X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FMsaWSThread.java;h=0dedce2f7b64f72d7b932ff49adb4dba37fcd505;hb=7e1a8203d671e11bdc3eedf19c808f30f7a7c348;hp=2946ba88a4915b94236cdf44f7c015b97a488dec;hpb=4822456539ebf9fe5a5b0fb2728f52465418e4fc;p=jalview.git

diff --git a/src/jalview/ws/MsaWSThread.java b/src/jalview/ws/MsaWSThread.java
index 2946ba8..0dedce2 100644
--- a/src/jalview/ws/MsaWSThread.java
+++ b/src/jalview/ws/MsaWSThread.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -24,7 +24,6 @@ import jalview.analysis.*;
 import jalview.bin.*;
 import jalview.datamodel.*;
 import jalview.datamodel.Alignment;
-import jalview.datamodel.Sequence;
 import jalview.gui.*;
 import vamsas.objects.simple.MsaResult;
 
@@ -59,7 +58,8 @@ class MsaWSThread
 
   // order
 
-  class MsaWSJob extends WSThread.WSJob
+  class MsaWSJob
+      extends WSThread.WSJob
   {
     // hold special input for this
     vamsas.objects.simple.SequenceSet seqs = new vamsas.objects.simple.
@@ -127,20 +127,20 @@ class MsaWSThread
         {
           seqarray[n] = new vamsas.objects.simple.Sequence();
           seqarray[n].setId(newname);
-          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequence()
+          seqarray[n++].setSeq( (submitGaps) ? seqs[i].getSequenceAsString()
                                : AlignSeq.extractGaps(
                                    jalview.util.Comparison.GapChars, seqs[i]
-                                   .getSequence()));
+                                   .getSequenceAsString()));
         }
         else
         {
           String empty = null;
           if (seqs[i].getEnd() >= seqs[i].getStart())
           {
-            empty = (submitGaps) ? seqs[i].getSequence()
+            empty = (submitGaps) ? seqs[i].getSequenceAsString()
                 : AlignSeq.extractGaps(
                     jalview.util.Comparison.GapChars, seqs[i]
-                    .getSequence());
+                    .getSequenceAsString());
           }
           emptySeqs.add(new String[]
                         {newname, empty});
@@ -158,7 +158,8 @@ class MsaWSThread
     public boolean hasResults()
     {
       if (subjobComplete && result != null && result.isFinished()
-          && ((MsaResult) result).getMsa() != null && ((MsaResult) result).getMsa().getSeqs() != null)
+          && ( (MsaResult) result).getMsa() != null &&
+          ( (MsaResult) result).getMsa().getSeqs() != null)
       {
         return true;
       }
@@ -173,10 +174,10 @@ class MsaWSThread
         SequenceI[] alseqs = null;
         char alseq_gapchar = '-';
         int alseq_l = 0;
-        if (((MsaResult) result).getMsa() != null)
+        if ( ( (MsaResult) result).getMsa() != null)
         {
-          alseqs = getVamsasAlignment(((MsaResult) result).getMsa());
-          alseq_gapchar = ((MsaResult) result).getMsa().getGapchar().charAt(0);
+          alseqs = getVamsasAlignment( ( (MsaResult) result).getMsa());
+          alseq_gapchar = ( (MsaResult) result).getMsa().getGapchar().charAt(0);
           alseq_l = alseqs.length;
         }
         if (emptySeqs.size() > 0)
@@ -224,7 +225,7 @@ class MsaWSThread
               if (nw > sw)
               {
                 // pad at end
-                alseqs[i].setSequence(t_alseqs[i].getSequence() +
+                alseqs[i].setSequence(t_alseqs[i].getSequenceAsString() +
                                       insbuff.substring(0, sw - nw));
               }
             }
@@ -267,26 +268,31 @@ class MsaWSThread
       }
       return null;
     }
+
     /**
      * mark subjob as cancelled and set result object appropriatly
      */
-    void cancel() {
-      cancelled=true;
+    void cancel()
+    {
+      cancelled = true;
       subjobComplete = true;
       result = null;
     }
+
     /**
      *
      * @return boolean true if job can be submitted.
      */
-    boolean hasValidInput() {
-      if (seqs.getSeqs()!=null)
+    boolean hasValidInput()
+    {
+      if (seqs.getSeqs() != null)
+      {
         return true;
+      }
       return false;
     }
   }
 
-
   String alTitle; // name which will be used to form new alignment window.
   Alignment dataset; // dataset to which the new alignment will be
 
@@ -306,14 +312,10 @@ class MsaWSThread
               AlignmentView alview,
               String wsname, boolean subgaps, boolean presorder)
   {
+    super(alFrame, wsinfo, alview, wsname, wsUrl);
     this.server = server;
-    this.WsUrl = wsUrl;
-    this.wsInfo = wsinfo;
-    this.WebServiceName = wsname;
-    this.input = alview;
     this.submitGaps = subgaps;
     this.preserveOrder = presorder;
-    this.alignFrame = alFrame;
   }
 
