more subtle rearrangements
authorjprocter <Jim Procter>
Sun, 5 Jun 2005 17:01:52 +0000 (17:01 +0000)
committerjprocter <Jim Procter>
Sun, 5 Jun 2005 17:01:52 +0000 (17:01 +0000)
src/jalview/ws/JPredClient.java
src/jalview/ws/MsaWSClient.java

index 232d6d6..8d3ae35 100755 (executable)
@@ -11,344 +11,424 @@ import java.awt.*;
 import jalview.analysis.AlignSeq;\r
 import ext.vamsas.*;\r
 \r
-\r
-public class JPredClient extends WSClient\r
+public class JPredClient\r
+    extends WSClient\r
 {\r
   ext.vamsas.JPredWS server;\r
   String altitle = "";\r
   java.util.Hashtable SequenceInfo = null;\r
-  private void setWebService() {\r
+  private WebserviceInfo setWebService()\r
+  {\r
     WebServiceName = "JNetWS";\r
     WebServiceJobTitle = "JNet secondary structure prediction";\r
-    WebServiceReference="\"Cuff J. A and Barton G.J (1999) Application of enhanced "\r
+    WebServiceReference =\r
+        "\"Cuff J. A and Barton G.J (1999) Application of enhanced "\r
         + "multiple sequence alignment profiles to improve protein secondary structure prediction, "\r
         + "Proteins 40:502-511\".";\r
-    WsURL="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
-  }\r
-  public JPredClient(String title, SequenceI[] msf)\r
-  {\r
-    setWebService();\r
-    wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);\r
-    SequenceI seq = msf[0];\r
-    altitle = "JNet prediction on "+seq.getName()+" using alignment from "+title;\r
+    WsURL = "http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred";\r
+    WebserviceInfo wsInfo = new WebserviceInfo(WebServiceJobTitle,\r
+                                               WebServiceReference);\r
 \r
-    wsInfo.setProgressText("Job details for MSA based prediction ("+title+") on sequence :\n>"\r
-                   + seq.getName() + "\n"\r
-                   + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
+    return wsInfo;\r
+  }\r
 \r
-    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+    private boolean locateWebService()\r
+    {\r
 \r
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
-    // JBPNote url will be set from properties\r
-    try {\r
-      this.server = loc.getjpred(new java.net.URL(WsURL));\r
-    }\r
-    catch (Exception ex) {\r
-      JOptionPane.showMessageDialog(Desktop.desktop, "The Secondary Structure Prediction Service named "\r
-                                    +WebServiceName+" at "+WsURL+" couldn't be located.",\r
-                                    "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
-      wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"\r
-                     +WsURL+"\n"+ex.getMessage());\r
+      JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
+      try\r
+      {\r
+        this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
+        ( (JpredSoapBindingStub)this.server).setTimeout(60000); // one minute stub\r
+      }\r
+      catch (Exception ex)\r
+      {\r
+        JOptionPane.showMessageDialog(Desktop.desktop,\r
+            "The Secondary Structure Prediction Service named "\r
+                                      + WebServiceName + " at " + WsURL +\r
+                                      " couldn't be located.",\r
+                                      "Internal Jalview Error",\r
+                                      JOptionPane.WARNING_MESSAGE);\r
+        wsInfo.setProgressText("Serious! " + WebServiceName +\r
+                               " Service location failed\nfor URL :"\r
+                               + WsURL + "\n" + ex.getMessage());\r
+        wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+        return false;\r
+      }\r
+      return true;\r
     }\r
 \r
-    JPredThread jthread = new JPredThread(msf);\r
-    jthread.start();\r
-  }\r
-\r
-  public JPredClient(String title, SequenceI seq)\r
-  {\r
-    setWebService();\r
-    wsInfo = new WebserviceInfo(WebServiceJobTitle, WebServiceReference);\r
-    wsInfo.setProgressText("Job details for prediction on sequence :\n>"\r
-                   + seq.getName() + "\n" + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
-    altitle = "JNet prediction for sequence "+seq.getName()+" from "+title;\r
-    SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
-\r
-    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
