X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FJPredClient.java;h=863e80e2c166f7de7471fa331ac92207239bcb02;hb=4d2e0d36506302cc00677527725bcccbdf27d766;hp=55e65a50c9158addc367ef8c8964722e1ebafb9a;hpb=b2d54d33d6313efd9da96bd7586dfaa7a0d7a182;p=jalview.git

diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java
index 55e65a5..863e80e 100755
--- a/src/jalview/ws/JPredClient.java
+++ b/src/jalview/ws/JPredClient.java
@@ -43,11 +43,12 @@ public class JPredClient
      * @param title String
      * @param msa boolean - true - submit alignment as a sequence profile
      * @param alview AlignmentView
+     * @param viewonly TODO
      */
-    public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame) {
+    public JPredClient(ext.vamsas.ServiceHandle sh, String title, boolean msa, AlignmentView alview, AlignFrame parentFrame, boolean viewonly) {
     super();
     wsInfo=setWebService(sh);
-    startJPredClient(title, msa, alview, parentFrame);
+    startJPredClient(title, msa, alview, parentFrame, viewonly);
 
   }
   /**
@@ -59,9 +60,10 @@ public class JPredClient
    * @param title String
    * @param msa boolean
    * @param alview AlignmentView
+   * @param viewonly if true then the prediction will be made just on the concatenated visible regions
    */
   private void startJPredClient(String title, boolean msa,
-                                jalview.datamodel.AlignmentView alview, AlignFrame parentFrame)
+                                jalview.datamodel.AlignmentView alview, AlignFrame parentFrame, boolean viewonly)
   {
     AlignmentView input = alview;
     if (wsInfo == null)
@@ -74,30 +76,68 @@ public class JPredClient
       Cache.log.warn("Couldn't find a Jpred webservice to invoke!");
       return;
     }
+    SeqCigar[] msf=null;
+    SequenceI seq=null;
+    int[] delMap=null;
+    // original JNetClient behaviour - submit full length of sequence or profile
+    // and mask result.
+    msf = input.getSequences();
+    seq = msf[0].getSeq('-');
+
+    if (viewonly) {
+      int[] viscontigs = alview.getVisibleContigs();
+      int spos=0;
+      int i=0;
+      if (viscontigs!=null) {
+        // Construct the delMap - mapping from the positions within the input to Jnet to the contigs in the original sequence
+
+        delMap = new int[seq.getEnd()-seq.getStart()+1];
+        int gapMap[] = seq.gapMap();
+        for (int contig = 0; contig<viscontigs.length; contig += 2)
+        {
 
-    SeqCigar[] msf = input.getSequences();
-    SequenceI seq = msf[0].getSeq('-');
+          while (spos<gapMap.length && gapMap[spos]<viscontigs[contig]) {
+            spos++;
+          }
+          while (spos<gapMap.length && gapMap[spos]<=viscontigs[contig+1]) {
+            delMap[i++] = spos++;
+          }
+        }
+        int tmap[] = new int[i];
+        System.arraycopy(delMap, 0, tmap, 0, i);
+        delMap=tmap;
+      }
+    }
     if (msa && msf.length > 1)
     {
 
-      String altitle = "JNet prediction on " + seq.getName() +
+      String altitle = "JNet prediction on "+(viewonly?"visible ":"") + seq.getName() +
           " using alignment from " + title;
 
-      wsInfo.setProgressText("Job details for MSA based prediction (" +
-                             title + ") on sequence :\n>" + seq.getName() +
-                             "\n" +
-                             AlignSeq.extractGaps("-. ", seq.getSequence()) +
-                             "\n");
       SequenceI aln[] = new SequenceI[msf.length];
       for (int i = 0, j = msf.length; i < j; i++)
       {
         aln[i] = msf[i].getSeq('-');
       }
 