   /**
@@ -339,6 +341,7 @@ class MsaWSThread
     OutputHeader = wsInfo.getProgressText();
     alTitle = title;
     dataset = seqset;
+
     SequenceI[][] conmsa = _msa.getVisibleContigs('-');
     if (conmsa != null)
     {
@@ -355,11 +358,14 @@ class MsaWSThread
           jobs[j] = new MsaWSJob(0, conmsa[j]);
         }
         if (njobs > 0)
+        {
           wsinfo.setProgressName("region " + jobs[j].jobnum, jobs[j].jobnum);
+        }
         wsinfo.setProgressText(jobs[j].jobnum, OutputHeader);
       }
     }
   }
+
   public boolean isCancellable()
   {
     return true;
@@ -383,7 +389,7 @@ class MsaWSThread
             {
               // CANCELLED_JOB
               cancelledMessage = "Job cancelled.";
-              ((MsaWSJob) jobs[job]).cancel();
+              ( (MsaWSJob) jobs[job]).cancel();
               wsInfo.setStatus(jobs[job].jobnum,
                                WebserviceInfo.STATE_CANCELLED_OK);
             }
@@ -409,7 +415,8 @@ class MsaWSThread
             cancelledMessage +=
                 ("\nProblems cancelling the job : Exception received...\n"
                  + exc + "\n");
-            Cache.log.warn("Exception whilst cancelling "+jobs[job].jobId,exc);
+            Cache.log.warn("Exception whilst cancelling " + jobs[job].jobId,
+                           exc);
           }
           wsInfo.setProgressText(jobs[job].jobnum, OutputHeader
                                  + cancelledMessage + "\n");
@@ -432,13 +439,19 @@ class MsaWSThread
       }
     }
   }
-  void pollJob(WSJob job) throws Exception {
-    ((MsaWSJob) job).result = server.getResult(((MsaWSJob) job).jobId);
+
+  void pollJob(WSJob job)
+      throws Exception
+  {
+    ( (MsaWSJob) job).result = server.getResult( ( (MsaWSJob) job).jobId);
   }
+
   void StartJob(WSJob job)
   {
-    if (!(job instanceof MsaWSJob)) {
-      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance "+job.getClass());
+    if (! (job instanceof MsaWSJob))
+    {
+      throw new Error("StartJob(MsaWSJob) called on a WSJobInstance " +
+                      job.getClass());
     }
     MsaWSJob j = (MsaWSJob) job;
     if (j.submitted)
@@ -456,7 +469,7 @@ class MsaWSThread
       j.result = new MsaResult();
       j.result.setFinished(true);
       j.result.setStatus("Empty Alignment Job");
-      ((MsaResult) j.result).setMsa(null);
+      ( (MsaResult) j.result).setMsa(null);
     }
     try
     {
@@ -534,7 +547,8 @@ class MsaWSThread
         if (jobs[j].submitted && jobs[j].subjobComplete && jobs[j].hasResults())
         {
           results++;
-          vamsas.objects.simple.Alignment valign = ((MsaResult) jobs[j].result).getMsa();
+          vamsas.objects.simple.Alignment valign = ( (MsaResult) jobs[j].result).
+              getMsa();
           if (valign != null)
           {
             wsInfo.appendProgressText(jobs[j].jobnum,
@@ -579,49 +593,59 @@ class MsaWSThread
         }
       });
       wsInfo.setResultsReady();
-    } else
+    }
+    else
+    {
       wsInfo.setFinishedNoResults();
+    }
   }
 
   void displayResults(boolean newFrame)
   {
     // view input or result data for each block
     Vector alorders = new Vector();
-    SequenceI[][] results=new SequenceI[jobs.length][];
+    SequenceI[][] results = new SequenceI[jobs.length][];
     AlignmentOrder[] orders = new AlignmentOrder[jobs.length];
-    SequenceI[] first=null;
-    for (int j=0; j<jobs.length; j++) {
-      if (jobs[j].hasResults()) {
+
+    for (int j = 0; j < jobs.length; j++)
+    {
+      if (jobs[j].hasResults())
+      {
         Object[] res = ( (MsaWSJob) jobs[j]).getAlignment();
         alorders.add(res[1]);
         results[j] = (SequenceI[]) res[0];
         orders[j] = (AlignmentOrder) res[1];
 //    SequenceI[] alignment = input.getUpdated
-      } else {
-        results[j]=null;
+      }
+      else
+      {
+        results[j] = null;
       }
     }
     Object[] newview = input.getUpdatedView(results, orders, '-');
     // trash references to original result data
-    for (int j=0; j<jobs.length; j++) {
+    for (int j = 0; j < jobs.length; j++)
+    {
       results[j] = null;
       orders[j] = null;
     }
     SequenceI[] alignment = (SequenceI[]) newview[0];
     ColumnSelection columnselection = (ColumnSelection) newview[1];
     Alignment al = new Alignment(alignment);
+
     if (dataset != null)
     {
       al.setDataset(dataset);
     }
 
+    propagateDatasetMappings(al);
     // JBNote- TODO: warn user if a block is input rather than aligned data ?
 
     if (newFrame)
     {
       AlignFrame af = new AlignFrame(al, columnselection,
-                                           AlignFrame.DEFAULT_WIDTH,
-                                           AlignFrame.DEFAULT_HEIGHT);
+                                     AlignFrame.DEFAULT_WIDTH,
+                                     AlignFrame.DEFAULT_HEIGHT);
 
       // >>>This is a fix for the moment, until a better solution is
       // found!!<<<
@@ -643,7 +667,7 @@ class MsaWSThread
           {
             String orderName = new String(" Region " + i);
             int j = i + 1;
-            int r = l;
+
             while (j < l)
             {
               if ( ( (AlignmentOrder) alorders.get(i)).equals( ( (
@@ -671,7 +695,7 @@ class MsaWSThread
           for (int i = 0, l = alorders.size(); i < l; i++)
           {
             af.addSortByOrderMenuItem(WebServiceName
-                                      +( (String) names.get(i)) +
+                                      + ( (String) names.get(i)) +
                                       " Ordering",
                                       (AlignmentOrder) alorders.get(i));
           }
@@ -690,6 +714,7 @@ class MsaWSThread
     }
   }
 
+
   public boolean canMergeResults()
   {
     return false;