Import RNAalifold removed from RNAStructReader. @XmlSeeAlso line added

to ScoreManager.

diff --git a/datamodel/compbio/data/sequence/RNAStructReader.java b/datamodel/compbio/data/sequence/RNAStructReader.java
index 7ebba4c..5eec46f 100644 (file)
--- a/datamodel/compbio/data/sequence/RNAStructReader.java
+++ b/datamodel/compbio/data/sequence/RNAStructReader.java
@@ -13,8 +13,6 @@ import java.util.regex.Pattern;
 \r
 import org.apache.log4j.Logger;\r
 \r
-import compbio.runner.structure.RNAalifold;\r
-\r
 // Utility class for reading alifold output\r
 \r
 public class RNAStructReader {\r
@@ -157,7 +155,7 @@ public class RNAStructReader {
                return new RNAStructScoreManager(structs, data);\r
        }\r
        \r
-       // Just for the purpose of creating nee TreeSet<Score> objects of length one\r
+       // Just for the purpose of creating new TreeSet<Score> objects of length one\r
        // for adding to a 'data' list to make a ScoreManager\r
        private static TreeSet<Score> newSetScore(Enum<?> res, List<Float> scores) {\r
                // first convert List<Float> to float[]\r

diff --git a/datamodel/compbio/data/sequence/RNAStructScoreManager.java b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
index e792969..d2da2e1 100644 (file)
--- a/datamodel/compbio/data/sequence/RNAStructScoreManager.java
+++ b/datamodel/compbio/data/sequence/RNAStructScoreManager.java
@@ -28,6 +28,7 @@ public class RNAStructScoreManager extends ScoreManager {
        \r
 \r
        public RNAStructScoreManager(List<String> structs, List<TreeSet<Score>> data) {\r
+               \r
                assert(structs.size() == data.size());\r
                \r
                List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
@@ -57,6 +58,7 @@ public class RNAStructScoreManager extends ScoreManager {
                        data.add(sch.scores);\r
                }\r
                return data;\r
+               \r
        }\r
 \r
        // Send this data Structure back to something approximating the stdoutFile\r

diff --git a/datamodel/compbio/data/sequence/ScoreManager.java b/datamodel/compbio/data/sequence/ScoreManager.java
index 9b1803d..3c1bc21 100644 (file)
--- a/datamodel/compbio/data/sequence/ScoreManager.java
+++ b/datamodel/compbio/data/sequence/ScoreManager.java
@@ -28,8 +28,10 @@ import java.util.TreeSet;
 \r
 import javax.xml.bind.annotation.XmlAccessType;\r
 import javax.xml.bind.annotation.XmlAccessorType;\r
+import javax.xml.bind.annotation.XmlSeeAlso;\r
 import javax.xml.bind.annotation.XmlTransient;\r
 \r
+@XmlSeeAlso({RNAStructScoreManager.class})\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
 public class ScoreManager {\r
 \r
@@ -49,6 +51,9 @@ public class ScoreManager {
        }\r
 \r
        private ScoreManager(Map<String, Set<Score>> data) {\r
+               System.out.println("A ScoreManager was created!!");\r
+\r
+               \r
                List<ScoreHolder> seqScores = new ArrayList<ScoreHolder>();\r
                for (Map.Entry<String, Set<Score>> singleSeqScores : data.entrySet()) {\r
                        seqScores.add(new ScoreHolder(singleSeqScores.getKey(),\r
@@ -58,11 +63,18 @@ public class ScoreManager {
        }\r
 \r
        public static ScoreManager newInstance(Map<String, Set<Score>> data) {\r
+               System.out.println("A ScoreManager was created!!");\r
+\r
+               \r
                return new ScoreManager(data);\r
        }\r
 \r
        public static ScoreManager newInstanceSingleScore(\r
                        Map<String, Score> seqScoresMap) {\r
+               \r
+               System.out.println("A ScoreManager was created!!");\r
+\r
+               \r
                Map<String, Set<Score>> multipleScoresMap = new TreeMap<String, Set<Score>>();\r
                for (Map.Entry<String, Score> seqScore : seqScoresMap.entrySet()) {\r
                        Set<Score> scores = new TreeSet<Score>();\r
@@ -73,6 +85,9 @@ public class ScoreManager {
        }\r
 \r
        public static ScoreManager newInstanceSingleSequence(Set<Score> data) {\r
+               System.out.println("A ScoreManager was created!!");\r
+\r
+               \r
                return new ScoreManager(ScoreManager.SINGLE_ENTRY_KEY,\r
                                new TreeSet(data));\r
        }\r

