Merge branch 'bug/JAL-3120restoreFeatureColour' into merge/JAL-3120

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

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index c88a24a..78c6da2 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -21,14 +21,14 @@
 package jalview.workers;
 
 import jalview.analysis.AAFrequency;
-import jalview.analysis.Profile;
 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;
 
 public class ConsensusThread extends AlignCalcWorker
 {
@@ -50,19 +50,21 @@ public class ConsensusThread extends AlignCalcWorker
     try
     {
       AlignmentAnnotation consensus = getConsensusAnnotation();
-      if (consensus == null || calcMan.isPending(this))
+      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)
@@ -91,7 +93,7 @@ public class ConsensusThread extends AlignCalcWorker
 
       if (ap != null)
       {
-        ap.paintAlignment(true);
+        ap.paintAlignment(true, true);
       }
     } catch (OutOfMemoryError error)
     {
@@ -116,7 +118,15 @@ public class ConsensusThread extends AlignCalcWorker
   protected void eraseConsensus(int aWidth)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    consensus.annotations = new Annotation[aWidth];
+    if (consensus != null)
+    {
+      consensus.annotations = new Annotation[aWidth];
+    }
+    AlignmentAnnotation gap = getGapAnnotation();
+    if (gap != null)
+    {
+      gap.annotations = new Annotation[aWidth];
+    }
   }
 
   /**
@@ -124,10 +134,11 @@ public class ConsensusThread extends AlignCalcWorker
    */
   protected void computeConsensus(AlignmentI alignment)
   {
-    Profile[] hconsensus = new Profile[alignment.getWidth()];
 
     SequenceI[] aseqs = getSequences();
-    AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
+    int width = alignment.getWidth();
+    ProfilesI hconsensus = AAFrequency.calculate(aseqs, width, 0, width,
+            true);
 
     alignViewport.setSequenceConsensusHash(hconsensus);
     setColourSchemeConsensus(hconsensus);
@@ -144,13 +155,12 @@ public class ConsensusThread extends AlignCalcWorker
   /**
    * @param hconsensus
    */
-  protected void setColourSchemeConsensus(Profile[] hconsensus)
+  protected void setColourSchemeConsensus(ProfilesI hconsensus)
   {
-    ColourSchemeI globalColourScheme = alignViewport
-            .getGlobalColourScheme();
-    if (globalColourScheme != null)
+    ResidueShaderI cs = alignViewport.getResidueShading();
+    if (cs != null)
     {
-      globalColourScheme.setConsensus(hconsensus);
+      cs.setConsensus(hconsensus);
     }
   }
 
@@ -165,6 +175,16 @@ public class ConsensusThread extends AlignCalcWorker
   }
 
   /**
+   * 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.
    */
@@ -177,11 +197,16 @@ public class ConsensusThread extends AlignCalcWorker
   public void updateResultAnnotation(boolean immediate)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    Profile[] hconsensus = (Profile[]) getViewportConsensus();
+    ProfilesI hconsensus = (ProfilesI) getViewportConsensus();
     if (immediate || !calcMan.isWorking(this) && consensus != null
             && hconsensus != null)
     {
       deriveConsensus(consensus, hconsensus);
+      AlignmentAnnotation gap = getGapAnnotation();
+      if (gap != null)
+      {
+        deriveGap(gap, hconsensus);
+      }
     }
   }
 
@@ -195,20 +220,39 @@ public class ConsensusThread extends AlignCalcWorker
    *          the computed consensus data
    */
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
-          Profile[] hconsensus)
+          ProfilesI hconsensus)
   {
+
     long nseq = getSequences().length;
-    AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,
-            hconsensus.length, alignViewport.isIgnoreGapsConsensus(),
+    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()
+  protected Object getViewportConsensus()
   {
     // TODO convert ComplementConsensusThread to use Profile
     return alignViewport.getSequenceConsensusHash();