-    try {\r
-      this.server = loc.getjpred(new java.net.URL(WsURL)); // JBPNote will be set from properties\r
-      ((JpredSoapBindingStub) this.server).setTimeout(60000); // one minute stub\r
-    }\r
-    catch (Exception ex) {\r
-      JOptionPane.showMessageDialog(Desktop.desktop, "The Secondary Structure Prediction Service named "\r
-                                    +WebServiceName+" at "+WsURL+" couldn't be located.",\r
-                                    "Internal Jalview Error", JOptionPane.WARNING_MESSAGE);\r
-      wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"\r
-                     +WsURL+"\n"+ex.getMessage());\r
-      wsInfo.setStatus(wsInfo.STATE_STOPPED_SERVERERROR);\r
+    public JPredClient(String title, SequenceI[] msf)\r
+    {\r
+      wsInfo = setWebService();\r
+      SequenceI seq = msf[0];\r
+      altitle = "JNet prediction on " + seq.getName() +\r
+          " using alignment from " + title;\r
+\r
+      wsInfo.setProgressText("Job details for MSA based prediction (" + title +\r
+                             ") on sequence :\n>"\r
+                             + seq.getName() + "\n"\r
+                             + AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
+                             "\n");\r
+\r
+      SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
+      if (!locateWebService())\r
+        return;\r
+\r
+      JPredThread jthread = new JPredThread(msf);\r
+      jthread.start();\r
     }\r
 \r
-    JPredThread jthread = new JPredThread(seq);\r
-    jthread.start();\r
-  }\r
+    public JPredClient(String title, SequenceI seq)\r
+    {\r
+      wsInfo = setWebService();\r
+      wsInfo.setProgressText("Job details for prediction on sequence :\n>"\r
+                             + seq.getName() + "\n" +\r
+                             AlignSeq.extractGaps("-. ", seq.getSequence()) +\r
+                             "\n");\r
+      altitle = "JNet prediction for sequence " + seq.getName() + " from " +\r
+          title;\r
 \r
+      SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(seq);\r
 \r
-  class JPredThread\r
-      extends Thread\r
-  {\r
-    String OutputHeader;\r
-    ext.vamsas.JpredResult result;\r
-    ext.vamsas.Sequence sequence;\r
-    ext.vamsas.Msfalignment msa;\r
-    String jobId;\r
-    boolean jobComplete = false;\r
-    int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
-    JPredThread(SequenceI seq)\r
-    {\r
-      OutputHeader = wsInfo.getProgressText();\r
-      this.sequence = new ext.vamsas.Sequence();\r
-      this.sequence.setId(seq.getName());\r
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ",seq.getSequence()));\r
-    }\r
+      if (!locateWebService())\r
+              return;\r
 \r
-    JPredThread(SequenceI[] msf)\r
-    {\r
-      OutputHeader = wsInfo.getProgressText();\r
-      this.sequence = new ext.vamsas.Sequence();\r
-      this.sequence.setId(msf[0].getName());\r
-      this.sequence.setSeq(AlignSeq.extractGaps("-. ",msf[0].getSequence()));\r
-      jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
-      this.msa = new ext.vamsas.Msfalignment();\r
-      msa.setMsf(mwrite.print(msf));\r
+      JPredThread jthread = new JPredThread(seq);\r
+      jthread.start();\r
     }\r
 \r
-\r
-    public void run()\r
+    class JPredThread\r
+        extends Thread\r
     {\r
+      String OutputHeader;\r
+      ext.vamsas.JpredResult result;\r
+      ext.vamsas.Sequence sequence;\r
+      ext.vamsas.Msfalignment msa;\r
+      String jobId;\r
+      boolean jobComplete = false;\r
+      int allowedServerExceptions = 3; // thread dies if too many exceptions.\r
+      JPredThread(SequenceI seq)\r
+      {\r
+        OutputHeader = wsInfo.getProgressText();\r
+        this.sequence = new ext.vamsas.Sequence();\r
+        this.sequence.setId(seq.getName());\r
+        this.sequence.setSeq(AlignSeq.extractGaps("-. ", seq.getSequence()));\r
+      }\r
 \r
-      StartJob();\r
+      JPredThread(SequenceI[] msf)\r
+      {\r
+        OutputHeader = wsInfo.getProgressText();\r
+        this.sequence = new ext.vamsas.Sequence();\r
+        this.sequence.setId(msf[0].getName());\r
+        this.sequence.setSeq(AlignSeq.extractGaps("-. ", msf[0].getSequence()));\r
+        jalview.io.PileUpfile mwrite = new jalview.io.PileUpfile();\r
