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diff --git a/src/jalview/io/JPredClient.java b/src/jalview/io/JPredClient.java
deleted file mode 100755 (executable)
index c463c51..0000000
--- a/src/jalview/io/JPredClient.java
+++ /dev/null
@@ -1,302 +0,0 @@
-package jalview.io;\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
-            }\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.QuerySeqPosition;\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.Scores;\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