X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fws%2FMsaWSClient.java;h=eb6ee388d91d90b1937bb9491b8a13d1d190ff1e;hb=aad4f693fc478138fd225741acf1f8d44defd162;hp=49c879b4d1d7748e515ee4b498cd4f0b8e79eb5d;hpb=7570956d4b58f313d402cdd0507737c0628f1544;p=jalview.git

diff --git a/src/jalview/ws/MsaWSClient.java b/src/jalview/ws/MsaWSClient.java
index 49c879b..eb6ee38 100755
--- a/src/jalview/ws/MsaWSClient.java
+++ b/src/jalview/ws/MsaWSClient.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -63,7 +63,7 @@ public class MsaWSClient
                      Alignment seqdataset,
                      AlignFrame _alignFrame)
   {
-
+    super();
     alignFrame = _alignFrame;
     if (!sh.getAbstractName().equals("MsaWS"))
     {
@@ -76,7 +76,7 @@ public class MsaWSClient
       return;
     }
 
-    if ((wsInfo = this.setWebService(sh))==null)
+    if ((wsInfo = setWebService(sh))==null)
      {
        JOptionPane.showMessageDialog(Desktop.desktop,
                                      "The Multiple Sequence Alignment Service named " +
@@ -102,8 +102,10 @@ public class MsaWSClient
     wsInfo.setProgressText( ( (submitGaps) ? "Re-alignment" : "Alignment") +
                            " of " + altitle + "\nJob details\n");
 
-    MsaWSThread musclethread = new MsaWSThread(WebServiceName +
-                                               " alignment of " + altitle, msa,
+    MsaWSThread musclethread = new MsaWSThread(server, WsURL, wsInfo, alignFrame,
+                                               WebServiceName,
+                                               WebServiceName+" alignment of " + altitle,
+                                               msa,
                                                submitGaps, preserveOrder, seqdataset);
     wsInfo.setthisService(musclethread);
     musclethread.start();
@@ -150,393 +152,4 @@ public class MsaWSClient
   {
     return "Multiple Sequence Alignment";
   }
-
-  protected class MsaWSThread
-      extends Thread implements WSClientI
-  {
-    String ServiceName = WebServiceName;
-    String OutputHeader;
-    vamsas.objects.simple.MsaResult result = null;
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
-        SequenceSet();
-    Hashtable SeqNames = null;
-    boolean submitGaps = false; // pass sequences including gaps to alignment service
-    boolean preserveOrder = true; // and always store and recover sequence order
-    String jobId;
-    String alTitle; // name which will be used to form new alignment window.
-    int allowedServerExceptions = 3; // thread dies if too many exceptions.
-    boolean jobComplete = false;
-
-    Alignment dataset; // dataset to which the new alignment will be associated.
-
-    MsaWSThread(String title, AlignmentView _msa, boolean subgaps,
-                boolean presorder, Alignment seqset)
-    {
-      // jbpnote - transformation should be above here - this is per sequence set contig, not for many contigs.
-      alTitle = title;
-      submitGaps = subgaps;
-      preserveOrder = presorder;
-      dataset = seqset;
-      OutputHeader = wsInfo.getProgressText();
-      SeqNames = new Hashtable();
-      SeqCigar[] msa = _msa.getSequences();
-      vamsas.objects.simple.Sequence[] seqarray = new vamsas.objects.simple.