+        this.msa = new ext.vamsas.Msfalignment();\r
+        msa.setMsf(mwrite.print(msf));\r
+      }\r
 \r
-      while (!jobComplete && (allowedServerExceptions > 0))\r
+      public void run()\r
       {\r
-        try\r
-        {\r
-          if ((result = server.getresult(jobId))==null)\r
-            throw(new Exception("Timed out when communicating with server\nTry again later.\n"));\r
 \r
-         if( result.isRunning() )\r
-           wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
-         else if( result.isQueued() )\r
-           wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+        StartJob();\r
 \r
-          if (result.isFinished())\r
+        while (!jobComplete && (allowedServerExceptions > 0))\r
+        {\r
+          try\r
           {\r
-            parseResult();\r
-            jobComplete = true;\r
-            jobsRunning--;\r
+            if ( (result = server.getresult(jobId)) == null)\r
+            {\r
+              throw (new Exception(\r
+                  "Timed out when communicating with server\nTry again later.\n"));\r
+            }\r
+\r
+            if (result.isRunning())\r
+            {\r
+              wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+            }\r
+            else if (result.isQueued())\r
+            {\r
+              wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\r
+            }\r
+\r
+            if (result.isFinished())\r
+            {\r
+              parseResult();\r
+              jobComplete = true;\r
+              jobsRunning--;\r
+            }\r
+            else\r
+            {\r
+              wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
+              if (! (result.isJobFailed() || result.isServerError()))\r
+              {\r
+                try\r
+                {\r
+                  Thread.sleep(5000);\r
+                }\r
+                catch (InterruptedException ex1)\r
+                {\r
+                }\r
+                //  System.out.println("I'm alive "+seqid+" "+jobid);\r
+              }\r
+              else\r
+              {\r
+                wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+              }\r
+            }\r
           }\r
-          else\r
+          catch (Exception ex)\r
           {\r
-            wsInfo.setProgressText(OutputHeader + "\n" + result.getStatus());\r
-            if (! (result.isJobFailed() || result.isServerError()))\r
+            allowedServerExceptions--;\r
+            wsInfo.appendProgressText("\nJPredWS Server exception!\n" +\r
+                                      ex.getMessage());\r
+            try\r
             {\r
-              try\r
+              if (allowedServerExceptions > 0)\r
               {\r
                 Thread.sleep(5000);\r
               }\r
-              catch (InterruptedException ex1)\r
-              {\r
-              }\r
-              //  System.out.println("I'm alive "+seqid+" "+jobid);\r
-            } else {\r
-              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+            }\r
+            catch (InterruptedException ex1)\r
+            {\r
             }\r
           }\r
         }\r
-        catch (Exception ex)\r
+\r
+        if (! (result.isJobFailed() || result.isServerError()))\r
         {\r
-          allowedServerExceptions--;\r
-          wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());\r
-          try\r
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
+        }\r
+        else\r
+        {\r
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+        }\r
+      }\r
+\r
+      void StartJob()\r
+      {\r
+        try\r
+        {\r
+          if (msa != null)\r
           {\r
-            if (allowedServerExceptions>0)\r
-              Thread.sleep(5000);\r
+            jobId = server.predictOnMsa(msa);\r
+          }\r
+          else\r
+          {\r
+            jobId = server.predict(sequence);\r
+          }\r
+          if (jobId != null)\r
+          {\r
+            if (jobId.startsWith("Broken"))\r
+            {\r
+              throw new Exception("Submission " + jobId);\r
+            }\r
+            else\r
+            {\r
+              System.out.println(WsURL + " Job Id '" + jobId + "'");\r
+            }\r
           }\r
-          catch (InterruptedException ex1)\r
+          else\r
