From 129ad37552c4bd5b241e90e0caf8b7f32a32bfb7 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Mon, 14 Aug 2006 12:52:03 +0000
Subject: [PATCH] multiple subjobs can be cancelled and gui only allows
 results when a subjob actually completes.

---
 src/jalview/ws/MsaWSThread.java | 1203 +++++++++++++++++++++++++--------------
 1 file changed, 769 insertions(+), 434 deletions(-)

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 090af4e..803bf44 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -1,95 +1,94 @@
 package jalview.ws;
 
-import jalview.datamodel.AlignmentView;
-import jalview.datamodel.AlignmentOrder;
-import jalview.datamodel.ColumnSelection;
-import jalview.gui.WebserviceInfo;
-import jalview.analysis.AlignSeq;
-import jalview.bin.Cache;
-import jalview.gui.AlignFrame;
-import javax.swing.JOptionPane;
+import java.util.*;
 
-import vamsas.objects.simple.MsaResult;
-import vamsas.objects.simple.Result;
+import javax.swing.*;
+
+import jalview.analysis.*;
+import jalview.bin.*;
+import jalview.datamodel.*;
 import jalview.datamodel.Alignment;
-import jalview.datamodel.SeqCigar;
-import jalview.gui.Desktop;
-import jalview.datamodel.SequenceI;
-import java.util.Hashtable;
-import java.util.Vector;
+import jalview.gui.*;
+import vamsas.objects.simple.MsaResult;
 
 /**
  * <p>
  * Title:
  * </p>
- * 
+ *
  * <p>
  * Description:
  * </p>
- * 
+ *
  * <p>
  * Copyright: Copyright (c) 2004
  * </p>
- * 
+ *
  * <p>
  * Company: Dundee University
  * </p>
- * 
+ *
  * @author not attributable
  * @version 1.0
  */
-class MsaWSThread extends Thread implements WSClientI {
+class MsaWSThread
+    extends Thread implements WSClientI
+{
   jalview.gui.AlignFrame alignFrame;
-  
+
   WebserviceInfo wsInfo = null;
-  
+
   String WebServiceName = null;
-  
+
   String OutputHeader;
   AlignmentView input;
   boolean submitGaps = false; // pass sequences including gaps to alignment
-  
+
   // service
-  
+
   boolean preserveOrder = true; // and always store and recover sequence
-  
+
   // order
-  
-  class MsaWSJob {
+
+  class MsaWSJob
+  {
     int jobnum = 0; // WebServiceInfo pane for this job
-    
+
     String jobId; // ws job ticket
-    
+
     vamsas.objects.simple.MsaResult result = null;
-    
-    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.SequenceSet();
-    
+
+    vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
+        SequenceSet();
+
     /**
      * MsaWSJob
-     * 
+     *
      * @param jobNum
      *            int
      * @param jobId
      *            String
      */
-    public MsaWSJob(int jobNum, SequenceI[] inSeqs) {
+    public MsaWSJob(int jobNum, SequenceI[] inSeqs)
+    {
       this.jobnum = jobNum;
-      if (!prepareInput(inSeqs,2)) {
-        submitted=true;
-        subjobComplete=true;
+      if (!prepareInput(inSeqs, 2))
+      {
+        submitted = true;
+        subjobComplete = true;
         result = new MsaResult();
         result.setFinished(true);
         result.setStatus("Job never ran - input returned to user.");
       }
-        
+
     }
-    
+
     int allowedServerExceptions = 3; // thread dies if too many
-    
+
     // exceptions.
-    boolean submitted=false;
+    boolean submitted = false;
     boolean subjobComplete = false;
-    
+
     Hashtable SeqNames = new Hashtable();
     Vector emptySeqs = new Vector();
     /**
@@ -98,154 +97,217 @@ class MsaWSThread extends Thread implements WSClientI {
      * @param minlen minimum number of residues required for this MsaWS service
      * @return true if seqs contains sequences to be submitted to service.
      */
-    private boolean prepareInput(SequenceI[] seqs, int minlen) {
+    private boolean prepareInput(SequenceI[] seqs, int minlen)
+    {
       int nseqs = 0;
-      if (minlen<0)
+      if (minlen < 0)
+      {
         throw new Error("Implementation error: minlen must be zero or more.");
-      for (int i = 0; i < seqs.length; i++) {
-        if (seqs[i].getEnd()-seqs[i].getStart()>minlen-1) {
+      }
+      for (int i = 0; i < seqs.length; i++)
+      {
+        if (seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
           nseqs++;
         }
       }
-      boolean valid=nseqs>1; // need at least two seqs
-      vamsas.objects.simple.Sequence[] seqarray = 
-          (valid) 
-        ? new vamsas.objects.simple.Sequence[nseqs]
-                                             :null;
-        for (int i = 0, n = 0; i < seqs.length; i++) {
-          
-          String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
-          // for
-          // any
-          // subjob
-          SeqNames.put(newname, jalview.analysis.SeqsetUtils
-              .SeqCharacterHash(seqs[i]));
-          if (valid && seqs[i].getEnd()-seqs[i].getStart()>minlen-1) {
-            seqarray[n] = new vamsas.objects.simple.Sequence();
-            seqarray[n].setId(newname);
-            seqarray[n++].setSeq((submitGaps) ? seqs[i].getSequence()
+      boolean valid = nseqs > 1; // need at least two seqs
+      vamsas.objects.simple.Sequence[] seqarray =
+          (valid)
+          ? new vamsas.objects.simple.Sequence[nseqs]
+          : null;
+      for (int i = 0, n = 0; i < seqs.length; i++)
+      {
+
+        String newname = jalview.analysis.SeqsetUtils.unique_name(i); // same
+        // for
+        // any
+        // subjob
+        SeqNames.put(newname, jalview.analysis.SeqsetUtils
+                     .SeqCharacterHash(seqs[i]));
+        if (valid && seqs[i].getEnd() - seqs[i].getStart() > minlen - 1)
+        {
+          seqarray[n] = new vamsas.objects.simple.Sequence();
+          seqarray[n].setId(newname);
+          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequence()
+                               : AlignSeq.extractGaps(
+                                   jalview.util.Comparison.GapChars, seqs[i]
+                                   .getSequence()));
+        }
+        else
+        {
+          String empty = null;
+          if (seqs[i].getEnd() >= seqs[i].getStart())
+          {
+            empty = (submitGaps) ? seqs[i].getSequence()
                 : AlignSeq.extractGaps(
                     jalview.util.Comparison.GapChars, seqs[i]
-                                                           .getSequence()));
-          } else {
-            String empty=null;
-            if (seqs[i].getEnd()>=seqs[i].getStart()) {
-              empty = (submitGaps) ? seqs[i].getSequence()
-                    : AlignSeq.extractGaps(
-                        jalview.util.Comparison.GapChars, seqs[i]
-                                                               .getSequence());              
-            }
-            emptySeqs.add(new String[] { newname, empty});
+                    .getSequence());
           }
+          emptySeqs.add(new String[]
+                        {newname, empty});
         }
-        this.seqs = new vamsas.objects.simple.SequenceSet();
-        this.seqs.setSeqs(seqarray);
-        return valid;
+      }
+      this.seqs = new vamsas.objects.simple.SequenceSet();
+      this.seqs.setSeqs(seqarray);
+      return valid;
     }
+
     /**
-     * 
+     *
      * @return true if getAlignment will return a valid alignment result.
