  <message name="testAllServices">
+    <part name="parameters" element="tns:testAllServices"/>
+  </message>
+  <message name="testAllServicesResponse">
+    <part name="parameters" element="tns:testAllServicesResponse"/>
+  </message>
   <message name="getLastTested">
     <part name="parameters" element="tns:getLastTested"/>
   </message>
@@ -24,12 +30,6 @@
   <message name="getLastTestedOnResponse">
     <part name="parameters" element="tns:getLastTestedOnResponse"/>
   </message>
-  <message name="testAllServices">
-    <part name="parameters" element="tns:testAllServices"/>
-  </message>
-  <message name="testAllServicesResponse">
-    <part name="parameters" element="tns:testAllServicesResponse"/>
-  </message>
   <message name="testService">
     <part name="parameters" element="tns:testService"/>
   </message>
@@ -47,6 +47,10 @@
       <input wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/getSupportedServicesRequest" message="tns:getSupportedServices"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/getSupportedServicesResponse" message="tns:getSupportedServicesResponse"/>
     </operation>
+    <operation name="testAllServices">
+      <input wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/testAllServicesRequest" message="tns:testAllServices"/>
+      <output wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/testAllServicesResponse" message="tns:testAllServicesResponse"/>
+    </operation>
     <operation name="getLastTested">
       <input wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/getLastTestedRequest" message="tns:getLastTested"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/getLastTestedResponse" message="tns:getLastTestedResponse"/>
@@ -55,10 +59,6 @@
       <input wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/getLastTestedOnRequest" message="tns:getLastTestedOn"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/getLastTestedOnResponse" message="tns:getLastTestedOnResponse"/>
     </operation>
-    <operation name="testAllServices">
-      <input wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/testAllServicesRequest" message="tns:testAllServices"/>
-      <output wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/testAllServicesResponse" message="tns:testAllServicesResponse"/>
-    </operation>
     <operation name="testService">
       <input wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/testServiceRequest" message="tns:testService"/>
       <output wsam:Action="http://msa.data.compbio/01/12/2010/RegistryWS/testServiceResponse" message="tns:testServiceResponse"/>
@@ -79,7 +79,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLastTested">
+    <operation name="testAllServices">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -88,7 +88,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLastTestedOn">
+    <operation name="getLastTested">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -97,7 +97,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="testAllServices">
+    <operation name="getLastTestedOn">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/TcoffeeWS.wsdl b/webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
index 415612b..6781837 100644 (file)
--- a/webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
+++ b/webservices/compbio/ws/server/resource/TcoffeeWS.wsdl
@@ -45,18 +45,18 @@
   <message name="alignResponse">
     <part name="parameters" element="tns:alignResponse"/>
   </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="pullExecStatistics">
+    <part name="parameters" element="tns:pullExecStatistics"/>
+  </message>
+  <message name="pullExecStatisticsResponse">
+    <part name="parameters" element="tns:pullExecStatisticsResponse"/>
+  </message>
   <message name="getJobStatus">
     <part name="parameters" element="tns:getJobStatus"/>
   </message>
@@ -69,11 +69,11 @@
   <message name="getLimitResponse">
     <part name="parameters" element="tns:getLimitResponse"/>
   </message>
-  <message name="getRunnerOptions">
-    <part name="parameters" element="tns:getRunnerOptions"/>
+  <message name="getLimits">
+    <part name="parameters" element="tns:getLimits"/>
   </message>
-  <message name="getRunnerOptionsResponse">
-    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
+  <message name="getLimitsResponse">
+    <part name="parameters" element="tns:getLimitsResponse"/>
   </message>
   <message name="getPresets">
     <part name="parameters" element="tns:getPresets"/>
@@ -81,11 +81,11 @@
   <message name="getPresetsResponse">
     <part name="parameters" element="tns:getPresetsResponse"/>
   </message>
-  <message name="getLimits">
-    <part name="parameters" element="tns:getLimits"/>
+  <message name="getRunnerOptions">
+    <part name="parameters" element="tns:getRunnerOptions"/>
   </message>
-  <message name="getLimitsResponse">
-    <part name="parameters" element="tns:getLimitsResponse"/>
+  <message name="getRunnerOptionsResponse">
+    <part name="parameters" element="tns:getRunnerOptionsResponse"/>
   </message>
   <portType name="MsaWS">
     <operation name="getResult">
@@ -116,14 +116,14 @@
       <fault message="tns:LimitExceededException" name="LimitExceededException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/LimitExceededException"/>
       <fault message="tns:JobSubmissionException" name="JobSubmissionException" wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/align/Fault/JobSubmissionException"/>
     </operation>
-    <operation name="pullExecStatistics">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
-    </operation>
     <operation name="cancelJob">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobRequest" message="tns:cancelJob"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/cancelJobResponse" message="tns:cancelJobResponse"/>
     </operation>
+    <operation name="pullExecStatistics">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsRequest" message="tns:pullExecStatistics"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/pullExecStatisticsResponse" message="tns:pullExecStatisticsResponse"/>
+    </operation>
     <operation name="getJobStatus">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusRequest" message="tns:getJobStatus"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getJobStatusResponse" message="tns:getJobStatusResponse"/>
@@ -132,17 +132,17 @@
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitRequest" message="tns:getLimit"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitResponse" message="tns:getLimitResponse"/>
     </operation>
-    <operation name="getRunnerOptions">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
+    <operation name="getLimits">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
     </operation>
     <operation name="getPresets">
       <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsRequest" message="tns:getPresets"/>
       <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getPresetsResponse" message="tns:getPresetsResponse"/>
     </operation>
-    <operation name="getLimits">
-      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsRequest" message="tns:getLimits"/>
-      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getLimitsResponse" message="tns:getLimitsResponse"/>
+    <operation name="getRunnerOptions">
+      <input wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsRequest" message="tns:getRunnerOptions"/>
+      <output wsam:Action="http://msa.data.compbio/01/01/2010/MsaWS/getRunnerOptionsResponse" message="tns:getRunnerOptionsResponse"/>
     </operation>
   </portType>
   <binding name="TcoffeeWSPortBinding" type="tns:MsaWS">
@@ -219,7 +219,7 @@
         <soap:fault name="JobSubmissionException" use="literal"/>
       </fault>
     </operation>
-    <operation name="pullExecStatistics">
+    <operation name="cancelJob">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -228,7 +228,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="cancelJob">
+    <operation name="pullExecStatistics">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -255,7 +255,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getRunnerOptions">
+    <operation name="getLimits">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>
@@ -273,7 +273,7 @@
         <soap:body use="literal"/>
       </output>
     </operation>
-    <operation name="getLimits">
+    <operation name="getRunnerOptions">
       <soap:operation soapAction=""/>
       <input>
         <soap:body use="literal"/>

diff --git a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
index 9f5bbee..18262c9 100644 (file)
--- a/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
+++ b/webservices/compbio/ws/server/resource/TcoffeeWS_schema1.xsd
@@ -152,32 +152,6 @@
     </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>
@@ -209,6 +183,32 @@
     </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="getLimit">
     <xs:sequence>
       <xs:element name="presetName" type="xs:string" minOccurs="0"/>