           {\r
+            throw new Exception("Server timed out - try again later\n");\r
+\r
           }\r
         }\r
+        catch (Exception e)\r
+        {\r
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
+          allowedServerExceptions = 0;\r
+          jobComplete = false;\r
+          wsInfo.appendProgressText("Failed to submit the prediction: " +\r
+                                    e.toString() + "\nJust close the window\n");\r
+          System.err.println(\r
+              "JPredWS Client: Failed to submit the prediction\n" +\r
+              e.toString() + "\n");\r
+          // e.printStackTrace(); TODO: JBPNote DEBUG\r
+        }\r
       }\r
 \r
-      if (! (result.isJobFailed() || result.isServerError()))\r
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);\r
-      else\r
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
-    }\r
-\r
-    void StartJob()\r
-    {\r
-      try\r
+      private void addFloatAnnotations(Alignment al, int[] gapmap,\r
+                                       Vector values, String Symname,\r
+                                       String Visname, float min, float max,\r
+                                       int winLength)\r
       {\r
-        if (msa!=null)  {\r
-          jobId = server.predictOnMsa(msa);\r
-        } else {\r
-          jobId = server.predict(sequence);\r
-        }\r
-        if (jobId!=null) {\r
-          if (jobId.startsWith("Broken")) {\r
-            throw new Exception("Submission " + jobId);\r
-          } else {\r
-            System.out.println(WsURL+" Job Id '"+jobId+"'");\r
-          }\r
-        } else {\r
-          throw new Exception("Server timed out - try again later\n");\r
 \r
+        Annotation[] annotations = new Annotation[al.getWidth()];\r
+        for (int j = 0; j < values.size(); j++)\r
+        {\r
+          float value = Float.parseFloat(values.get(j).toString());\r
+          annotations[gapmap[j]] = new Annotation("", value + "", ' ', value);\r
         }\r
+        al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations,\r
+                                                 min, max, winLength));\r
       }\r
-      catch (Exception e)\r
-      {\r
-         wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);\r
-         allowedServerExceptions=0;\r
-         jobComplete=false;\r
-         wsInfo.appendProgressText("Failed to submit the prediction: "+e.toString()+"\nJust close the window\n");\r
-         System.err.println("JPredWS Client: Failed to submit the prediction\n" +\r
-                            e.toString() + "\n");\r
-         // e.printStackTrace(); TODO: JBPNote DEBUG\r
-      }\r
-    }\r
 \r
-    private void addFloatAnnotations(Alignment al, int[] gapmap, Vector values, String Symname, String Visname, float min, float max, int winLength) {\r
-\r
-      Annotation[] annotations = new Annotation[al.getWidth()];\r
-      for (int j = 0; j < values.size(); j++)\r
+      void parseResult()\r
       {\r
-        float value = Float.parseFloat(values.get(j).toString());\r
-        annotations[gapmap[j]] = new Annotation("", value+"",' ',value);\r
-      }\r
-      al.addAnnotation(new AlignmentAnnotation(Symname, Visname, annotations, min, max, winLength));\r
-    }\r
-\r
-    void parseResult()\r
-    {\r
-      // OutputHeader = output.getText();\r
-      if (result.isFailed()) {\r
-        OutputHeader +="Job failed.\n";\r
-      }\r
-      if (result.getStatus()!=null) {\r
-        OutputHeader += "\n"+result.getStatus();\r
-      }\r
-      if (result.getPredfile()!=null) {\r
-        OutputHeader += "\n"+result.getPredfile();\r
-      // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
-      }\r
-      if (result.getAligfile()!=null) {\r
-        OutputHeader += "\n"+result.getAligfile();\r
-      }\r
-      wsInfo.setProgressText(OutputHeader);\r
-      try {\r
-        // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
-        jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.getPredfile(), "Paste");\r
-        SequenceI[] preds = prediction.getSeqsAsArray();\r
-        Alignment al;\r
-        int FirstSeq; // the position of the query sequence in Alignment al\r
-        boolean noMsa = true; // set if no MSA has been returned by JPred\r
-\r
-        if (this.msa!=null && result.getAligfile()!=null) {\r
