X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=b97c4c58ecfb6b787b040140b71a74a375cc1758;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=8cde493b8fa91d50218929ca394b8d345142f2f9;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 8cde493..b97c4c5 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -21,22 +21,17 @@
 package jalview.workers;
 
 import jalview.analysis.AAFrequency;
-import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ProfilesI;
 import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
+import jalview.renderer.ResidueShaderI;
 
-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)
   {
@@ -46,100 +41,112 @@ public class ConsensusThread extends AlignCalcWorker implements
   @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 = alignViewport
-              .getAlignmentConsensusAnnotation();
-      if (consensus == 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);
-          }
-          Thread.sleep(200);
-        } catch (Exception ex)
-        {
-          ex.printStackTrace();
-        }
-      }
-      if (alignViewport.isClosed())
-      {
-        abortAndDestroy();
-        return;
-      }
-      AlignmentI alignment = alignViewport.getAlignment();
-
-      int aWidth = -1;
+      abortAndDestroy();
+      return;
+    }
+    AlignmentI alignment = alignViewport.getAlignment();
 
-      if (alignment == null || (aWidth = alignment.getWidth()) < 0)
-      {
-        calcMan.workerComplete(this);
-        // .updatingConservation = false;
-        // AlignViewport.UPDATING_CONSERVATION = false;
+    int aWidth = -1;
 
-        return;
-      }
-      consensus = alignViewport.getAlignmentConsensusAnnotation();
+    if (alignment == null || (aWidth = alignment.getWidth()) < 0)
+    {
+      return;
+    }
 
-      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);
-      updateResultAnnotation(true);
-      ColourSchemeI globalColourScheme = alignViewport
-              .getGlobalColourScheme();
-      if (globalColourScheme != null)
-      {
-        globalColourScheme.setConsensus(hconsensus);
-      }
+    eraseConsensus(aWidth);
+    computeConsensus(alignment);
+    updateResultAnnotation(true);
 
-    } catch (OutOfMemoryError error)
+    if (ap != null)
     {
-      calcMan.workerCannotRun(this);
+      ap.paintAlignment(true, true);
+    }
+  }
 
-      // consensus = null;
-      // hconsensus = null;
-      ap.raiseOOMWarning("calculating consensus", error);
+  /**
+   * 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();
+    if (consensus != null)
+    {
+      consensus.annotations = new Annotation[aWidth];
+    }
+    AlignmentAnnotation gap = getGapAnnotation();
+    if (gap != null)
+    {
+      gap.annotations = new Annotation[aWidth];
     }
+  }
 
-    calcMan.workerComplete(this);
-    if (ap != null)
+  /**
+   * @param alignment
+   */
+  protected void computeConsensus(AlignmentI alignment)
+  {
+
+    SequenceI[] aseqs = getSequences();
+    int width = alignment.getWidth();
+    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+            true);
+
+    alignViewport.setSequenceConsensusHash(hconsensus);
+    setColourSchemeConsensus(hconsensus);
+  }
+
+  /**
+   * @return
+   */
+  protected SequenceI[] getSequences()
+  {
+    return alignViewport.getAlignment().getSequencesArray();
+  }
+
+  /**
+   * @param hconsensus
+   */
+  protected void setColourSchemeConsensus(ProfilesI hconsensus)
+  {
+    ResidueShaderI cs = alignViewport.getResidueShading();
+    if (cs != null)
     {
-      ap.paintAlignment(true);
+      cs.setConsensus(hconsensus);
     }
   }
 
   /**
+   * Get the Consensus annotation for the alignment
+   * 
+   * @return
+   */
+  protected AlignmentAnnotation getConsensusAnnotation()
+  {
+    return alignViewport.getAlignmentConsensusAnnotation();
+  }
+
+  /**
+   * Get the Gap annotation for the alignment
+   * 
+   * @return
+   */
+  protected AlignmentAnnotation getGapAnnotation()
+  {
+    return alignViewport.getAlignmentGapAnnotation();
+  }
+
+  /**
    * update the consensus annotation from the sequence profile data using
    * current visualization settings.
    */
@@ -151,15 +158,64 @@ public class ConsensusThread extends AlignCalcWorker implements
 
   public void updateResultAnnotation(boolean immediate)
   {
-    AlignmentAnnotation consensus = alignViewport
-            .getAlignmentConsensusAnnotation();
-    Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
+    AlignmentAnnotation consensus = getConsensusAnnotation();
+    ProfilesI hconsensus = (ProfilesI) 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);
+      AlignmentAnnotation gap = getGapAnnotation();
+      if (gap != null)
+      {
+        deriveGap(gap, hconsensus);
+      }
     }
   }
+
+  /**
+   * Convert the computed consensus data into the desired annotation for
+   * display.
+   * 
+   * @param consensusAnnotation
+   *          the annotation to be populated
+   * @param hconsensus
+   *          the computed consensus data
+   */
+  protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
+          ProfilesI hconsensus)
+  {
+    long nseq = getSequences().length;
+    AAFrequency.completeConsensus(consensusAnnotation, hconsensus,
+            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+            alignViewport.isIgnoreGapsConsensus(),
+            alignViewport.isShowSequenceLogo(), nseq);
+  }
+
+  /**
+   * Convert the computed consensus data into a gap annotation row for display.
+   * 
+   * @param gapAnnotation
+   *          the annotation to be populated
+   * @param hconsensus
+   *          the computed consensus data
+   */
+  protected void deriveGap(AlignmentAnnotation gapAnnotation,
+          ProfilesI hconsensus)
+  {
+    long nseq = getSequences().length;
+    AAFrequency.completeGapAnnot(gapAnnotation, hconsensus,
+            hconsensus.getStartColumn(), hconsensus.getEndColumn() + 1,
+            nseq);
+  }
+
+  /**
+   * Get the consensus data stored on the viewport.
+   * 
+   * @return
+   */
+  protected Object getViewportConsensus()
+  {
+    // TODO convert ComplementConsensusThread to use Profile
+    return alignViewport.getSequenceConsensusHash();
+  }
 }