JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / workers / ConsensusThread.java

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index c754ee3..5f0ec84 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -21,7 +21,6 @@
 package jalview.workers;
 
 import jalview.analysis.AAFrequency;
-import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
@@ -32,11 +31,8 @@ import jalview.schemes.ColourSchemeI;
 
 import java.util.Hashtable;
 
-public class ConsensusThread extends AlignCalcWorker implements
-        AlignCalcWorkerI
+public class ConsensusThread extends AlignCalcWorker
 {
-  private long nseq = -1;
-
   public ConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
@@ -54,8 +50,7 @@ public class ConsensusThread extends AlignCalcWorker implements
     long started = System.currentTimeMillis();
     try
     {
-      AlignmentAnnotation consensus = alignViewport
-              .getAlignmentConsensusAnnotation();
+      AlignmentAnnotation consensus = getConsensusAnnotation();
       if (consensus == null || calcMan.isPending(this))
       {
         calcMan.workerComplete(this);
@@ -88,58 +83,89 @@ public class ConsensusThread extends AlignCalcWorker implements
       if (alignment == null || (aWidth = alignment.getWidth()) < 0)
       {
         calcMan.workerComplete(this);
-        // .updatingConservation = false;
-        // AlignViewport.UPDATING_CONSERVATION = false;
-
         return;
       }
-      consensus = alignViewport.getAlignmentConsensusAnnotation();
 
-      consensus.annotations = null;
-      consensus.annotations = new Annotation[aWidth];
-      Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
-      hconsensus = new Hashtable[aWidth];
-      try
-      {
-        SequenceI aseqs[] = alignment.getSequencesArray();
-        nseq = aseqs.length;
-        AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus,
-                true);
-      } catch (ArrayIndexOutOfBoundsException x)
-      {
-        // this happens due to a race condition -
-        // alignment was edited at same time as calculation was running
-        //
-        // calcMan.workerCannotRun(this);
-        calcMan.workerComplete(this);
-        return;
-      }
-      alignViewport.setSequenceConsensusHash(hconsensus);
+      eraseConsensus(aWidth);
+      computeConsensus(alignment);
       updateResultAnnotation(true);
-      ColourSchemeI globalColourScheme = alignViewport
-              .getGlobalColourScheme();
-      if (globalColourScheme != null)
+
+      if (ap != null)
       {
-        globalColourScheme.setConsensus(hconsensus);
+        ap.paintAlignment(true);
       }
-
     } catch (OutOfMemoryError error)
     {
-      calcMan.workerCannotRun(this);
-
-      // consensus = null;
-      // hconsensus = null;
+      calcMan.disableWorker(this);
       ap.raiseOOMWarning("calculating consensus", error);
+    } finally
+    {
+      /*
+       * e.g. ArrayIndexOutOfBoundsException can happen due to a race condition
+       * - alignment was edited at same time as calculation was running
+       */
+      calcMan.workerComplete(this);
     }
+  }
+
+  /**
+   * Clear out any existing consensus annotations
+   * 
+   * @param aWidth
+   *          the width (number of columns) of the annotated alignment
+   */
+  protected void eraseConsensus(int aWidth)
+  {
+    AlignmentAnnotation consensus = getConsensusAnnotation();
+    consensus.annotations = new Annotation[aWidth];
+  }
+
+  /**
+   * @param alignment
+   */
+  protected void computeConsensus(AlignmentI alignment)
+  {
+    Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+
+    SequenceI[] aseqs = getSequences();
+    AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
+
+    alignViewport.setSequenceConsensusHash(hconsensus);
+    setColourSchemeConsensus(hconsensus);
+  }
 
-    calcMan.workerComplete(this);
-    if (ap != null)
+  /**
+   * @return
+   */
+  protected SequenceI[] getSequences()
+  {
+    return alignViewport.getAlignment().getSequencesArray();
+  }
+
+  /**
+   * @param hconsensus
+   */
+  protected void setColourSchemeConsensus(Hashtable[] hconsensus)
+  {
+    ColourSchemeI globalColourScheme = alignViewport
+            .getGlobalColourScheme();
+    if (globalColourScheme != null)
     {
-      ap.paintAlignment(true);
+      globalColourScheme.setConsensus(hconsensus);
     }
   }
 
   /**
+   * Get the Consensus annotation for the alignment
+   * 
+   * @return
+   */
+  protected AlignmentAnnotation getConsensusAnnotation()
+  {
+    return alignViewport.getAlignmentConsensusAnnotation();
+  }
+
+  /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
@@ -151,15 +177,40 @@ public class ConsensusThread extends AlignCalcWorker implements
 
   public void updateResultAnnotation(boolean immediate)
   {
-    AlignmentAnnotation consensus = alignViewport
-            .getAlignmentConsensusAnnotation();
-    Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
+    AlignmentAnnotation consensus = getConsensusAnnotation();
+    Hashtable[] hconsensus = getViewportConsensus();
     if (immediate || !calcMan.isWorking(this) && consensus != null
             && hconsensus != null)
     {
-      AAFrequency.completeConsensus(consensus, hconsensus, 0,
-              hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
-              alignViewport.isShowSequenceLogo(), nseq);
+      deriveConsensus(consensus, hconsensus);
     }
   }
+
+  /**
+   * Convert the computed consensus data into the desired annotation for
+   * display.
+   * 
+   * @param consensusAnnotation
+   *          the annotation to be populated
+   * @param consensusData
+   *          the computed consensus data
+   */
+  protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
+          Hashtable[] consensusData)
+  {
+    long nseq = getSequences().length;
+    AAFrequency.completeConsensus(consensusAnnotation, consensusData, 0,
+            consensusData.length, alignViewport.isIgnoreGapsConsensus(),
+            alignViewport.isShowSequenceLogo(), nseq);
+  }
+
+  /**
+   * Get the consensus data stored on the viewport.
+   * 
+   * @return
+   */
+  protected Hashtable[] getViewportConsensus()
+  {
+    return alignViewport.getSequenceConsensusHash();
+  }
 }