-      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
 
+      Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.uniquify(aln, true);
+      if (viewonly) {
+        // Remove hidden regions from sequence objects.
+        String seqs[] = alview.getSequenceStrings('-');
+        for (int i = 0, j = msf.length; i < j; i++)
+        {
+          aln[i].setSequence(seqs[i]);
+        }
+        seq.setSequence(seqs[0]);
+      }
+      wsInfo.setProgressText("Job details for "+(viewonly?"visible ":"")+"MSA based prediction (" +
+          title + ") on sequence :\n>" + seq.getName() +
+          "\n" +
+          AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
+          "\n");
       JPredThread jthread = new JPredThread(wsInfo, altitle, server,
-                                            SequenceInfo, aln, alview, parentFrame);
+                                            SequenceInfo, aln, delMap, alview, parentFrame, WsURL);
       wsInfo.setthisService(jthread);
       jthread.start();
     }
@@ -105,19 +145,23 @@ public class JPredClient
     {
       if (!msa && msf.length>1)
         throw new Error("Implementation Error! Multiple single sequence prediction jobs are not yet supported.");
-      wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
-                             seq.getName() + "\n" +
-                             AlignSeq.extractGaps("-. ", seq.getSequence()) +
-                             "\n");
-      String altitle = "JNet prediction for sequence " + seq.getName() +
+      String altitle = "JNet prediction for "+(viewonly?"visible ":"")+"sequence " + seq.getName() +
           " from " +
           title;
-
+      String seqname = seq.getName();
       Hashtable SequenceInfo = jalview.analysis.SeqsetUtils.SeqCharacterHash(
           seq);
-
-      JPredThread jthread = new JPredThread(wsInfo, altitle, server,
-                                            SequenceInfo, seq, alview, parentFrame);
+      if (viewonly) {
+        // Remove hidden regions from input sequence
+        String seqs[] = alview.getSequenceStrings('-');
+        seq.setSequence(seqs[0]);
+      }
+      wsInfo.setProgressText("Job details for prediction on "+(viewonly?"visible ":"")+"sequence :\n>" +
+          seqname + "\n" +
+          AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
+          "\n");
+      JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL,
+                                            SequenceInfo, seq, delMap, alview, parentFrame);
       wsInfo.setthisService(jthread);
       jthread.start();
     }
@@ -159,7 +203,7 @@ public class JPredClient
 
     wsInfo.setProgressText("Job details for MSA based prediction (" +
                            title + ") on sequence :\n>" + seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
                            "\n");
     SequenceI aln[] = new SequenceI[msf.length];
     for (int i = 0, j = msf.length; i < j; i++)
@@ -175,7 +219,7 @@ public class JPredClient
       return;
     }
 
-    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, parentFrame);
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, aln,null, null, parentFrame, WsURL);
     wsInfo.setthisService(jthread);
     jthread.start();
   }
@@ -188,7 +232,7 @@ public class JPredClient
     }
     wsInfo.setProgressText("Job details for prediction on sequence :\n>" +
                            seq.getName() + "\n" +
-                           AlignSeq.extractGaps("-. ", seq.getSequence()) +
+                           AlignSeq.extractGaps("-. ", seq.getSequenceAsString()) +
                            "\n");
     String altitle = "JNet prediction for sequence " + seq.getName() + " from " +
         title;
@@ -201,7 +245,7 @@ public class JPredClient
       return;
     }
 
-    JPredThread jthread = new JPredThread(wsInfo, altitle, server, SequenceInfo, seq,null, parentFrame);
+    JPredThread jthread = new JPredThread(wsInfo, altitle, server, WsURL, SequenceInfo, seq,null, null, parentFrame);
     wsInfo.setthisService(jthread);
     jthread.start();
   }
@@ -251,520 +295,5 @@ public class JPredClient
 