      */
-    public boolean hasResults() {
-      if (subjobComplete && result!=null && jobs[0].result.isFinished())
+    public boolean hasResults()
+    {
+      if (subjobComplete && result != null && result.isFinished()
+          && result.getMsa() != null && result.getMsa().getSeqs() != null)
+      {
         return true;
+      }
       return false;
     }
-    public Object[] getAlignment() {
-      
-      if (result!=null && result.isFinished()) {
-        SequenceI[] alseqs=null;
-        char alseq_gapchar='-';
-        int alseq_l=0;
-        if (result.getMsa() != null) {
+
+    public Object[] getAlignment()
+    {
+
+      if (result != null && result.isFinished())
+      {
+        SequenceI[] alseqs = null;
+        char alseq_gapchar = '-';
+        int alseq_l = 0;
+        if (result.getMsa() != null)
+        {
           alseqs = getVamsasAlignment(result.getMsa());
-          alseq_gapchar=result.getMsa().getGapchar().charAt(0);
+          alseq_gapchar = result.getMsa().getGapchar().charAt(0);
           alseq_l = alseqs.length;
         }
-        if (emptySeqs.size()>0) {
-          SequenceI[] t_alseqs = new SequenceI[alseq_l+emptySeqs.size()];
+        if (emptySeqs.size() > 0)
+        {
+          SequenceI[] t_alseqs = new SequenceI[alseq_l + emptySeqs.size()];
           // get width
-          int i,w=0;
-          if (alseq_l>0) {
-            for (i=0,w=alseqs[0].getLength(); i<alseq_l; i++) {
-              if (w<alseqs[i].getLength())
-                w=alseqs[i].getLength();
+          int i, w = 0;
+          if (alseq_l > 0)
+          {
+            for (i = 0, w = alseqs[0].getLength(); i < alseq_l; i++)
+            {
+              if (w < alseqs[i].getLength())
+              {
+                w = alseqs[i].getLength();
+              }
               t_alseqs[i] = alseqs[i];
               alseqs[i] = null;
             }
           }
           // check that aligned width is at least as wide as emptySeqs width.
-          int ow=w,nw=w;
-          for (i=0, w=emptySeqs.size(); i<w; i++) {
-            String[] es=(String[]) emptySeqs.get(i);
-            if (es!=null && es[1]!=null) {
-              int sw=es[1].length();
-              if (nw<sw)
-                nw=sw;
+          int ow = w, nw = w;
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es != null && es[1] != null)
+            {
+              int sw = es[1].length();
+              if (nw < sw)
+              {
+                nw = sw;
+              }
             }
           }
           // make a gapped string.
-          StringBuffer insbuff=new StringBuffer(w);
-          for (i=0; i<nw; i++)
+          StringBuffer insbuff = new StringBuffer(w);
+          for (i = 0; i < nw; i++)
+          {
             insbuff.append(alseq_gapchar);
-          if (ow<nw) {
-            for (i=0; i<alseq_l; i++) {
-              int sw=t_alseqs[i].getLength();
-              if (nw>sw) {
+          }
+          if (ow < nw)
+          {
+            for (i = 0; i < alseq_l; i++)
+            {
+              int sw = t_alseqs[i].getLength();
+              if (nw > sw)
+              {
                 // pad at end
-                alseqs[i].setSequence(t_alseqs[i].getSequence()+insbuff.substring(0,sw-nw));
+                alseqs[i].setSequence(t_alseqs[i].getSequence() +
+                                      insbuff.substring(0, sw - nw));
               }
             }
           }
-          for (i=0, w=emptySeqs.size(); i<w; i++) {
-            String[] es=(String[]) emptySeqs.get(i);
-            if (es[1]==null)
-              t_alseqs[i+alseq_l] = new jalview.datamodel.Sequence(es[0], insbuff.toString(),1,0);
-            else {
-              if (es[1].length()<nw) {
-                t_alseqs[i+alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]+insbuff.substring(0, nw-es[1].length()),1,1+es[1].length());
-              } else {
-                t_alseqs[i+alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
+          for (i = 0, w = emptySeqs.size(); i < w; i++)
+          {
+            String[] es = (String[]) emptySeqs.get(i);
+            if (es[1] == null)
+            {
+              t_alseqs[i +
+                  alseq_l] = new jalview.datamodel.Sequence(es[0],
+                  insbuff.toString(), 1, 0);
+            }
+            else
+            {
+              if (es[1].length() < nw)
+              {
+                t_alseqs[i +
+                    alseq_l] = new jalview.datamodel.Sequence(es[0],
+                    es[1] + insbuff.substring(0, nw - es[1].length()), 1,
+                    1 + es[1].length());
+              }
+              else
+              {
+                t_alseqs[i +
+                    alseq_l] = new jalview.datamodel.Sequence(es[0], es[1]);
               }
             }
           }
           alseqs = t_alseqs;
-        } 
+        }
         AlignmentOrder msaorder = new AlignmentOrder(alseqs);
         // always recover the order - makes parseResult()'s life easier.
