X-Git-Url: http://source.jalview.org/gitweb/?p=jalviewjs.git;a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FStrucConsensusThread.java;h=4a0f41d39d5f6e78e6a54d964b0b41868424619e;hp=6f816761d928984a90f5011aa0063a945a08d489;hb=7301a2415adab88038b291fc54caeeb3a5a47a44;hpb=6154cb57a6eac3bb1344b8342495f5bb701ee921

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 6f81676..4a0f41d 100644
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -31,16 +31,27 @@ import jalview.datamodel.SequenceI;
 
 import java.util.Hashtable;
 
+/**
+ * 
+ * untested
+ * 
+ * @author Bob Hanson 
+ *
+ */
 public class StrucConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
 
+	private AlignmentAnnotation rnaStruc = null;
   private AlignmentAnnotation strucConsensus;
 
   private Hashtable[] hStrucConsensus;
 
   private long nseq = -1;
 
+	private AlignmentAnnotation[] aa;
+	private SequenceI[] arr;
+
 
   @Override
 	public AlignCalcWorkerI getNewWorker() {
@@ -53,108 +64,106 @@ public class StrucConsensusThread extends AlignCalcWorker implements
     super(alignViewport, alignPanel);
   }
 
-  @Override
-  public void run()
-  {
-    try
-    {
-      if (calcMan.isPending(this))
-      {
-        return;
-      }
-      calcMan.notifyStart(this);
-      while (!calcMan.notifyWorking(this))
-      {
-        try
-        {
-          if (ap != null)
-          {
-            // ap.paintAlignment(false);
-          }
-
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-      if (alignViewport.isClosed())
-      {
-        abortAndDestroy();
-        return;
-      }
-      AlignmentI alignment = alignViewport.getAlignment();
-
-      int aWidth = -1;
-
-      if (alignment == null || (aWidth = alignment.getWidth()) < 0)
-      {
-        calcMan.workerComplete(this);
-        return;
-      }
-      strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
-      hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
-      strucConsensus.annotations = null;
-      strucConsensus.annotations = new Annotation[aWidth];
-
-      hStrucConsensus = new Hashtable[aWidth];
-
-      AlignmentAnnotation[] aa = alignViewport.getAlignment()
-              .getAlignmentAnnotation();
-      AlignmentAnnotation rnaStruc = null;
-      // select rna struct to use for calculation
-      for (int i = 0; i < aa.length; i++)
-      {
-        if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
-        {
-          rnaStruc = aa[i];
-          break;
-        }
-      }
-      // check to see if its valid
-
-      if (rnaStruc == null || !rnaStruc.isValidStruc())
-      {
-        calcMan.workerComplete(this);
-        return;
-      }
-
-      try
-      {
-        final SequenceI[] arr = alignment.getSequencesArray();
-        nseq = arr.length;
-        StructureFrequency.calculate(arr, 0,
+	@Override
+	protected void run1(int state) {
+		if (alignViewport.isClosed()) {
+			abortAndDestroy();
+			return;
+		}
+		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;
+					}
+					alignment = alignViewport.getAlignment();
+					aWidth = -1;
+					if (alignment == null || (aWidth = alignment.getWidth()) < 0) {
+						state = DONE;
+					}
+					strucConsensus = alignViewport.getAlignmentStrucConsensusAnnotation();
+					hStrucConsensus = alignViewport.getRnaStructureConsensusHash();
+					strucConsensus.annotations = null;
+					strucConsensus.annotations = new Annotation[aWidth];
+
+					hStrucConsensus = new Hashtable[aWidth];
+
+					aa = alignViewport.getAlignment().getAlignmentAnnotation();
+		      // select rna struct to use for calculation
+		      for (int i = 0; i < aa.length; i++)
+		      {
+		        if (aa[i].getRNAStruc() != null && aa[i].isValidStruc())
+		        {
+		          rnaStruc = aa[i];
+		          break;
+		        }
+		      }
+		      // check to see if its valid
+
+		      if (rnaStruc == null || !rnaStruc.isValidStruc())
+		      {
+		        calcMan.workerComplete(this);
+		        return;
+		      }
+	        arr = alignment.getSequencesArray();
+	        nseq = arr.length;
+
+					state = LOOP_CALCULATE;
+					break;
+				case LOOP_CALCULATE:
+					iFirst = iLast;
+					iLast = Math.min(iLast + nPer, aWidth);
+					if (iLast == iFirst) {
+						state = DONE;
+					} else {
+		        StructureFrequency.calculate(arr, 0,
                 alignment.getWidth(), hStrucConsensus, true, rnaStruc);
-      } catch (ArrayIndexOutOfBoundsException x)
-      {
-        calcMan.workerComplete(this);
-        return;
-      }
-      alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
-      // TODO AlignmentAnnotation rnaStruc!!!
-      updateResultAnnotation(true);
-      if (alignViewport.getGlobalColourScheme() != null)
-      {
-        alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
-      }
-
-    } catch (OutOfMemoryError error)
-    {
-      calcMan.workerCannotRun(this);
-
-      // consensus = null;
-      // hconsensus = null;
-      ap.raiseOOMWarning("calculating RNA structure consensus", error);
-    } finally
-    {
-      calcMan.workerComplete(this);
-      if (ap != null)
-      {
-        ap.paintAlignment(true);
-      }
-    }
-
-  }
+						if (sleepAndReturn(0, state))
+							return;
+					}
+					break;
+				case DONE:
+		      alignViewport.setRnaStructureConsensusHash(hStrucConsensus);
+		      // TODO AlignmentAnnotation rnaStruc!!!
+		      updateResultAnnotation(true);
+		      if (alignViewport.getGlobalColourScheme() != null)
+		      {
+		        alignViewport.getGlobalColourScheme().setConsensus(hStrucConsensus);
+		      }
+					notifyDone();
+					return;
+				}
+			} catch (OutOfMemoryError error) {
+				calcMan.workerCannotRun(this);
+	      ap.raiseOOMWarning("calculating RNA structure consensus", error);
+			} catch (Throwable e) {
+				System.out.println("Error in ConsensusThread: " + e);
+				e.printStackTrace();
+				calcMan.workerComplete(this);
+			}
+		}
+	}
 
   /**
    * update the consensus annotation from the sequence profile data using
@@ -178,10 +187,4 @@ public class StrucConsensusThread extends AlignCalcWorker implements
     }
   }
 
-	@Override
-	protected void run1(int state) {
-		// TODO Auto-generated method stub
-		
-	}
-
 }