     return server;
   }
-
-  class JPredThread
-      extends WSThread
-      implements WSClientI
-  {
-    class JPredJob
-        extends WSThread.WSJob
-    {
-
-      vamsas.objects.simple.Sequence sequence;
-      vamsas.objects.simple.Msfalignment msa;
-      java.util.Hashtable SequenceInfo = null;
-      /**
-       *
-       * @return true if getResultSet will return a valid alignment and prediction result.
-       */
-      public boolean hasResults()
-      {
-        if (subjobComplete && result != null && result.isFinished()
-            && ( (JpredResult) result).getPredfile() != null &&
-            ( (JpredResult) result).getAligfile() != null)
-        {
-          return true;
-        }
-        return false;
-      }
-
-      boolean hasValidInput()
-      {
-        if (sequence != null)
-        {
-          return true;
-        }
-        return false;
-      }
-
-      public Alignment getResultSet()
-          throws Exception
-      {
-        if (result == null || !result.isFinished())
-        {
-          return null;
-        }
-        Alignment al = null;
-        int FirstSeq = -1; // the position of the query sequence in Alignment al
-
-        JpredResult result = (JpredResult)this.result;
-
-        jalview.bin.Cache.log.debug("Parsing output from JNet job.");
-        // JPredFile prediction = new JPredFile("C:/JalviewX/files/jpred.txt", "File");
-        jalview.io.JPredFile prediction = new jalview.io.JPredFile(result.
-            getPredfile(),
-            "Paste");
-        SequenceI[] preds = prediction.getSeqsAsArray();
-        jalview.bin.Cache.log.debug("Got prediction profile.");
-
-        if ( (this.msa != null) && (result.getAligfile() != null))
-        {
-          jalview.bin.Cache.log.debug("Getting associated alignment.");
-          // we ignore the returned alignment if we only predicted on a single sequence
-          String format = new jalview.io.IdentifyFile().Identify(result.
-              getAligfile(),
-              "Paste");
-
-          if (jalview.io.FormatAdapter.isValidFormat(format))
-          {
-            al = new Alignment(new FormatAdapter().readFile(result.getAligfile(),
-                "Paste", format));
-            SequenceI sqs[] = new SequenceI[al.getHeight()];
-            for (int i = 0, j = al.getHeight(); i < j; i++)
-            {
-              sqs[i] = al.getSequenceAt(i);
-            }
-            if (!jalview.analysis.SeqsetUtils.deuniquify( (Hashtable)
-                SequenceInfo, sqs))
-            {
-              throw (new Exception(
-                  "Couldn't recover sequence properties for alignment."));
-            }
-
-            FirstSeq = 0;
-            al.setDataset(null);
-
-            jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
-                                                          false);
-
-          }
-          else
-          {
-            throw (new Exception(
-                "Unknown format "+format+" for file : \n" +
-                result.getAligfile()));
-          }
-        }
-        else
-        {
-          al = new Alignment(preds);
-          FirstSeq = prediction.getQuerySeqPosition();
-          if (!jalview.analysis.SeqsetUtils.SeqCharacterUnhash(
-              al.getSequenceAt(FirstSeq), SequenceInfo))
-          {
-            throw (new Exception(
-                "Couldn't recover sequence properties for JNet Query sequence!"));
-          } else {
-            al.setDataset(null);
-            jalview.io.JnetAnnotationMaker.add_annotation(prediction, al, FirstSeq,
-                true);
-          }
-        }
-
-        return al; // , FirstSeq, noMsa};
-      }
-      public JPredJob(Hashtable SequenceInfo, SequenceI seq)
-      {
-        super();
-        String sq = AlignSeq.extractGaps(Comparison.GapChars, seq.getSequence());
-        if (sq.length() >= 20)
-        {
-          this.SequenceInfo = SequenceInfo;
-          sequence = new vamsas.objects.simple.Sequence();
-          sequence.setId(seq.getName());
-          sequence.setSeq(sq);
-        }
-      }
-
-      public JPredJob(Hashtable SequenceInfo, SequenceI[] msf)
-      {
-        this(SequenceInfo, msf[0]);
-        if (sequence != null)
-        {
-          if (msf.length > 1)
-          {
-            msa = new vamsas.objects.simple.Msfalignment();
-            jalview.io.PileUpfile pileup = new jalview.io.PileUpfile();
-            msa.setMsf(pileup.print(msf));
-          }
-        }
-      }
-    }
-    ext.vamsas.Jpred server;
-    String altitle = "";
-    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, AlignmentView alview, AlignFrame alframe) {
-      this.altitle = altitle;
-      this.server = server;
-      this.wsInfo = wsinfo;
-      this.input = alview;
-      this.alignFrame = alframe;
-    }
-
-//    String OutputHeader;
-//    vamsas.objects.simple.JpredResult result;
-
-    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo,SequenceI seq, AlignmentView alview, AlignFrame alframe)
-    {
-      this(wsinfo, altitle, server,alview, alframe);