         jalview.analysis.AlignmentSorter.recoverOrder(alseqs);
         // account for any missing sequences
         jalview.analysis.SeqsetUtils.deuniquify(SeqNames, alseqs);
-        return new Object[] { alseqs, msaorder};
+        return new Object[]
+            {
+            alseqs, msaorder};
       }
       return null;
     }
+
+    boolean cancelled = false;
+    /**
+     * mark subjob as cancelled and set result object appropriatly
+     */
+    void cancel() {
+      cancelled=true;
+      subjobComplete = true;
+      result = null;
+    }
   }
+
   MsaWSJob jobs[] = null;
-  
+
   String alTitle; // name which will be used to form new alignment window.
-  
+
   boolean jobComplete = false;
-  
+
   Alignment dataset; // dataset to which the new alignment will be
-  
+
   // associated.
-  
+
   ext.vamsas.MuscleWS server = null;
-  
+
   String WsUrl = null;
-  
+
   /**
    * set basic options for this (group) of Msa jobs
-   * 
+   *
    * @param subgaps
    *            boolean
    * @param presorder
    *            boolean
    */
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-      WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame, AlignmentView alview,
-      String wsname, boolean subgaps, boolean presorder) {
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              AlignmentView alview,
+              String wsname, boolean subgaps, boolean presorder)
+  {
     this.server = server;
     this.WsUrl = wsUrl;
     this.wsInfo = wsinfo;
@@ -255,10 +317,10 @@ class MsaWSThread extends Thread implements WSClientI {
     this.preserveOrder = presorder;
     this.alignFrame = alFrame;
   }
-  
+
   /**
    * create one or more Msa jobs to align visible seuqences in _msa
-   * 
+   *
    * @param title
    *            String
    * @param _msa
@@ -271,69 +333,88 @@ class MsaWSThread extends Thread implements WSClientI {
    *            Alignment
    */
   MsaWSThread(ext.vamsas.MuscleWS server, String wsUrl,
-      WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
-      String wsname, String title, AlignmentView _msa, boolean subgaps,
-      boolean presorder, Alignment seqset) {
+              WebserviceInfo wsinfo, jalview.gui.AlignFrame alFrame,
+              String wsname, String title, AlignmentView _msa, boolean subgaps,
+              boolean presorder, Alignment seqset)
+  {
     this(server, wsUrl, wsinfo, alFrame, _msa, wsname, subgaps, presorder);
     OutputHeader = wsInfo.getProgressText();
     alTitle = title;
     dataset = seqset;
     SeqCigar[] msa = _msa.getSequences();
     int[] contigs = _msa.getContigs();
-    int njobs=1;
-    if (contigs != null && contigs.length > 0) {
+    int njobs = 1;
+    if (contigs != null && contigs.length > 0)
+    {
       int start = 0;
-      njobs=0;
+      njobs = 0;
       int width = _msa.getWidth();
-      for (int contig = 0; contig < contigs.length; contig += 3) {
-        if ((contigs[contig+1] - start) > 0) {
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if ( (contigs[contig + 1] - start) > 0)
+        {
           njobs++;
         }
-        width+=contigs[contig+2];// end up with full region width (including hidden regions)
-        start = contigs[contig+1] + contigs[contig + 2];
+        width += contigs[contig + 2]; // end up with full region width (including hidden regions)
+        start = contigs[contig + 1] + contigs[contig + 2];
       }
-      if (start<width) {
+      if (start < width)
+      {
         njobs++;
       }
       jobs = new MsaWSJob[njobs];
-      start=0;
-      int j=0;
-      for (int contig = 0; contig < contigs.length; contig += 3) {
-        if (contigs[contig+1] - start > 0) {
+      start = 0;
+      int j = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        if (contigs[contig + 1] - start > 0)
+        {
           SequenceI mseq[] = new SequenceI[msa.length];
-          for (int s = 0; s < mseq.length; s++) {
+          for (int s = 0; s < mseq.length; s++)
+          {
             mseq[s] = msa[s].getSeq('-').getSubSequence(start,
-                contigs[contig+1]);
+                contigs[contig + 1]);
           }
-          if (j!=0) {
+          if (j != 0)
+          {
             jobs[j] = new MsaWSJob(wsinfo.addJobPane(), mseq);
-          } else {
+          }
+          else
+          {
             jobs[j] = new MsaWSJob(0, mseq);
           }
-          wsinfo.setProgressName("region "+jobs[j].jobnum,jobs[j].jobnum);
+          wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
           wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
           j++;
         }
-        start = contigs[contig+1] + contigs[contig + 2];
+        start = contigs[contig + 1] + contigs[contig + 2];
       }
-      if (start<width) {
+      if (start < width)
+      {
         SequenceI mseq[] = new SequenceI[msa.length];
-        for (int s = 0; s < mseq.length; s++) {
+        for (int s = 0; s < mseq.length; s++)
+        {
           mseq[s] = msa[s].getSeq('-').getSubSequence(start,
-              width+1);
+              width + 1);
         }
-        if (j!=0) {
+        if (j != 0)
+        {
           jobs[j] = new MsaWSJob(wsinfo.addJobPane(), mseq);
-        } else {
+        }
+        else
+        {
           jobs[j] = new MsaWSJob(0, mseq);
         }
-        wsinfo.setProgressName("region "+jobs[j].jobnum,jobs[j].jobnum);
+        wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
         wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
-        j++;        
+        j++;
       }
-    } else {
+    }
+    else
+    {
       SequenceI mseq[] = new SequenceI[msa.length];
-      for (int s = 0; s < mseq.length; s++) {
+      for (int s = 0; s < mseq.length; s++)
+      {
         mseq[s] = msa[s].getSeq('-');
       }
       jobs = new MsaWSJob[1];
@@ -341,428 +422,682 @@ class MsaWSThread extends Thread implements WSClientI {
       jobs[0] = new MsaWSJob(0, mseq);
     }
   }
-  
-  public boolean isCancellable() {
+
+  public boolean isCancellable()
+  {
     return true;
   }
-  
-  public void cancelJob() {
-    if (!jobComplete && jobs != null) {
+
+  public void cancelJob()
+  {
+    if (!jobComplete && jobs != null)
+    {
       boolean cancelled = true;
-      for (int job = 0; job < jobs.length; job++) {
+      for (int job = 0; job < jobs.length; job++)
+      {
         if (jobs[job].submitted && !jobs[job].subjobComplete)
-        { 
+        {
           String cancelledMessage = "";
-          try {
+          try
+          {
             vamsas.objects.simple.WsJobId cancelledJob = server
-            .cancel(jobs[job].jobId);
-            if (cancelledJob.getStatus() == 2) {
+                .cancel(jobs[job].jobId);
+            if (cancelledJob.getStatus() == 2)
+            {
               // CANCELLED_JOB
               cancelledMessage = "Job cancelled.";
-              jobs[job].subjobComplete = true;
-              jobs[job].result = null;
-              wsInfo.setStatus(jobs[job].jobnum, WebserviceInfo.STATE_CANCELLED_OK);
-            } else if (cancelledJob.getStatus() == 3) {
+              jobs[job].cancel();
+              wsInfo.setStatus(jobs[job].jobnum,
+                               WebserviceInfo.STATE_CANCELLED_OK);
+            }
+            else if (cancelledJob.getStatus() == 3)
+            {
               // VALID UNSTOPPABLE JOB
-              cancelledMessage += "Server cannot cancel this job. just close the window.\n";
+              cancelledMessage +=
+                  "Server cannot cancel this job. just close the window.\n";
               cancelled = false;
-              wsInfo.setStatus(jobs[job].jobnum, WebserviceInfo.STATE_CANCELLED_OK);
+              // wsInfo.setStatus(jobs[job].jobnum,
+              //                 WebserviceInfo.STATE_RUNNING);
             }
-            
-            if (cancelledJob.getJobId() != null) {
+
+            if (cancelledJob.getJobId() != null)
+            {
               cancelledMessage += ("[" + cancelledJob.getJobId() + "]");
             }
-            
+
             cancelledMessage += "\n";
-          } catch (Exception exc) {
-            cancelledMessage += ("\nProblems cancelling the job : Exception received...\n"
-                + exc + "\n");
-            exc.printStackTrace();
+          }
+          catch (Exception exc)
+          {
+            cancelledMessage +=
+                ("\nProblems cancelling the job : Exception received...\n"
+                 + exc + "\n");
+            Cache.log.warn("Exception whilst cancelling "+jobs[job].jobId,exc);
           }
           wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
-              + cancelledMessage + "\n");
+                                 + cancelledMessage + "\n");
         }
       }
-      if (cancelled) {
+      if (cancelled)
+      {
         wsInfo.setStatus(WebserviceInfo.STATE_CANCELLED_OK);
         jobComplete = true;
       }
-    } else {
-      if (!jobComplete) {
+      this.interrupt(); // kick thread to update job states.