-          // we ignore the returned alignment if we only predicted on a single sequence\r
-          String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), "Paste");\r
-          if (jalview.io.FormatAdapter.formats.contains(format))\r
+        // OutputHeader = output.getText();\r
+        if (result.isFailed())\r
+        {\r
+          OutputHeader += "Job failed.\n";\r
+        }\r
+        if (result.getStatus() != null)\r
+        {\r
+          OutputHeader += "\n" + result.getStatus();\r
+        }\r
+        if (result.getPredfile() != null)\r
+        {\r
+          OutputHeader += "\n" + result.getPredfile();\r
+          // JBPNote The returned files from a webservice could be hidden behind icons in the monitor window that, when clicked, pop up their corresponding data\r
+        }\r
+        if (result.getAligfile() != null)\r
+        {\r
+          OutputHeader += "\n" + result.getAligfile();\r
+        }\r
+        wsInfo.setProgressText(OutputHeader);\r
+        try\r
+        {\r
+          // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");\r
+          jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.\r
+              getPredfile(), "Paste");\r
+          SequenceI[] preds = prediction.getSeqsAsArray();\r
+          Alignment al;\r
+          int FirstSeq; // the position of the query sequence in Alignment al\r
+          boolean noMsa = true; // set if no MSA has been returned by JPred\r
+\r
+          if (this.msa != null && result.getAligfile() != null)\r
           {\r
-            al = new Alignment(jalview.io.FormatAdapter.readFile(result.getAligfile(),"Paste",format));\r
-            noMsa = false;\r
-            FirstSeq = 0;\r
+            // we ignore the returned alignment if we only predicted on a single sequence\r
+            String format = jalview.io.IdentifyFile.Identify(result.getAligfile(),\r
+                "Paste");\r
+            if (jalview.io.FormatAdapter.formats.contains(format))\r
+            {\r
+              al = new Alignment(jalview.io.FormatAdapter.readFile(result.\r
+                  getAligfile(), "Paste", format));\r
+              noMsa = false;\r
+              FirstSeq = 0;\r
+            }\r
+            else\r
+            {\r
+              throw (new Exception("Unknown format 'format' for file : \n" +\r
+                                   result.getAligfile()));\r
+            }\r
+\r
           }\r
           else\r
           {\r
-            throw (new Exception("Unknown format 'format' for file : \n" +\r
-                             result.getAligfile()));\r
+            al = new Alignment(preds);\r
+            FirstSeq = prediction.getQuerySeqPosition();\r
           }\r
 \r
-        } else {\r
-          al = new Alignment(preds);\r
-          FirstSeq = prediction.getQuerySeqPosition();\r
-        }\r
-\r
-        if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al.getSequenceAt(FirstSeq), SequenceInfo))\r
-          throw (new Exception("Couldn't recover sequence properties for JNet Query sequence!"));\r
-\r
-        AlignmentAnnotation annot;\r
-        Annotation [] annotations = null;\r
-        int i = 0;\r
-        int width = preds[0].getSequence().length();\r
+          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(al.getSequenceAt(\r
+              FirstSeq), SequenceInfo))\r
+          {\r
+            throw (new Exception(\r
+                "Couldn't recover sequence properties for JNet Query sequence!"));\r
+          }\r
 \r
+          AlignmentAnnotation annot;\r
+          Annotation[] annotations = null;\r
+          int i = 0;\r
+          int width = preds[0].getSequence().length();\r
 \r
-        int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
+          int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
 \r
-        if (gapmap.length!=width) {\r
-          throw (new Exception("Jnet Client Error\nNumber of residues in supposed query sequence :\n"\r
-                               +al.getSequenceAt(FirstSeq).getName()+"\n"\r
-                               +al.getSequenceAt(FirstSeq).getSequence()\r
-                               +"\nDiffer from number of prediction sites in \n"+result.getPredfile()+"\n"));\r
-        }\r
-        // JBPNote Should also rename the query sequence sometime...\r
-        i=0;\r