-      JPredJob job = new JPredJob(SequenceInfo, seq);
-      if (job.hasValidInput())
-      {
-        OutputHeader = wsInfo.getProgressText();
-        jobs = new WSJob[]
-            {
-            job};
-        job.jobnum = 0;
-      }
-    }
-
-    JPredThread(WebserviceInfo wsinfo, String altitle, ext.vamsas.Jpred server, Hashtable SequenceInfo, SequenceI[] msf, AlignmentView alview, AlignFrame alframe)
-    {
-      this(wsinfo, altitle, server,alview, alframe);
-      JPredJob job = new JPredJob(SequenceInfo, msf);
-      if (job.hasValidInput())
-      {
-        jobs = new WSJob[]
-            {
-            job};
-        OutputHeader = wsInfo.getProgressText();
-        job.jobnum = 0;
-      }
-    }
-
-    /*
-        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"));
-              }
-              if (result.getState()==0)
-                jalview.bin.Cache.log.debug("Finished "+jobId);
-              if (result.isRunning())
-              {
-                wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-              }
-              if (result.isQueued())
-              {
-                wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-              }
-
-              wsInfo.setProgressText(OutputHeader + "\n" +
-                                     result.getStatus());
-
-              if (result.isFinished())
-              {
-
-                parseResult();
-                jobComplete = true;
-                jobsRunning--;
-              } else {
-                // catch exceptions
-                if (! (result.isJobFailed() || result.isServerError()))
-                {
-                  try
-                  {
-                    Thread.sleep(5000);
-                  }
-                  catch (InterruptedException ex1)
-                  {
-                  }
-
-                  //  System.out.println("I'm alive "+seqid+" "+jobid);
-                }
-                else
-                {
-                  wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-                  jobsRunning--;
-                  jobComplete = true;
-                }
-              }
-            }
-            catch (Exception ex)
-            {
-              allowedServerExceptions--;
-
-              wsInfo.appendProgressText("\nJPredWS Server exception!\n" +
-                                        ex.getMessage());
-
-              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("JPredClient: "+er);
-              System.gc();
-            }
-          }
-          if (result!=null)
-            if (! (result.isJobFailed() || result.isServerError()))
-            {
-              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-            }
-            else
-            {
-              wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-            }
-        }
-     */
-    void StartJob(WSJob j)
-    {
-      if (! (j instanceof JPredJob))
-      {
-        throw new Error("Implementation error - StartJob(JpredJob) called on " +
-                        j.getClass());
-      }
-      try
-      {
-        JPredJob job = (JPredJob) j;
-        if (job.msa != null)
-        {
-          job.jobId = server.predictOnMsa(job.msa);
-        }
-        else
-          if (job.sequence!=null)
-          {
-            job.jobId = server.predict(job.sequence); // debug like : job.jobId = "/jobs/www-jpred/jp_Yatat29";//
-          }
-
-        if (job.jobId != null)
-        {
-          if (job.jobId.startsWith("Broken"))
-          {
-            job.result = (vamsas.objects.simple.Result)new JpredResult();
-            job.result.setInvalid(true);
-            job.result.setStatus("Submission " + job.jobId);
-          }
-          else
-          {
-            job.submitted = true;
-            job.subjobComplete = false;
-            Cache.log.info(WsURL + " Job Id '" + job.jobId + "'");
-          }
-        }
-        else
-        {
-          throw new Exception("Server timed out - try again later\n");
-        }
-      }
-      catch (Exception e)
-      {
-        if (e.getMessage().indexOf("Exception") > -1)
-        {
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
-          wsInfo.setProgressText(j.jobnum,
-                                 "Failed to submit the prediction. (Just close the window)\n"
-                                 +
-                                 "It is most likely that there is a problem with the server.\n");
-          System.err.println(
-              "JPredWS Client: Failed to submit the prediction. Quite possibly because of a server error - see below)\n" +
-              e.getMessage() + "\n");
-
-          jalview.bin.Cache.log.warn("Server Exception", e);
-        }
-        else
-        {
-          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-          // JBPNote - this could be a popup informing the user of the problem.
-          wsInfo.appendProgressText(j.jobnum,
-                                    "Failed to submit the prediction:\n"
-                                    + e.getMessage() +
-                                    wsInfo.getProgressText());
