JAL-98 ProfileI interface for Profile

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

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index f04ce1f..2b11477 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 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -26,11 +26,10 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ProfileI;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
-import java.util.Hashtable;
-
 public class ConsensusThread extends AlignCalcWorker
 {
   public ConsensusThread(AlignViewportI alignViewport,
@@ -125,7 +124,7 @@ public class ConsensusThread extends AlignCalcWorker
    */
   protected void computeConsensus(AlignmentI alignment)
   {
-    Hashtable[] hconsensus = new Hashtable[alignment.getWidth()];
+    ProfileI[] hconsensus = new ProfileI[alignment.getWidth()];
 
     SequenceI[] aseqs = getSequences();
     AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
@@ -145,7 +144,7 @@ public class ConsensusThread extends AlignCalcWorker
   /**
    * @param hconsensus
    */
-  protected void setColourSchemeConsensus(Hashtable[] hconsensus)
+  protected void setColourSchemeConsensus(ProfileI[] hconsensus)
   {
     ColourSchemeI globalColourScheme = alignViewport
             .getGlobalColourScheme();
@@ -178,7 +177,7 @@ public class ConsensusThread extends AlignCalcWorker
   public void updateResultAnnotation(boolean immediate)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    Hashtable[] hconsensus = getViewportConsensus();
+    ProfileI[] hconsensus = (ProfileI[]) getViewportConsensus();
     if (immediate || !calcMan.isWorking(this) && consensus != null
             && hconsensus != null)
     {
@@ -192,15 +191,15 @@ public class ConsensusThread extends AlignCalcWorker
    * 
    * @param consensusAnnotation
    *          the annotation to be populated
-   * @param consensusData
+   * @param hconsensus
    *          the computed consensus data
    */
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
-          Hashtable[] consensusData)
+          ProfileI[] hconsensus)
   {
     long nseq = getSequences().length;
-    AAFrequency.completeConsensus(consensusAnnotation, consensusData, 0,
-            consensusData.length, alignViewport.isIgnoreGapsConsensus(),
+    AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,
+            hconsensus.length, alignViewport.isIgnoreGapsConsensus(),
             alignViewport.isShowSequenceLogo(), nseq);
   }
 
@@ -209,8 +208,9 @@ public class ConsensusThread extends AlignCalcWorker
    * 
    * @return
    */
-  protected Hashtable[] getViewportConsensus()
+  protected Object[] getViewportConsensus()
   {
+    // TODO convert ComplementConsensusThread to use Profile
     return alignViewport.getSequenceConsensusHash();
   }
 }