-        while (i < preds.length)\r
-        {\r
-          String id = preds[i].getName().toUpperCase();\r
-          if(id.startsWith("LUPAS") || id.startsWith("JNET") || id.startsWith("JPRED"))\r
+          if (gapmap.length != width)\r
           {\r
-            annotations = new Annotation[al.getWidth()];\r
-\r
-            if(id.equals("JNETPRED")\r
-               || id.equals("JNETPSSM")\r
-               || id.equals("JNETFREQ")\r
-               || id.equals("JNETHMM")\r
-               || id.equals("JNETALIGN")\r
-               || id.equals("JPRED"))\r
-            {\r
-              for (int j = 0; j < width; j++)\r
-                annotations[gapmap[j]] = new Annotation("", "", preds[i].getCharAt(j), 0);\r
-            }\r
-            else if(id.equals("JNETCONF"))\r
+            throw (new Exception(\r
+                "Jnet Client Error\nNumber of residues in supposed query sequence :\n"\r
+                + al.getSequenceAt(FirstSeq).getName() + "\n"\r
+                + al.getSequenceAt(FirstSeq).getSequence()\r
+                + "\nDiffer from number of prediction sites in \n" +\r
+                result.getPredfile() + "\n"));\r
+          }\r
+          // JBPNote Should also rename the query sequence sometime...\r
+          i = 0;\r
+          while (i < preds.length)\r
+          {\r
+            String id = preds[i].getName().toUpperCase();\r
+            if (id.startsWith("LUPAS") || id.startsWith("JNET") ||\r
+                id.startsWith("JPRED"))\r
             {\r
-              for (int j = 0; j < width; j++)\r
+              annotations = new Annotation[al.getWidth()];\r
+\r
+              if (id.equals("JNETPRED")\r
+                  || id.equals("JNETPSSM")\r
+                  || id.equals("JNETFREQ")\r
+                  || id.equals("JNETHMM")\r
+                  || id.equals("JNETALIGN")\r
+                  || id.equals("JPRED"))\r
               {\r
-                float value = Float.parseFloat(preds[i].getCharAt(j)+"");\r
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "",preds[i].getCharAt(j),value);\r
+                for (int j = 0; j < width; j++)\r
+                {\r
+                  annotations[gapmap[j]] = new Annotation("", "",\r
+                      preds[i].getCharAt(j), 0);\r
+                }\r
               }\r
-            }\r
-            else\r
-            {\r
-              for (int j = 0; j < width; j++) {\r
-                annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j)+"", "", ' ', 0);\r
+              else if (id.equals("JNETCONF"))\r
+              {\r
+                for (int j = 0; j < width; j++)\r
+                {\r
+                  float value = Float.parseFloat(preds[i].getCharAt(j) + "");\r
+                  annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +\r
+                      "", "", preds[i].getCharAt(j), value);\r
+                }\r
+              }\r
+              else\r
+              {\r
+                for (int j = 0; j < width; j++)\r
+                {\r
+                  annotations[gapmap[j]] = new Annotation(preds[i].getCharAt(j) +\r
+                      "", "", ' ', 0);\r
+                }\r
+              }\r
+\r
+              if (id.equals("JNETCONF"))\r
+              {\r
+                annot = new AlignmentAnnotation(preds[i].getName(),\r
+                                                "JNet Output",\r
+                                                annotations, 0f, 10f, 1);\r
               }\r
-            }\r
 \r
-            if(id.equals("JNETCONF"))\r
-              annot = new AlignmentAnnotation(preds[i].getName(),\r
-                                           "JNet Output",\r
-                                           annotations,0f,10f,1);\r
-\r
-            else   annot = new AlignmentAnnotation(preds[i].getName(),\r
-                                            "JNet Output",\r
-                                            annotations);\r
-            al.addAnnotation(annot);\r
-            if (noMsa)\r
-              al.deleteSequence(preds[i]);\r
+              else\r
+              {\r
+                annot = new AlignmentAnnotation(preds[i].getName(),\r
+                                                "JNet Output",\r
+                                                annotations);\r
+              }\r