+    }
+    else
+    {
+      if (!jobComplete)
+      {
         wsInfo
-        .setProgressText(OutputHeader
-            + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
+            .setProgressText(OutputHeader
+                             + "Server cannot cancel this job because it has not been submitted properly. just close the window.\n");
       }
     }
   }
-  
-  public void run() {
-    
-    while (!jobComplete) {
-      int running=0;
-      int queuing=0;
-      int finished=0;
-      int error=0;
-      int serror=0;
-      for (int j=0; j<jobs.length; j++) {
-        
-        if (!jobs[j].submitted && jobs[j].seqs.getSeqs()!=null)
-          StartJob(jobs[j]);          
-        
-        if (jobs[j].submitted && !jobs[j].subjobComplete) {
-          try {
-            if ((jobs[j].result = server.getResult(jobs[j].jobId)) == null) {
+
+  class JobStateSummary {
+    int running = 0;
+    int queuing = 0;
+    int finished = 0;
+    int error = 0;
+    int serror = 0;
+    int cancelled=0;
+    int results=0;
+    void updateJobPanelState(WebserviceInfo wsInfo, MsaWSJob j) {
+      if (j.result != null)
+      {
+        String progheader = "";
+        // Parse state of job[j]
+        if (j.result.isRunning())
+        {
+          running++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_RUNNING);
+        }
+        else if (j.result.isQueued())
+        {
+          queuing++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_QUEUING);
+        }
+        else if (j.result.isFinished())
+        {
+          finished++;
+          j.subjobComplete = true;
+          if (j.hasResults())
+            results++;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_OK);
+        }
+        else if (j.result.isFailed())
+        {
+          progheader += "Job failed.\n";
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+          error++;
+        }
+        else if (j.result.isServerError())
+        {
+          serror++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum,
+                           WebserviceInfo.STATE_STOPPED_SERVERERROR);
+        }
+        else if (j.result.isBroken() || j.result.isFailed())
+        {
+          error++;
+          j.subjobComplete = true;
+          wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        // and pass on any sub-job messages to the user
+        wsInfo.setProgressText(j.jobnum, OutputHeader);
+        wsInfo.appendProgressText(j.jobnum, progheader);
+        if (j.result.getStatus() != null)
+        {
+          wsInfo.appendProgressText(j.jobnum, j.result.getStatus());
+        }
+      }
+      else
+      {
+        if (j.submitted && j.subjobComplete)
+        {
+          if (j.allowedServerExceptions == 0)
+          {
+            serror++;
+          }
+          else if (j.result == null)
+          {
+            error++;
+          }
+        }
+      }
+    }
+  }
+  public void run()
+  {
+    JobStateSummary jstate=null;
+    while (!jobComplete)
+    {
+      jstate = new JobStateSummary();
+      for (int j = 0; j < jobs.length; j++)
+      {
+
+        if (!jobs[j].submitted && jobs[j].seqs.getSeqs() != null)
+        {
+          StartJob(jobs[j]);
+        }
+
+        if (jobs[j].submitted && !jobs[j].subjobComplete)
+        {
+          try
+          {
+            if ( (jobs[j].result = server.getResult(jobs[j].jobId)) == null)
+            {
               throw (new Exception(
-              "Timed out when communicating with server\nTry again later.\n"));
+                  "Timed out when communicating with server\nTry again later.\n"));
             }
-            jalview.bin.Cache.log.debug("Job "+j+" Result state " + jobs[j].result.getState()
-                + "(ServerError=" + jobs[j].result.isServerError() + ")");
-          } catch (Exception ex) {
+            jalview.bin.Cache.log.debug("Job " + j + " Result state " +
+                                        jobs[j].result.getState()
+                                        + "(ServerError=" +
+                                        jobs[j].result.isServerError() + ")");
+          }
+          catch (Exception ex)
+          {
             // Deal with Transaction exceptions
             wsInfo.appendProgressText(jobs[j].jobnum, "\n" + WebServiceName
-                + " Server exception!\n" + ex.getMessage());
+                                      + " Server exception!\n" + ex.getMessage());
             Cache.log.warn(WebServiceName + " job(" + jobs[j].jobnum
-                + ") Server exception: " + ex.getMessage());
-            
-            if (jobs[j].allowedServerExceptions > 0) {
+                           + ") Server exception: " + ex.getMessage());
+
+            if (jobs[j].allowedServerExceptions > 0)
+            {
               jobs[j].allowedServerExceptions--;
               Cache.log.debug("Sleeping after a server exception.");
-              try {
+              try
+              {
                 Thread.sleep(5000);
               }
-              catch (InterruptedException ex1) {
+              catch (InterruptedException ex1)
+              {
               }
-            } else {
-              Cache.log.warn("Dropping job "+j+" "+jobs[j].jobId);
-              jobs[j].subjobComplete=true;
-              wsInfo.setStatus(jobs[j].jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
+            }
+            else
+            {
+              Cache.log.warn("Dropping job " + j + " " + jobs[j].jobId);
+              jobs[j].subjobComplete = true;
+              wsInfo.setStatus(jobs[j].jobnum,
+                               WebserviceInfo.STATE_STOPPED_SERVERERROR);
             }
           }
-          catch (OutOfMemoryError er) {   
+          catch (OutOfMemoryError er)
+          {
             jobComplete = true;
-            jobs[j].subjobComplete=true;
-            jobs[j].result=null; // may contain out of date result object
+            jobs[j].subjobComplete = true;
+            jobs[j].result = null; // may contain out of date result object
             wsInfo.setStatus(jobs[j].jobnum,
-                WebserviceInfo.STATE_STOPPED_ERROR);
+                             WebserviceInfo.STATE_STOPPED_ERROR);
             JOptionPane
-            .showInternalMessageDialog(
-                Desktop.desktop,
-                "Out of memory handling result for job !!"
-                + "\nSee help files for increasing Java Virtual Machine memory.",
-                "Out of memory", JOptionPane.WARNING_MESSAGE);
-            Cache.log.error("Out of memory when retrieving Job "+j+" id:" + WsUrl+"/"+jobs[j].jobId, er);
+                .showInternalMessageDialog(
+                    Desktop.desktop,
+                    "Out of memory handling result for job !!"
