X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=78c6da24a0caf2ee7852d06aad41f39211c0565e;hb=3c8a25936a2d805e7e3d7ab82f83b13135406d18;hp=86cebc42a89e56a8e2beece8b1f5f209fc9ffcc4;hpb=a8f483d04205bb8273ee311c12968b7e86d205fa;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 86cebc4..78c6da2 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,40 +1,37 @@
 /*
- * 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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)
   {
@@ -52,21 +49,22 @@ public class ConsensusThread extends AlignCalcWorker implements
     long started = System.currentTimeMillis();
     try
     {
-      AlignmentAnnotation consensus = alignViewport
-              .getAlignmentConsensusAnnotation();
-      if (consensus == null || calcMan.isPending(this))
+      AlignmentAnnotation consensus = getConsensusAnnotation();
+      AlignmentAnnotation gap = getGapAnnotation();
+      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.");
+        // System.err.println("Thread
+        // (Consensus"+Thread.currentThread().getName()+") Waiting around.");
         try
         {
           if (ap != null)
           {
-            ap.paintAlignment(false);
+            ap.paintAlignment(false, false);
           }
           Thread.sleep(200);
         } catch (Exception ex)
@@ -77,6 +75,7 @@ public class ConsensusThread extends AlignCalcWorker implements
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -85,58 +84,107 @@ 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, 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();
+    if (consensus != null)
+    {
+      consensus.annotations = new Annotation[aWidth];
     }
+    AlignmentAnnotation gap = getGapAnnotation();
+    if (gap != null)
+    {
+      gap.annotations = new Annotation[aWidth];
+    }
+  }
+
+  /**
+   * @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();
+  }
 
-    calcMan.workerComplete(this);
-    if (ap != null)
+  /**
+   * @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.
    */
@@ -148,15 +196,65 @@ 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();
+  }
 }