+              al.addAnnotation(annot);\r
+              if (noMsa)\r
+              {\r
+                al.deleteSequence(preds[i]);\r
+              }\r
+            }\r
+            i++;\r
           }\r
-          i++;\r
-        }\r
 \r
-        Hashtable scores = prediction.getScores();\r
-      /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),\r
-                            "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
+          Hashtable scores = prediction.getScores();\r
+          /*  addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPH"),\r
+                                "JnetpropH", "Jnet Helix Propensity", 0f,1f,1);\r
 \r
-        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),\r
-                            "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
+            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPB"),\r
+           "JnetpropB", "Jnet Beta Sheet Propensity", 0f,1f,1);\r
 \r
-        addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),\r
-                            "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
-       */\r
-        AlignFrame af = new AlignFrame(al);\r
+            addFloatAnnotations(al, gapmap,  (Vector)scores.get("JNETPROPC"),\r
+                                "JnetpropC", "Jnet Coil Propensity", 0f,1f,1);\r
+           */\r
+          AlignFrame af = new AlignFrame(al);\r
 \r
+          Desktop.addInternalFrame(af,\r
+                                   altitle,\r
+                                   AlignFrame.NEW_WINDOW_WIDTH,\r
+                                   AlignFrame.NEW_WINDOW_HEIGHT);\r
+        }\r
+        catch (Exception ex)\r
+        {\r
+          ex.printStackTrace();\r
+        }\r
 \r
-        Desktop.addInternalFrame(af,\r
-                                 altitle,\r
-                                 AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
-      }catch(Exception ex){ex.printStackTrace();}\r
+      }\r
 \r
     }\r
-\r
   }\r
-}\r
-\r
index faf2faf..91f0786 100755 (executable)
@@ -22,7 +22,7 @@ public class MsaWSClient
      * server is a WSDL2Java generated stub for an archetypal MsaWSI service.
      */
     ext.vamsas.MuscleWS server;
-
+    // JBPNote Nasty object-global state setting methods shouldn't be allowed
   private boolean setWebService(String MsaWSName) {
     if (MsaWServices.info.containsKey(MsaWSName)) {
       WebServiceName = MsaWSName;
@@ -36,6 +36,23 @@ public class MsaWSClient
     }
   }
 
+  private boolean locateWebService() {
+      // TODO: MuscleWS transmuted to generic MsaWS client
+      MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
+      try {
+        this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
+        ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
+      }
+      catch (Exception ex) {
+        wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
+                       +WsURL+"\n"+ex.getMessage());
+        wsInfo.setStatus(wsInfo.ERROR);
+        ex.printStackTrace();
+        return false;
+      }
+      loc.getEngine().setOption("axis","1");
+      return true;
+  }
 
   public MsaWSClient(String MsaWSName, String altitle, SequenceI[] msa, boolean submitGaps, boolean preserveOrder)
   {
@@ -47,21 +64,11 @@ public class MsaWSClient
 
     wsInfo = new jalview.gui.WebserviceInfo(WebServiceJobTitle, WebServiceReference);
 
+    if (!locateWebService())
+      return;
+
     wsInfo.setProgressText(((submitGaps) ? "Re-alignment" : "Alignment")+" of "+altitle+"\nJob details\n");
 
-    // TODO: MuscleWS transmuted to generic MsaWS client
-    MuscleWSServiceLocator loc = new MuscleWSServiceLocator(); // Default
-    try {
-      this.server = (MuscleWS) loc.getMuscleWS(new java.net.URL(WsURL));
-      ((MuscleWSSoapBindingStub) this.server).setTimeout(60000); // One minute timeout
-    }
-    catch (Exception ex) {
-      wsInfo.setProgressText("Serious! "+WebServiceName+" Service location failed\nfor URL :"
-                     +WsURL+"\n"+ex.getMessage());
-      wsInfo.setStatus(wsInfo.ERROR);
-      ex.printStackTrace();
-    }
-    loc.getEngine().setOption("axis","1");
     MsaWSThread musclethread = new MsaWSThread(WebServiceName+" alignment of "+altitle, msa, submitGaps, preserveOrder);
     wsInfo.setthisService(musclethread);
     musclethread.start();