-
-          jalview.bin.Cache.log.debug("Failed Submission of job " + j.jobnum, e);
-
-        }
-        j.allowedServerExceptions = -1;
-        j.subjobComplete = true;
-      }
-    }
-
-    /*  private void addFloatAnnotations(Alignment al, int[] gapmap,
-                                       Vector values, String Symname,
-                                       String Visname, float min,
-                                       float max, int winLength)
-      {
-        Annotation[] annotations = new Annotation[al.getWidth()];
-
-        for (int j = 0; j < values.size(); j++)
-        {
-          float value = Float.parseFloat(values.get(j).toString());
-          annotations[gapmap[j]] = new Annotation("", value + "", ' ',
-                                                  value);
-        }
-
-        al.addAnnotation(new AlignmentAnnotation(Symname, Visname,
-     annotations, min, max, winLength));
-      }*/
-
-    void parseResult()
-    {
-      int results = 0; // number of result sets received
-      JobStateSummary finalState = new JobStateSummary();
-      try
-      {
-        for (int j = 0; j < jobs.length; j++)
-        {
-          finalState.updateJobPanelState(wsInfo, OutputHeader, jobs[j]);
-          if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
-          {
-            results++;
-          }
-        }
-      }
-      catch (Exception ex)
-      {
-
-        Cache.log.error("Unexpected exception when processing results for " +
-                        altitle, ex);
-        wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
-      }
-      if (results > 0)
-      {
-        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();
-      }
-      else
-      {
-        wsInfo.setFinishedNoResults();
-      }
-    }
-
-    void displayResults(boolean newWindow)
-    {
-      // TODO: cope with multiple subjobs.
-      if (jobs != null)
-      {
-        Alignment res = null;
-        boolean msa=false;
-        for (int jn = 0; jn < jobs.length; jn++)
-        {
-          Alignment jobres = null;
-          JPredJob j = (JPredJob) jobs[jn];
-
-          if (j.hasResults())
-          {
-            // hack - we only deal with all single seuqence predictions or all profile predictions
-            msa = (j.msa!=null) ? true : msa;
-            try
-            {
-              jalview.bin.Cache.log.debug("Parsing output of job " + jn);
-              jobres = j.getResultSet();
-              jalview.bin.Cache.log.debug("Finished parsing output.");
-              if (jobs.length==1)
-                res = jobres;
-              else {
-                  // do merge with other job results
-                  throw new Error("Multiple JNet subjob merging not yet implemented.");
-              }
-            }
-            catch (Exception e)
-            {
-              jalview.bin.Cache.log.error(
-                  "JNet Client: JPred Annotation Parse Error",
-                  e);
-              wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
-              wsInfo.appendProgressText(j.jobnum,
-                                        OutputHeader + "\n" +
-                                        j.result.getStatus() +
-                                        "\nInvalid JNet job result data!\n" +
-                                        e.getMessage());
-              j.result.setBroken(true);
-            }
-          }
-        }
-
-        if (res != null)
-        {
-          if (newWindow)
-          {
-            AlignFrame af;
-           if (input==null) {
-             af = new AlignFrame(res);
-           } else {
-             java.lang.Object[] alandcolsel = input.getAlignmentAndColumnSelection(alignFrame.getViewport().getGapCharacter());
-
-             if (((SequenceI[])alandcolsel[0])[0].getLength()!=res.getWidth()) {
-               if (msa) {
-                 throw new Error("Implementation Error! ColumnSelection from input alignment will not map to result alignment!");
-               } else {
-                 // test this.
-                 ((ColumnSelection) alandcolsel[1]).pruneDeletions(ShiftList.parseMap(((SequenceI[]) alandcolsel[0])[0].gapMap()));//gapMap returns insert list, interpreted as delete list by pruneDeletions
-               }
-             }
-             af = new AlignFrame(res, (ColumnSelection) alandcolsel[1]);
-           }
-            Desktop.addInternalFrame(af, altitle,
-                                     AlignFrame.NEW_WINDOW_WIDTH,
-                                     AlignFrame.NEW_WINDOW_HEIGHT);
-          }
-          else
-          {
-            Cache.log.info("Append results onto existing alignment.");
-          }
-        }
-      }
-    }
-    void pollJob(WSJob job)
-        throws Exception
-    {
-      job.result = server.getresult(job.jobId);
-    }
-    public boolean isCancellable()
-    {
-      return false;
-    }
-
-    public void cancelJob()
-    {
-      throw new Error("Implementation error!");
-    }
-
-    public boolean canMergeResults()
-    {
-      return false;
-    }
-
-  }
 }