diff --git a/testsrc/compbio/ws/client/TestRNAalifoldWS.java b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
index fd8fb9b..5452c4e 100644 (file)
--- a/testsrc/compbio/ws/client/TestRNAalifoldWS.java
+++ b/testsrc/compbio/ws/client/TestRNAalifoldWS.java
@@ -27,6 +27,7 @@ import compbio.data.sequence.Alignment;
 import compbio.data.sequence.ClustalAlignmentUtil;
 import compbio.data.sequence.ConservationMethod;
 import compbio.data.sequence.FastaSequence;
+import compbio.data.sequence.RNAStructScoreManager;
 import compbio.data.sequence.ScoreManager;
 import compbio.data.sequence.SequenceUtil;
 import compbio.data.sequence.UnknownFileFormatException;
@@ -40,6 +41,7 @@ import compbio.metadata.RunnerConfig;
 import compbio.metadata.UnsupportedRuntimeException;
 import compbio.metadata.WrongParameterException;
 import compbio.runner.conservation.AACon;
+import compbio.runner.structure.RNAalifold;
 import compbio.util.SysPrefs;
 import compbio.ws.server.RNAalifoldWS;
 
@@ -47,6 +49,7 @@ import compbio.ws.server.RNAalifoldWS;
 public class TestRNAalifoldWS {
        
        SequenceAnnotation<RNAalifoldWS> foldws;
+//     RNAalifoldWS foldws;
        
        @BeforeTest(groups = {AllTestSuit.test_group_webservices})
        void initConnection() {
@@ -54,6 +57,7 @@ public class TestRNAalifoldWS {
                try {
                        JABAService client = Jws2Client.connect(
                                        "http://localhost:8080/jabaws", Services.RNAalifoldWS);
+//                     foldws = (RNAalifoldWS) client;
                        foldws = (SequenceAnnotation<RNAalifoldWS>) client;
                } catch (ConnectException e) {
                        e.printStackTrace();
@@ -69,6 +73,7 @@ public class TestRNAalifoldWS {
        public void testFold() throws FileNotFoundException, IOException,
                        UnknownFileFormatException {
                
+               
 //             String CURRENT_DIRECTORY = SysPrefs.getCurrentDirectory()
 //                             + File.separator;
                
@@ -87,7 +92,10 @@ public class TestRNAalifoldWS {
                        
                        String jobId = foldws.customAnalize(fsl, options);
                        System.out.println("J: " + jobId);
-                       ScoreManager result = foldws.getAnnotation(jobId);
+                       RNAStructScoreManager result = (RNAStructScoreManager)foldws.getAnnotation(jobId);
+
+                       
+                       // standard and RNAStruct specific ways of formatting scoremanager
                        System.out.println("fold results: \n" + result.toString());
                        
                        Writer writer = new OutputStreamWriter(System.out);

diff --git a/webservices/compbio/data/msa/jaxws/CancelJob.java b/webservices/compbio/data/msa/jaxws/CancelJob.java
index 32660d9..9b1f062 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/CancelJob.java
+++ b/webservices/compbio/data/msa/jaxws/CancelJob.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "cancelJob", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "cancelJob", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "cancelJob", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class CancelJob {\r
 \r
     @XmlElement(name = "jobId", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/CancelJobResponse.java b/webservices/compbio/data/msa/jaxws/CancelJobResponse.java
index 7ccc190..00a92e2 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/CancelJobResponse.java
+++ b/webservices/compbio/data/msa/jaxws/CancelJobResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "cancelJobResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class CancelJobResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/GetJobStatus.java b/webservices/compbio/data/msa/jaxws/GetJobStatus.java
index 5fd70f5..438b3a0 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetJobStatus.java
+++ b/webservices/compbio/data/msa/jaxws/GetJobStatus.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getJobStatus", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getJobStatus", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getJobStatus", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getJobStatus", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetJobStatus {\r
 \r
     @XmlElement(name = "jobId", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java b/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java
index 0f8ba68..0f81c39 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetJobStatusResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getJobStatusResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetJobStatusResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/GetLimit.java b/webservices/compbio/data/msa/jaxws/GetLimit.java
index 6b04bc0..64514ba 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetLimit.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimit.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getLimit", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getLimit", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getLimit", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getLimit", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetLimit {\r
 \r
     @XmlElement(name = "presetName", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/GetLimitResponse.java b/webservices/compbio/data/msa/jaxws/GetLimitResponse.java
index 249e7e4..8147fa6 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetLimitResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimitResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getLimitResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetLimitResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/GetLimits.java b/webservices/compbio/data/msa/jaxws/GetLimits.java
index b8668d9..152f72e 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetLimits.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimits.java
@@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getLimits", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getLimits", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getLimits", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getLimits", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetLimits {\r
 \r
 \r