-          Sequence[msa.length];
-
-      for (int i = 0,n=0; i < msa.length; i++)
-      {
-        String newname = jalview.analysis.SeqsetUtils.unique_name(i);
-        SequenceI mseq = msa[i].getSeq('-');
-        // uniquify as we go
-        // TODO: JBPNote: this is a ubiquitous transformation - set of jalview seq objects to vamsas sequences with name preservation
-        SeqNames.put(newname,
-                     jalview.analysis.SeqsetUtils.SeqCharacterHash(mseq));
-        seqarray[i] = new vamsas.objects.simple.Sequence();
-        seqarray[i].setId(newname);
-        seqarray[i].setSeq( (submitGaps) ? mseq.getSequence()
-                           : AlignSeq.extractGaps(
-                               jalview.util.Comparison.GapChars,
-                               mseq.getSequence()));
-      }
-
-      this.seqs = new vamsas.objects.simple.SequenceSet();
-      this.seqs.setSeqs(seqarray);
-    }
-
-    public boolean isCancellable()
-    {
-      return true;
-    }
-
-    public void cancelJob()
-    {
-      if ( (jobId != null) && !jobId.equals("") && !jobComplete)
-      {
-        String cancelledMessage = "";
-
-        try
-        {
-          vamsas.objects.simple.WsJobId cancelledJob = server.cancel(jobId);
-
-          if (cancelledJob.getStatus() == 2)
-          {
-            // CANCELLED_JOB
-            cancelledMessage = "Job cancelled.";
-            wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
-            jobComplete = true;
-            jobsRunning--;
-            result = null;
-          }
-          else if (cancelledJob.getStatus() == 3)
-          {
-            // VALID UNSTOPPABLE JOB
-            cancelledMessage +=
-                "Server cannot cancel this job. just close the window.\n";
-          }
-
-          if (cancelledJob.getJobId() != null)
-          {
-            cancelledMessage += ("[" + cancelledJob.getJobId() +
-                                 "]");
-          }
-
-          cancelledMessage += "\n";
-        }
-        catch (Exception exc)
-        {
-          cancelledMessage +=
-              ("\nProblems cancelling the job : Exception received...\n" +
-               exc + "\n");
-          exc.printStackTrace();
-        }
-
-        wsInfo.setProgressText(OutputHeader + cancelledMessage + "\n");
-      }
-      else
-      {
-        if (!jobComplete)
-        {
-          wsInfo.setProgressText(OutputHeader +
-                                 "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
-        }
-      }
-    }
-
-    public void run()
-    {
-      StartJob();
-
-      while (!jobComplete && (allowedServerExceptions > 0))
-      {
-        try
-        {
-          if ( (result = server.getResult(jobId)) == null)
-          {
-            throw (new Exception(
-                "Timed out when communicating with server\nTry again later.\n"));
-          }
-          jalview.bin.Cache.log.debug("Result state " + result.getState() +
-                                        "(ServerError=" + result.isServerError() +
-                                        ")");
-          if (result.isRunning())
-          {
-            wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-          }
-          else if (result.isQueued())
-          {
-            wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-          }
-
-          if (result.isFinished())
-          {
-            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-            wsInfo.showResultsNewFrame.addActionListener(new java.awt.event.ActionListener()
-                {
-                  public void actionPerformed(java.awt.event.ActionEvent evt)
-                  {
-                    displayResults(true);
-                  }
-                });
-           wsInfo.mergeResults.addActionListener(new java.awt.event.ActionListener()
-                {
-                  public void actionPerformed(java.awt.event.ActionEvent evt)
-                  {
-                    displayResults(false);
-                  }
-                });
-           wsInfo.setResultsReady();
-            parseResult();
-            jobComplete = true;
-            jobsRunning--;
-          }
-          else
-          {
-            if (result.getStatus() != null)
-            {
-              wsInfo.setProgressText(OutputHeader + "\n"+   result.getStatus());
-            }
-            if (result.isServerError())
-            {
-              jobComplete = true;
-              jobsRunning--;
-
-              break;
-            }
-            if (! (result.isJobFailed() || result.isServerError() ||
-                   result.isBroken() || result.isFailed()))
-            {
-              Thread.sleep(5000);
-
-              //  System.out.println("I'm alive "+seqid+" "+jobid);
-            }
-            else
-            {
-              jobComplete = true;
-              jobsRunning--;
-              break;
-            }
-          }
-        }
-        catch (Exception ex)
-        {
-          allowedServerExceptions--;
-          wsInfo.appendProgressText("\n" + ServiceName +
-                                    " Server exception!\n" + ex.getMessage());
-          System.err.println(ServiceName + " Server exception: " +
-                             ex.getMessage());
-
-          //          ex.printStackTrace(); JBPNote Debug
-          try
-          {
-            if (allowedServerExceptions > 0)
-            {
-              Thread.sleep(5000);
-            }
-          }
-          catch (InterruptedException ex1)
-          {
-          }
-        }
-        catch(OutOfMemoryError er)
-        {
-          jobComplete = true;
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-          JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "Out of memory handling result!!"
-             +"\nSee help files for increasing Java Virtual Machine memory."
