X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=b97c4c58ecfb6b787b040140b71a74a375cc1758;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=d6a4488ad25a637db7c9e8271f47929609ba2ba2;hpb=4389a166735bf1203894abdf3cf7dd57c4856dbc;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index d6a4488..b97c4c5 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -41,71 +41,33 @@ public class ConsensusThread extends AlignCalcWorker
   @Override
   public void run()
   {
-    if (calcMan.isPending(this))
+    AlignmentAnnotation consensus = getConsensusAnnotation();
+    AlignmentAnnotation gap = getGapAnnotation();
+    if ((consensus == null && gap == null))
     {
       return;
     }
-    calcMan.notifyStart(this);
-    long started = System.currentTimeMillis();
-    try
+    if (alignViewport.isClosed())
     {
-      AlignmentAnnotation consensus = getConsensusAnnotation();
-      AlignmentAnnotation gap = getOccupancyAnnotation();
-      if ((consensus == null && gap == null) || calcMan.isPending(this))
-      {
-        calcMan.workerComplete(this);
-        return;
-      }
-      while (!calcMan.notifyWorking(this))
-      {
-        // System.err.println("Thread
-        // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
-        try
-        {
-          if (ap != null)
-          {
-            ap.paintAlignment(false, false);
-          }
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-      if (alignViewport.isClosed())
-      {
-        abortAndDestroy();
-        return;
-      }
-      AlignmentI alignment = alignViewport.getAlignment();
+      abortAndDestroy();
+      return;
+    }
+    AlignmentI alignment = alignViewport.getAlignment();
 
-      int aWidth = -1;
+    int aWidth = -1;
 
-      if (alignment == null || (aWidth = alignment.getWidth()) < 0)
-      {
-        calcMan.workerComplete(this);
-        return;
-      }
+    if (alignment == null || (aWidth = alignment.getWidth()) < 0)
+    {
+      return;
+    }
 
-      eraseConsensus(aWidth);
-      computeConsensus(alignment);
-      updateResultAnnotation(true);
+    eraseConsensus(aWidth);
+    computeConsensus(alignment);
+    updateResultAnnotation(true);
 
-      if (ap != null)
-      {
-        ap.paintAlignment(true, true);
-      }
-    } catch (OutOfMemoryError error)
-    {
-      calcMan.disableWorker(this);
-      ap.raiseOOMWarning("calculating consensus", error);
-    } finally
+    if (ap != null)
     {
-      /*
-       * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
-       * - alignment was edited at same time as calculation was running
-       */
-      calcMan.workerComplete(this);
+      ap.paintAlignment(true, true);
     }
   }
 
@@ -118,8 +80,11 @@ public class ConsensusThread extends AlignCalcWorker
   protected void eraseConsensus(int aWidth)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    consensus.annotations = new Annotation[aWidth];
-    AlignmentAnnotation gap = getOccupancyAnnotation();
+    if (consensus != null)
+    {
+      consensus.annotations = new Annotation[aWidth];
+    }
+    AlignmentAnnotation gap = getGapAnnotation();
     if (gap != null)
     {
       gap.annotations = new Annotation[aWidth];
@@ -137,7 +102,7 @@ public class ConsensusThread extends AlignCalcWorker
     ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
             true);
 
-    alignViewport.setConsensusProfiles(hconsensus);
+    alignViewport.setSequenceConsensusHash(hconsensus);
     setColourSchemeConsensus(hconsensus);
   }
 
@@ -176,9 +141,9 @@ public class ConsensusThread extends AlignCalcWorker
    * 
    * @return
    */
-  protected AlignmentAnnotation getOccupancyAnnotation()
+  protected AlignmentAnnotation getGapAnnotation()
   {
-    return alignViewport.getOccupancyAnnotation();
+    return alignViewport.getAlignmentGapAnnotation();
   }
 
   /**
@@ -199,10 +164,10 @@ public class ConsensusThread extends AlignCalcWorker
             && hconsensus != null)
     {
       deriveConsensus(consensus, hconsensus);
-      AlignmentAnnotation occupancy = getOccupancyAnnotation();
-      if (occupancy != null)
+      AlignmentAnnotation gap = getGapAnnotation();
+      if (gap != null)
       {
-        deriveOccupancy(occupancy, hconsensus);
+        deriveGap(gap, hconsensus);
       }
     }
   }
@@ -234,11 +199,11 @@ public class ConsensusThread extends AlignCalcWorker
    * @param hconsensus
    *          the computed consensus data
    */
-  protected void deriveOccupancy(AlignmentAnnotation gapAnnotation,
+  protected void deriveGap(AlignmentAnnotation gapAnnotation,
           ProfilesI hconsensus)
   {
     long nseq = getSequences().length;
-    AAFrequency.completeOccupancyAnnot(gapAnnotation, hconsensus,
+    AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
             hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
             nseq);
   }
@@ -251,6 +216,6 @@ public class ConsensusThread extends AlignCalcWorker
   protected Object getViewportConsensus()
   {
     // TODO convert ComplementConsensusThread to use Profile
-    return alignViewport.getConsensusProfiles();
+    return alignViewport.getSequenceConsensusHash();
   }
 }