Added cancel interface for JPred Client and fixed some messages.

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
new file mode 100755 (executable)
index 0000000..2eecf46
--- /dev/null
+++ b/src/jalview/ws/JPredClient.java
@@ -0,0 +1,304 @@
+package jalview.ws;\r
+\r
+import org.apache.axis.client.*;\r
+import javax.xml.namespace.QName;\r
+import java.util.*;\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
+import javax.swing.*;\r
+import java.util.*;\r
+import java.awt.*;\r
+import jalview.analysis.AlignSeq;\r
+import ext.vamsas.*;\r
+\r
+\r
+public class JPredClient\r
+{\r
+  int jobsRunning = 0;\r
+  ext.vamsas.JpredSoapBindingStub server;\r
+  WebserviceInfo wsInfo;\r
+\r
+  public JPredClient(SequenceI[] msf)\r
+  {\r
+    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",\r
+          "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
+\r
+    SequenceI seq = msf[0];\r
+    wsInfo.setProgressText("Job details for MSA based prediction on sequence :\nName : "\r
+                   + seq.getName() + "\nSequence : "\r
+                   + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
+\r
+\r
+    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
+    try {\r
+      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties\r
+    }\r
+    catch (Exception ex) {\r
+      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
+                     +loc.getjpredAddress()+"\n"+ex.getMessage());\r
+    }\r
+\r
+    JPredThread jthread = new JPredThread(msf);\r
+    jthread.start();\r
+  }\r
+\r
+  public JPredClient(SequenceI seq)\r
+  {\r
+    wsInfo = new WebserviceInfo("JNet secondary structure prediction job",\r
+                                "\"Cuff J. A and Barton G.J (1999) Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction, Proteins 40:502-511\".");\r
+\r
+\r
+    wsInfo.setProgressText("Job details for prediction on sequence :\nName : "\r
+                   + seq.getName() + "\nSequence : " + AlignSeq.extractGaps("-. ",seq.getSequence()) + "\n");\r
+\r
+    JPredWSServiceLocator loc = new JPredWSServiceLocator(); // Default\r
+    try {\r
+      this.server = (JpredSoapBindingStub) loc.getjpred(); // JBPNote will be set from properties\r
+    }\r
+    catch (Exception ex) {\r
+      wsInfo.setProgressText("Serious! JPred Service location failed\nfor URL :"\r
+                     +loc.getjpredAddress()+"\n"+ex.getMessage());\r
+    }\r
+\r
+    JPredThread jthread = new JPredThread(seq);\r
+    jthread.start();\r
+  }\r
+\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
+\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.MSFfile mwrite = new jalview.io.MSFfile();\r
+      this.msa = new ext.vamsas.Msfalignment();\r
+      msa.setMsf(mwrite.print(msf));\r
+    }\r
+\r
+\r
+    public void run()\r
+    {\r
+\r
+      StartJob();\r
+\r
+      while (!jobComplete && (allowedServerExceptions > 0))\r
+      {\r
+        try\r
+        {\r
+          result = server.getresult(jobId);\r
+\r
+         if( result.isRunning() )\r
+           wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);\r
+         else if( result.isQueued() )\r
+           wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);\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
+              Thread.sleep(5000);\r
+              //  System.out.println("I'm alive "+seqid+" "+jobid);\r
+            } else {\r
+              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);\r
+            }\r
+          }\r
+        }\r
+        catch (Exception ex)\r
+        {\r
+          allowedServerExceptions--;\r
+          wsInfo.appendProgressText("\nJPredWS Server exception!\n" + ex.getMessage());\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
+      {\r
+        if (msa!=null)  {\r
+          jobId = server.predictOnMsa(msa);\r
+        } else {\r
+          jobId = server.predict(sequence);\r
+        }\r
+        System.out.println(jobId);\r
+      }\r
+      catch (Exception e)\r
+      {\r
+        System.out.println("JPredWS Client: Failed to submit the prediction\n" +\r
+                           e.toString() + "\n");\r
+        e.printStackTrace();\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
+      {\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
+          {\r
+            al = new Alignment(jalview.io.FormatAdapter.readFile(result.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
+        } else {\r
+          al = new Alignment(preds);\r
+          FirstSeq = prediction.getQuerySeqPosition();\r
+        }\r
+\r
+        AlignmentAnnotation annot;\r
+        Annotation [] annotations = null;\r
+        int i = 0;\r
+        int width = preds[0].getSequence().length();\r
+\r
+\r
+        int[] gapmap = al.getSequenceAt(FirstSeq).gapMap();\r
+        if (gapmap.length!=width) {\r
+          throw (new Exception("Jpred 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
+          {\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
+            {\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)+"", "",preds[i].getCharAt(j),value);\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
+              }\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
+          }\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
+\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
+\r
+\r
+        Desktop.addInternalFrame(af,\r
+                                 "JNet Prediction for sequence ",\r
+                                 AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
+      }catch(Exception ex){ex.printStackTrace();}\r
+\r
+    }\r
+\r
+  }\r
+}\r
+\r