X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConservationThread.java;h=ac37f463139a70d379435a17fa47d1ac44c3a5c6;hb=4231d40261fef32ce4570a6bbad0d35df44e8baf;hp=32e13f26c429c75e2c8071453f678607cd25378d;hpb=c07eb2c5794833bd0241000d6844d783fe10cb82;p=jalview.git

diff --git a/src/jalview/workers/ConservationThread.java b/src/jalview/workers/ConservationThread.java
index 32e13f2..ac37f46 100644
--- a/src/jalview/workers/ConservationThread.java
+++ b/src/jalview/workers/ConservationThread.java
@@ -49,81 +49,89 @@ public class ConservationThread extends AlignCalcWorker implements
 
   AlignmentAnnotation conservation, quality;
 
-  int alWidth;
+	@Override
+	protected void run1(int state) {
+		while (!interrupted()) {
+			try {
+				switch (state) {
+				case INIT:
+					if (calcMan.isPending(this))
+						return;
+					calcMan.notifyStart(this);
+					state = LOOP_STANDBY;
+					break;
+				case LOOP_STANDBY:
+					while (!calcMan.notifyWorking(this)) {
+						if (ap != null) {
+							ap.paintAlignment(false);
+						}
+						try {
+							if (sleepAndReturn(200, state))
+								return;
+						} catch (InterruptedException e) {
+							state = DONE;
+							break;
+						}
+					}
+					if (alignViewport.isClosed()) {
+						abortAndDestroy();
+						state = DONE;
+						break;
+					}
+		      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+		      alignment = alignViewport.getAlignment();
+		      conservation = alignViewport.getAlignmentConservationAnnotation();
+		      quality = alignViewport.getAlignmentQualityAnnot();
+		      ourAnnot.add(conservation);
+		      ourAnnot.add(quality);
+		      ourAnnots = ourAnnot;
+		      ConsPercGaps = alignViewport.getConsPercGaps();
+		      // AlignViewport.UPDATING_CONSERVATION = true;
+
+		      if (alignment == null || (aWidth = alignment.getWidth()) < 0)
+		      {
+		        calcMan.workerComplete(this);
+		        // .updatingConservation = false;
+		        // AlignViewport.UPDATING_CONSERVATION = false;
+
+		        return;
+		      }
+					state = LOOP_CALCULATE;
+					break;
+				case LOOP_CALCULATE:
+					iFirst = iLast;
+					nPer = aWidth  + 1; // for now - one big chunk
+					iLast = Math.min(iLast + nPer, aWidth);
+					if (iLast == iFirst) {
+						state = DONE;
+					} else {
+						computeConsensus();
+						if (sleepAndReturn(0, state))
+							return;
+					}
+					break;
+				case DONE:
+		      updateResultAnnotation(true);
+					return;
+				}
+			} catch (OutOfMemoryError error) {
+				calcMan.workerCannotRun(this);
+	      ap.raiseOOMWarning("calculating conservation", error);
+			} catch (Throwable e) {
+				System.out.println("Error in ConsensusThread: " + e);
+				e.printStackTrace();
+				calcMan.workerComplete(this);
+			}
+		}
+	}
+
+	private void computeConsensus() {
+    cons = Conservation.calculateConservation("All",
+        ResidueProperties.propHash, 3,
+        alignment.getSequences(), 0, aWidth - 1, false,
+        ConsPercGaps, quality != null);
+	}
 
-  @Override
-  public void run()
-  {
-    try
-    {
-      calcMan.notifyStart(this); // updatingConservation = true;
-
-      while (!calcMan.notifyWorking(this))
-      {
-        try
-        {
-          if (ap != null)
-          {
-            // ap.paintAlignment(false);
-          }
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-      if (alignViewport.isClosed())
-      {
-        abortAndDestroy();
-        return;
-      }
-      List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
-      AlignmentI alignment = alignViewport.getAlignment();
-      conservation = alignViewport.getAlignmentConservationAnnotation();
-      quality = alignViewport.getAlignmentQualityAnnot();
-      ourAnnot.add(conservation);
-      ourAnnot.add(quality);
-      ourAnnots = ourAnnot;
-      ConsPercGaps = alignViewport.getConsPercGaps();
-      // AlignViewport.UPDATING_CONSERVATION = true;
-
-      if (alignment == null || (alWidth = alignment.getWidth()) < 0)
-      {
-        calcMan.workerComplete(this);
-        // .updatingConservation = false;
-        // AlignViewport.UPDATING_CONSERVATION = false;
-
-        return;
-      }
-      try
-      {
-        cons = Conservation.calculateConservation("All",
-                ResidueProperties.propHash, 3,
-                alignment.getSequences(), 0, alWidth - 1, false,
-                ConsPercGaps, quality != null);
-      } catch (IndexOutOfBoundsException x)
-      {
-        // probable race condition. just finish and return without any fuss.
-        calcMan.workerComplete(this);
-        return;
-      }
-      updateResultAnnotation(true);
-    } catch (OutOfMemoryError error)
-    {
-      ap.raiseOOMWarning("calculating conservation", error);
-      calcMan.workerCannotRun(this);
-      // alignViewport.conservation = null;
-      // this.alignViewport.quality = null;
-
-    }
-    calcMan.workerComplete(this);
-
-    if (ap != null)
-    {
-      ap.paintAlignment(true);
-    }
-
-  }
 
   private void updateResultAnnotation(boolean b)
   {
@@ -131,7 +139,7 @@ public class ConservationThread extends AlignCalcWorker implements
             && conservation != null && quality != null)
     {
       alignViewport.setConservation(cons);
-      cons.completeAnnotations(conservation, quality, 0, alWidth);
+      cons.completeAnnotations(conservation, quality, 0, aWidth);
     }
   }
 
@@ -141,4 +149,5 @@ public class ConservationThread extends AlignCalcWorker implements
     updateResultAnnotation(false);
 
   }
+
 }