+                    +
+                "\nSee help files for increasing Java Virtual Machine memory.",
+                    "Out of memory", JOptionPane.WARNING_MESSAGE);
+            Cache.log.error("Out of memory when retrieving Job " + j + " id:" +
+                            WsUrl + "/" + jobs[j].jobId, er);
             System.gc();
           }
         }
-        if (jobs[j].result!=null) {
-          String progheader="";
-          // Parse state of job[j]
-          if (jobs[j].result.isRunning()) {
-            running++;
-            wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_RUNNING);
-          } else if (jobs[j].result.isQueued()) {
-            queuing++;
-            wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_QUEUING);
-          } else if (jobs[j].result.isFinished()) {
-            finished++;
-            jobs[j].subjobComplete = true;
-            wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_OK);
-          } else if (jobs[j].result.isFailed()) {
-            progheader += "Job failed.\n";
-            jobs[j].subjobComplete=true;
-            wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_ERROR);
-            error++;
-          } else if (jobs[j].result.isServerError()) {
-            serror++;
-            jobs[j].subjobComplete = true;
-            wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_SERVERERROR);
-          } else if (jobs[j].result.isBroken() || jobs[j].result.isFailed()) {
-            error++;
-            jobs[j].subjobComplete=true;
-            wsInfo.setStatus(jobs[j].jobnum,WebserviceInfo.STATE_STOPPED_ERROR);
-          }
-          // and pass on any sub-job messages to the user
-          wsInfo.setProgressText(jobs[j].jobnum, OutputHeader);
-          wsInfo.appendProgressText(jobs[j].jobnum, progheader);
-          if (jobs[j].result.getStatus() != null) {
-            wsInfo.appendProgressText(jobs[j].jobnum, jobs[j].result.getStatus());
-          }
-        } else {
-          if (jobs[j].submitted && jobs[j].subjobComplete) {
-            if (jobs[j].allowedServerExceptions==0) {
-              serror++;
-            } else if (jobs[j].result==null) {
-              error++;
-            } 
-          }
-        }
+        jstate.updateJobPanelState(wsInfo, jobs[j]);
       }
       // Decide on overall state based on collected jobs[] states
-      if (running>0) {
+      if (jstate.running > 0)
+      {
         wsInfo.setStatus(WebserviceInfo.STATE_RUNNING);
-      } else if (queuing>0) {
+      }
+      else if (jstate.queuing > 0)
+      {
         wsInfo.setStatus(WebserviceInfo.STATE_QUEUING);
-      } else {
-        jobComplete=true;
-        if (finished>0) {
+      }
+      else
+      {
+        jobComplete = true;
+        if (jstate.finished > 0)
+        {
           wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_OK);
-        } else if (error>0) {
-          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);          
-        } else if (serror>0) {
+        }
+        else if (jstate.error > 0)
+        {
+          wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
+        }
+        else if (jstate.serror > 0)
+        {
           wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
         }
       }
-      if (!jobComplete) {
-        try {
+      if (!jobComplete)
+      {
+        try
+        {
           Thread.sleep(5000);
         }
-        catch (InterruptedException e) {
-          Cache.log.debug("Interrupted sleep waiting for next job poll.",e);
+        catch (InterruptedException e)
+        {
+          Cache.log.debug("Interrupted sleep waiting for next job poll.", e);
         }
         // System.out.println("I'm alive "+alTitle);
       }
     }
-    if (jobComplete) {
+    if (jobComplete)
+    {
       parseResult(); // tidy up and make results available to user
     }
   }
-  
-  void StartJob(MsaWSJob j) {
-    if (j.submitted) {
-      if (Cache.log.isDebugEnabled()) {
-        Cache.log.debug("Tried to submit an already submitted job "+j.jobId);
+
+  void StartJob(MsaWSJob j)
+  {
+    if (j.submitted)
+    {
+      if (Cache.log.isDebugEnabled())
+      {
+        Cache.log.debug("Tried to submit an already submitted job " + j.jobId);
       }
       return;
     }
-    if (j.seqs.getSeqs()==null) {
+    if (j.seqs.getSeqs() == null)
+    {
       // special case - selection consisted entirely of empty sequences...
-      j.submitted=true;
-      j.result=new MsaResult();
+      j.submitted = true;
+      j.result = new MsaResult();
       j.result.setFinished(true);
       j.result.setStatus("Empty Alignment Job");
       j.result.setMsa(null);
     }
-    try {
+    try
+    {
       vamsas.objects.simple.WsJobId jobsubmit = server.align(j.seqs);
-      
-      if ((jobsubmit != null) && (jobsubmit.getStatus() == 1)) {
+
+      if ( (jobsubmit != null) && (jobsubmit.getStatus() == 1))
+      {
         j.jobId = jobsubmit.getJobId();
-        j.submitted=true;
+        j.submitted = true;
         j.subjobComplete = false;
         // System.out.println(WsURL + " Job Id '" + jobId + "'");
-      } else {
-        if (jobsubmit == null) {
+      }
+      else
+      {
+        if (jobsubmit == null)
+        {
           throw new Exception(
               "Server at "
               + WsUrl
-              + " returned null object, it probably cannot be contacted. Try again later ?");
+              +
+              " returned null object, it probably cannot be contacted. Try again later ?");
         }
-        
+
         throw new Exception(jobsubmit.getJobId());
       }
-    } catch (Exception e) {
+    }
+    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");
+          .println(WebServiceName
+                   + "Client: Failed to submit the sequences for alignment (probably a server side problem)\n"
+                   + "When contacting Server:" + WsUrl + "\n"
+                   + e.toString() + "\n");
       j.allowedServerExceptions = 0;
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo.setStatus(j.jobnum, WebserviceInfo.STATE_STOPPED_SERVERERROR);
       wsInfo
-      .appendProgressText(
-          j.jobnum,
-          "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");
-      
+          .appendProgressText(
+              j.jobnum,
+              "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.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++) {
+    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());
+                                              .getSeq());
     }
-    
+
     return msa;
   }
-  
-  void parseResult() {
-    try {
-      for (int j=0; j<jobs.length; j++) {
-        if (jobs[j].submitted && jobs[j].subjobComplete) {
-          if (jobs[j].result!=null) {
-            vamsas.objects.simple.Alignment valign = jobs[j].result.getMsa();
-            if (valign!= null) {
-              wsInfo.appendProgressText(jobs[j].jobnum,"\nAlignment Object Method Notes\n");
-              String[] lines = valign.getMethod();
-              for (int line = 0; line < lines.length; line++) {
-                wsInfo.appendProgressText(jobs[j].jobnum, 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
+
+  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, jobs[j]);
+        if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
+        {
+          results++;
+          vamsas.objects.simple.Alignment valign = jobs[j].result.getMsa();
+          if (valign != null)
+          {
+            wsInfo.appendProgressText(jobs[j].jobnum,
+                                      "\nAlignment Object Method Notes\n");
+            String[] lines = valign.getMethod();
+            for (int line = 0; line < lines.length; line++)
+            {
+              wsInfo.appendProgressText(jobs[j].jobnum, 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
           }
         }
       }
     }
-    catch (Exception ex) {
-      
-      Cache.log.error("Unexpected exception when processing results for "+alTitle,ex);
+    catch (Exception ex)
+    {
+
+      Cache.log.error("Unexpected exception when processing results for " +
+                      alTitle, ex);
       wsInfo.setStatus(WebserviceInfo.STATE_STOPPED_ERROR);
     }
-    
-    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();
+    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();
+    }
   }
-  void displayResults(boolean newFrame) {
+
+  void displayResults(boolean newFrame)
+  {
+    // view input or result data for each block
+    // warn user if a block is input rather than aligned data ?