diff --git a/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java b/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java
index f503c23..8bb6cc9 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetLimitsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getLimitsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetLimitsResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/GetPresets.java b/webservices/compbio/data/msa/jaxws/GetPresets.java
index 2e57fb8..04d5d12 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetPresets.java
+++ b/webservices/compbio/data/msa/jaxws/GetPresets.java
@@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getPresets", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getPresets", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getPresets", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getPresets", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetPresets {\r
 \r
 \r

diff --git a/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java b/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java
index ad2942b..7755793 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetPresetsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getPresetsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetPresetsResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/GetResultResponse.java b/webservices/compbio/data/msa/jaxws/GetResultResponse.java
index bbf4468..d8596b0 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetResultResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetResultResponse.java
@@ -13,14 +13,14 @@ import javax.xml.bind.annotation.XmlType;
 public class GetResultResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r
-    private compbio.data.sequence.RNAstruct _return;\r
+    private compbio.data.sequence.Alignment _return;\r
 \r
     /**\r
      * \r
      * @return\r
-     *     returns RNAstruct\r
+     *     returns Alignment\r
      */\r
-    public compbio.data.sequence.RNAstruct getReturn() {\r
+    public compbio.data.sequence.Alignment getReturn() {\r
         return this._return;\r
     }\r
 \r
@@ -29,7 +29,7 @@ public class GetResultResponse {
      * @param _return\r
      *     the value for the _return property\r
      */\r
-    public void setReturn(compbio.data.sequence.RNAstruct _return) {\r
+    public void setReturn(compbio.data.sequence.Alignment _return) {\r
         this._return = _return;\r
     }\r
 \r

diff --git a/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java b/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java
index 9128b3f..9d59cd3 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java
+++ b/webservices/compbio/data/msa/jaxws/GetRunnerOptions.java
@@ -6,9 +6,9 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getRunnerOptions", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetRunnerOptions {\r
 \r
 \r

diff --git a/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java b/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
index fb467ca..2278aa2 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/GetRunnerOptionsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "getRunnerOptionsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class GetRunnerOptionsResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
index a916bce..869aea5 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/JobSubmissionExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3\r
  * \r
  */\r
-@XmlRootElement(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "JobSubmissionException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class JobSubmissionExceptionBean {\r
 \r
     private String message;\r

diff --git a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
index 0ddadef..9e63199 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/LimitExceededExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3\r
  * \r
  */\r
-@XmlRootElement(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = {\r
+@XmlType(name = "LimitExceededException", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = {\r
     "actualNumberofSequences",\r
     "message",\r
     "numberOfSequencesAllowed",\r

diff --git a/webservices/compbio/data/msa/jaxws/PullExecStatistics.java b/webservices/compbio/data/msa/jaxws/PullExecStatistics.java
index db1be6e..7ab918b 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/PullExecStatistics.java
+++ b/webservices/compbio/data/msa/jaxws/PullExecStatistics.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/01/2010/", propOrder = {\r
+@XmlType(name = "pullExecStatistics", namespace = "http://msa.data.compbio/01/12/2010/", propOrder = {\r
     "jobId",\r
     "position"\r
 })\r