-             ,"Out of memory", JOptionPane.WARNING_MESSAGE );
-          System.out.println("MsaWSClient: "+er);
-          System.gc();
-        }
-      }
-
-      if (allowedServerExceptions == 0)
-      {
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-      }
-      else
-      {
-        if (result != null)
-        {
-          if ( !(result.isJobFailed() || result.isServerError()))
-          {
-            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-          }
-
-          if (result.isBroken() || result.isFailed())
-          {
-            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-          }
-
-          if (result.isServerError())
-          {
-            wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-          }
-        }
-      }
-    }
-
-    void StartJob()
-    {
-      try
-      {
-        vamsas.objects.simple.WsJobId jobsubmit = server.align(seqs);
-
-        if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
-        {
-          jobId = jobsubmit.getJobId();
-          System.out.println(WsURL + " Job Id '" + jobId + "'");
-        }
-        else
-        {
-          if (jobsubmit == null)
-          {
-            throw new Exception("Server at " + WsURL +
-                                " returned null object, it probably cannot be contacted. Try again later ?");
-          }
-
-          throw new Exception(jobsubmit.getJobId());
-        }
-      }
-      catch (Exception e)
-      {
-        // TODO: JBPNote catch timeout or other fault types explicitly
-        // For unexpected errors
-        System.err.println(WebServiceName +
-                           "Client: Failed to submit the sequences for alignment (probably a server side problem)\n" +
-                           "When contacting Server:" + WsURL + "\n" +
-                           e.toString() +
-                           "\n");
-        this.allowedServerExceptions = 0;
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
-        wsInfo.appendProgressText(
-            "Failed to submit sequences for alignment.\n" +
-            "It is most likely that there is a problem with the server.\n" +
-            "Just close the window\n");
-
-        // e.printStackTrace(); // TODO: JBPNote DEBUG
-      }
-    }
-
-    private jalview.datamodel.Sequence[] getVamsasAlignment(
-        vamsas.objects.simple.Alignment valign)
-    {
-      vamsas.objects.simple.Sequence[] seqs = valign.getSeqs().getSeqs();
-      jalview.datamodel.Sequence[] msa = new jalview.datamodel.Sequence[seqs.
-          length];
-
-      for (int i = 0, j = seqs.length; i < j; i++)
-      {
-        msa[i] = new jalview.datamodel.Sequence(seqs[i].getId(),
-                                                seqs[i].getSeq());
-      }
-
-      return msa;
-    }
-
-    void parseResult()
-    {
-
-      try
-      {
-        // OutputHeader = output.getText();
-        if (result.isFailed())
-        {
-          OutputHeader += "Job failed.\n";
-        }
-
-        if (result.getStatus() != null)
-        {
-          OutputHeader += ("\n" + result.getStatus());
-        }
-
-        if (result.getMsa() != null)
-        {
-          OutputHeader += "\nAlignment Object Method Notes\n";
-
-          String[] lines = result.getMsa().getMethod();
-
-          for (int line = 0; line < lines.length; line++)
-          {
-            OutputHeader += (lines[line] + "\n");
-          }
-
-          // JBPNote The returned files from a webservice could be
-          // hidden behind icons in the monitor window that,
-          // when clicked, pop up their corresponding data
-        }
-
-        wsInfo.setProgressText(OutputHeader);
-      }
-      catch (Exception ex)
-      {
-        ex.printStackTrace();
-      }
-    }
-
-    void displayResults(boolean newFrame)
-    {
-      SequenceI [] seqs = getVamsasAlignment(result.getMsa());
-
-      if (seqs != null)
-       {
-         AlignmentOrder msaorder = new AlignmentOrder(seqs);
-
-         if (preserveOrder)
-         {
-           jalview.analysis.AlignmentSorter.recoverOrder(seqs);
-         }
-
-         jalview.analysis.SeqsetUtils.deuniquify(SeqNames, seqs);
-
-         Alignment al = new Alignment(seqs);
-         if (dataset!=null)
-         {
-           al.setDataset(dataset);
-         }
-
-         if(newFrame)
-         {
-           // TODO: JBPNote Should also rename the query sequence sometime...
-           AlignFrame af = new AlignFrame(al);
-
-         //>>>This is a fix for the moment, until a better solution is found!!<<<
-           af.getFeatureRenderer().transferSettings(alignFrame.getFeatureRenderer());
-
-           af.addSortByOrderMenuItem(ServiceName + " Ordering",
-                                     msaorder);
-
-           Desktop.addInternalFrame(af, alTitle,
-                                    AlignFrame.NEW_WINDOW_WIDTH,
-                                    AlignFrame.NEW_WINDOW_HEIGHT);
-
-         }
-         else
-         {
-           System.out.println("MERGE WITH OLD FRAME");
-
-         }
-       }
-    }
-  }
 }