+
     int contigs[] = input.getContigs();
     SeqCigar[] seqs = input.getSequences();
     SequenceI[] alignment = new SequenceI[seqs.length];
     ColumnSelection columnselection = new ColumnSelection();
-    Vector alorders=new Vector();
-    if (contigs != null && contigs.length > 0) {
-      int cshift=0;
+    Vector alorders = new Vector();
+    if (contigs != null && contigs.length > 0)
+    {
       int start = 0;
       int nwidth = 0;
-      int j=0;
-      for (int contig = 0; contig < contigs.length; contig += 3) {
-        if (cshift+contigs[contig] - start > 0) {
-          Object[] subalg =  jobs[j++].getAlignment();
-          alorders.add(subalg[1]);
-          SequenceI mseq[] = (SequenceI[]) subalg[0];
-          int width = mseq[0].getLength();
-          for (int s = 0; s < mseq.length; s++) {
-            if (alignment[s]==null) {
-              alignment[s] = mseq[s];
-            } else {
-              alignment[s].setSequence(alignment[s].getSequence()+mseq[s].getSequence());
-              if (mseq[s].getStart()<=mseq[s].getEnd())
-                alignment[s].setEnd(mseq[s].getEnd());
-              ((AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
+      int owidth = input.getWidth();
+      int j = 0;
+      for (int contig = 0; contig < contigs.length; contig += 3)
+      {
+        owidth += contigs[contig + 2]; // recover final column width
+        if (contigs[contig + 1] - start > 0)
+        {
+          int width = 0; // subalignment width
+          if (jobs[j].hasResults())
+          {
+            Object[] subalg = jobs[j++].getAlignment();
+            alorders.add(subalg[1]);
+            SequenceI mseq[] = (SequenceI[]) subalg[0];
+            width = mseq[0].getLength();
+            for (int s = 0; s < mseq.length; s++)
+            {
+              if (alignment[s] == null)
+              {
+                alignment[s] = mseq[s];
+              }
+              else
+              {
+                alignment[s].setSequence(alignment[s].getSequence() +
+                                         mseq[s].getSequence());
+                if (mseq[s].getStart() <= mseq[s].getEnd())
+                {
+                  alignment[s].setEnd(mseq[s].getEnd());
+                }
+                ( (AlignmentOrder) subalg[1]).updateSequence(mseq[s],
+                    alignment[s]);
+              }
+            }
+          }
+          else
+          {
+            // recover input data or place gaps
+            if (true)
+            {
+              // recover input data
+              for (int s = 0; s < seqs.length; s++)
+              {
+                SequenceI oseq = seqs[s].getSeq('-').getSubSequence(start,
+                    contigs[contig + 1]);
+                if (width < oseq.getLength())
+                {
+                  width = oseq.getLength();
+                }
+                if (alignment[s] == null)
+                {
+                  alignment[s] = oseq;
+                }
+                else
+                {
+                  alignment[s].setSequence(alignment[s].getSequence() +
+                                           oseq.getSequence());
+                  if (oseq.getEnd() >= oseq.getStart())
+                  {
+                    alignment[s].setEnd(oseq.getEnd());
+                  }
+                }
+              }
+
             }
+            j++;
           }
-          nwidth+=width;
+          nwidth += width;
         }
         // advance to begining of visible region
-        start = cshift+contigs[contig] + contigs[contig + 2];
+        start = contigs[contig + 1] + contigs[contig + 2];
         // add hidden segment to right of next region
-        for (int s=0; s<seqs.length; s++) {
-          SequenceI hseq = seqs[s].getSeq('-').getSubSequence(cshift+contigs[contig], start);
-          if (alignment[s]==null) {
+        for (int s = 0; s < seqs.length; s++)
+        {
+          SequenceI hseq = seqs[s].getSeq('-').getSubSequence(contigs[contig +
+              1], start);
+          if (alignment[s] == null)
+          {
             alignment[s] = hseq;
-          } else {
-            alignment[s].setSequence(alignment[s].getSequence()+hseq.getSequence());
-            if (hseq.getEnd()>=hseq.getStart())
+          }
+          else
+          {
+            alignment[s].setSequence(alignment[s].getSequence() +
+                                     hseq.getSequence());
+            if (hseq.getEnd() >= hseq.getStart())
+            {
               alignment[s].setEnd(hseq.getEnd());
+            }
           }
         }
         // mark hidden segment as hidden in the new alignment
-        columnselection.hideColumns(nwidth, nwidth+contigs[contig+2]-1);
-        nwidth+=contigs[contig+2];
-        cshift+=contigs[contig+2];
+        columnselection.hideColumns(nwidth, nwidth + contigs[contig + 2] - 1);
+        nwidth += contigs[contig + 2];
       }
       // Do final job - if it exists
-      if (j<jobs.length && jobs[j].hasResults()) {
-        Object[] subalg =  jobs[j].getAlignment();
-        alorders.add(subalg[1]);
-        SequenceI mseq[] = (SequenceI[]) subalg[0];
-        int width = mseq[0].getLength();
-        for (int s = 0; s < mseq.length; s++) {
-          if (alignment[s]==null) {
-            alignment[s] = mseq[s];
-          } else {
-            alignment[s].setSequence(alignment[s].getSequence()+mseq[s].getSequence());
-            if (mseq[s].getEnd()>=mseq[s].getStart())
-              alignment[s].setEnd(mseq[s].getEnd());
-            ((AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
+      if (j < jobs.length)
+      {
+        int width = 0;
+        if (jobs[j].hasResults())
+        {