diff --git a/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java b/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java
index 068b404..ef36b8d 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java
+++ b/webservices/compbio/data/msa/jaxws/PullExecStatisticsResponse.java
@@ -7,9 +7,9 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;\r
 import javax.xml.bind.annotation.XmlType;\r
 \r
-@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "pullExecStatisticsResponse", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class PullExecStatisticsResponse {\r
 \r
     @XmlElement(name = "return", namespace = "")\r

diff --git a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
index 4561f5f..79f413a 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/ResultNotAvailableExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3\r
  * \r
  */\r
-@XmlRootElement(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "ResultNotAvailableException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class ResultNotAvailableExceptionBean {\r
 \r
     private String message;\r

diff --git a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
index 6927cf6..b349081 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/UnsupportedRuntimeExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3\r
  * \r
  */\r
-@XmlRootElement(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "UnsupportedRuntimeException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class UnsupportedRuntimeExceptionBean {\r
 \r
     private String message;\r

diff --git a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
index beb4d07..630d8a5 100644 (file)
--- a/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
+++ b/webservices/compbio/data/msa/jaxws/WrongParameterExceptionBean.java
@@ -13,9 +13,9 @@ import javax.xml.bind.annotation.XmlType;
  * Generated source version: 2.2.3\r
  * \r
  */\r
-@XmlRootElement(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlRootElement(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 @XmlAccessorType(XmlAccessType.FIELD)\r
-@XmlType(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/01/2010/")\r
+@XmlType(name = "WrongParameterException", namespace = "http://msa.data.compbio/01/12/2010/")\r
 public class WrongParameterExceptionBean {\r
 \r
     private String message;\r

diff --git a/webservices/compbio/ws/server/RNAalifoldWS.java b/webservices/compbio/ws/server/RNAalifoldWS.java
index d640e27..b07882a 100644 (file)
--- a/webservices/compbio/ws/server/RNAalifoldWS.java
+++ b/webservices/compbio/ws/server/RNAalifoldWS.java
@@ -31,17 +31,8 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
        public RNAalifoldWS() {\r
                super (new RNAalifold(), log);\r
        }\r
-\r
-       \r
-//     // for testing\r
-//     @Override\r
-//     public RNAStructScoreManager getAnnotation(String jobId) \r
-//                     throws ResultNotAvailableException {\r
-//             return WSUtil.getAnnotation(jobId, log);\r
-//     }\r
-       \r
        \r
-       // Only purpose of Overrides is to replace "analize" with "fold" method \r
+       // Only purpose is to replace "analize" with "fold" method \r
        // so that a clustal input file and not fasta will be generated\r
        @Override\r
        public String analize(List<FastaSequence> sequences)\r
@@ -53,7 +44,7 @@ public class RNAalifoldWS extends SequenceAnnotationService<RNAalifold>
                                getLimit(""));\r
        }\r
 \r
-       // Only purpose of Overrides is to replace "analize" with "fold" method \r
+       // Only purpose is to replace "analize" with "fold" method \r
                // so that a clustal input file and not fasta will be generated\r
        @Override\r
        public String customAnalize(List<FastaSequence> sequences,\r

diff --git a/webservices/compbio/ws/server/WSUtil.java b/webservices/compbio/ws/server/WSUtil.java
index e80b1e5..d230cde 100644 (file)
--- a/webservices/compbio/ws/server/WSUtil.java
+++ b/webservices/compbio/ws/server/WSUtil.java
@@ -27,6 +27,7 @@ import org.apache.log4j.Logger;
 \r
 import compbio.data.sequence.Alignment;\r
 import compbio.data.sequence.FastaSequence;\r
+import compbio.data.sequence.RNAStructScoreManager;\r
 import compbio.data.sequence.ScoreManager;\r
 import compbio.engine.AsyncExecutor;\r
 import compbio.engine.Configurator;\r
@@ -215,12 +216,12 @@ public final class WSUtil {
                ConfiguredExecutable<T> aacon = (ConfiguredExecutable<T>) asyncEngine\r
                                .getResults(jobId);\r
                \r
-               \r
                ScoreManager mas = aacon.getResults();\r
                \r
                log.trace(jobId + " getConservation : " + mas);\r
                return mas;\r
        }\r
+       \r
 \r
        /*\r
         * UNUSED\r