X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fworkers%2FConsensusThread.java;h=e12c5b8d87765b52779d4ba9dccff4e140615cf7;hb=refs%2Fheads%2Fj2s%2Fdevelop-bh;hp=9bdd714739bf2841be55a499f1f74cfb967f1ea3;hpb=f61b2748a32ef03e687abc37b97640873c2e44aa;p=jalview.git

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index 9bdd714..e12c5b8 100644
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -1,5 +1,27 @@
+/*
+ * 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.
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.workers;
 
+import java.util.Hashtable;
+
 import jalview.analysis.AAFrequency;
 import jalview.api.AlignCalcWorkerI;
 import jalview.api.AlignViewportI;
@@ -7,11 +29,11 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
-import java.util.Hashtable;
-
-public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
+public class ConsensusThread extends AlignCalcWorker implements
+        AlignCalcWorkerI
 {
   public ConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
@@ -22,16 +44,18 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
   @Override
   public void run()
   {
+  	
     if (calcMan.isPending(this))
     {
       return;
     }
     calcMan.notifyStart(this);
-    long started=System.currentTimeMillis();
+    long started = System.currentTimeMillis();
     try
     {
-      AlignmentAnnotation consensus = alignViewport.getAlignmentConsensusAnnotation();
-      if (consensus==null || calcMan.isPending(this))  {
+      AlignmentAnnotation consensus = getConsensusAnnotation();
+      if (consensus == null || calcMan.isPending(this))
+      {
         calcMan.workerComplete(this);
         return;
       }
@@ -42,7 +66,7 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
         {
           if (ap != null)
           {
-           ap.paintAlignment(false);
+            ap.paintAlignment(false);
           }
           Thread.sleep(200);
         } catch (Exception ex)
@@ -53,6 +77,7 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
       if (alignViewport.isClosed())
       {
         abortAndDestroy();
+        return;
       }
       AlignmentI alignment = alignViewport.getAlignment();
 
@@ -61,55 +86,90 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
       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 {
-       AAFrequency.calculate(alignment.getSequencesArray(), 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;
       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);
 
-    calcMan.workerComplete(this);
-    if (ap != null)
+    alignViewport.setSequenceConsensusHash(hconsensus);
+    setColourSchemeConsensus(hconsensus);
+  }
+
+  /**
+   * @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.
    */
@@ -121,14 +181,40 @@ public class ConsensusThread extends AlignCalcWorker implements AlignCalcWorkerI
 
   public void updateResultAnnotation(boolean immediate)
   {
-    AlignmentAnnotation consensus = alignViewport
-            .getAlignmentConsensusAnnotation();
-    Hashtable[] hconsensus = alignViewport.getSequenceConsensusHash();
-    if (immediate || !calcMan.isWorking(this) && consensus!=null && hconsensus!=null)
+    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());
+      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();
+  }
 }