+          Object[] subalg = jobs[j].getAlignment();
+          alorders.add(subalg[1]);
+          SequenceI mseq[] = (SequenceI[]) subalg[0];
+          width = mseq[0].getLength();
+          for (int s = 0; s < mseq.length; s++)
+          {
+            if (alignment[s] == null)
+            {
+              alignment[s] = mseq[s];
+            }
+            else
+            {
+              alignment[s].setSequence(alignment[s].getSequence() +
+                                       mseq[s].getSequence());
+              if (mseq[s].getEnd() >= mseq[s].getStart())
+              {
+                alignment[s].setEnd(mseq[s].getEnd());
+              }
+              ( (AlignmentOrder) subalg[1]).updateSequence(mseq[s], alignment[s]);
+            }
+          }
+        }
+        else
+        {
+          if (start < owidth)
+          {
+            // recover input data or place gaps
+            if (true)
+            {
+              // recover input data
+              for (int s = 0; s < seqs.length; s++)
+              {
+                SequenceI oseq = seqs[s].getSeq('-').getSubSequence(start,
+                    owidth + 1);
+                if (width < oseq.getLength())
+                {
+                  width = oseq.getLength();
+                }
+                if (alignment[s] == null)
+                {
+                  alignment[s] = oseq;
+                }
+                else
+                {
+                  alignment[s].setSequence(alignment[s].getSequence() +
+                                           oseq.getSequence());
+                  if (oseq.getEnd() >= oseq.getStart())
+                  {
+                    alignment[s].setEnd(oseq.getEnd());
+                  }
+                }
+              }
+              nwidth += width;
+            }
+            else
+            {
+              // place gaps.
+              throw new Error("Padding not yet implemented.");
+            }
           }
         }
-        nwidth+=width;  
       }
-    } else {
-      if (jobs[0].hasResults()) {
+    }
+    else
+    {
+      if (jobs[0].hasResults())
+      {
         Object[] alg = jobs[0].getAlignment();
         alignment = (SequenceI[]) alg[0];
         alorders.add(alg[1]);
-      } else {
-        alignment = SeqCigar.createAlignmentSequences(seqs, '-', columnselection,null);
+      }
+      else
+      {
+        alignment = SeqCigar.createAlignmentSequences(seqs, '-',
+            columnselection, null);
       }
     }
     Alignment al = new Alignment(alignment);
-    if (dataset != null) {
+    if (dataset != null)
+    {
       al.setDataset(dataset);
     }
-    
-    if (newFrame) {
+
+    if (newFrame)
+    {
       // TODO: JBPNote Should also rename the query sequence
       // sometime...
-      AlignFrame af = new AlignFrame(al,columnselection);
-      
+      AlignFrame af = new AlignFrame(al, columnselection);
+
       // >>>This is a fix for the moment, until a better solution is
       // found!!<<<
       af.getFeatureRenderer().transferSettings(
           alignFrame.getFeatureRenderer());
-      if (alorders.size()>0) {
-        if (alorders.size()==1) {
+      if (alorders.size() > 0)
+      {
+        if (alorders.size() == 1)
+        {
           af.addSortByOrderMenuItem(WebServiceName + " Ordering",
-              (AlignmentOrder) alorders.get(0));
-        } else {
+                                    (AlignmentOrder) alorders.get(0));
+        }
+        else
+        {
           // construct a non-redundant ordering set
-          Vector names=new Vector();
-          for (int i=0,l=alorders.size(); i<l; i++) {
-            String orderName = new String("Region "+i);
-            int j=i+1;
-            int r=l;
-            while (j<l) {
-              if (((AlignmentOrder) alorders.get(i)).equals(((AlignmentOrder) alorders.get(j)))) {
-                alorders.remove(j); l--;
-                orderName+=","+j;
-              } else
+          Vector names = new Vector();
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            String orderName = new String("Region " + i);
+            int j = i + 1;
+            int r = l;
+            while (j < l)
+            {
+              if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
+                  AlignmentOrder) alorders.get(j))))
+              {
+                alorders.remove(j);
+                l--;
+                orderName += "," + j;
+              }
+              else
+              {
                 j++;
+              }
             }
-            
-            if (i==0 && j==1)
+
+            if (i == 0 && j == 1)
+            {
               names.add(new String(""));
+            }
             else
+            {
               names.add(orderName);
+            }
           }
-          for (int i=0,l=alorders.size(); i<l; i++) {
-            af.addSortByOrderMenuItem(WebServiceName + ((String) names.get(i))+" Ordering",
-                (AlignmentOrder) alorders.get(i));              
+          for (int i = 0, l = alorders.size(); i < l; i++)
+          {
+            af.addSortByOrderMenuItem(WebServiceName + ( (String) names.get(i)) +
+                                      " Ordering",
+                                      (AlignmentOrder) alorders.get(i));
           }
         }
       }
-      
+
       Desktop.addInternalFrame(af, alTitle,
-          AlignFrame.NEW_WINDOW_WIDTH,
-          AlignFrame.NEW_WINDOW_HEIGHT);
-      
-    } else {
+                               AlignFrame.NEW_WINDOW_WIDTH,
+                               AlignFrame.NEW_WINDOW_HEIGHT);
+
+    }
+    else
+    {
       System.out.println("MERGE WITH OLD FRAME");
-      
+
     }
   }
 }
-- 
1.7.10.2