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 4bd8c48..2b11477 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -26,7 +26,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
-import jalview.datamodel.Profile;
+import jalview.datamodel.ProfileI;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 
@@ -124,7 +124,7 @@ public class ConsensusThread extends AlignCalcWorker
    */
   protected void computeConsensus(AlignmentI alignment)
   {
-    Profile[] hconsensus = new Profile[alignment.getWidth()];
+    ProfileI[] hconsensus = new ProfileI[alignment.getWidth()];
 
     SequenceI[] aseqs = getSequences();
     AAFrequency.calculate(aseqs, 0, alignment.getWidth(), hconsensus, true);
@@ -144,7 +144,7 @@ public class ConsensusThread extends AlignCalcWorker
   /**
    * @param hconsensus
    */
-  protected void setColourSchemeConsensus(Profile[] hconsensus)
+  protected void setColourSchemeConsensus(ProfileI[] hconsensus)
   {
     ColourSchemeI globalColourScheme = alignViewport
             .getGlobalColourScheme();
@@ -177,7 +177,7 @@ public class ConsensusThread extends AlignCalcWorker
   public void updateResultAnnotation(boolean immediate)
   {
     AlignmentAnnotation consensus = getConsensusAnnotation();
-    Profile[] hconsensus = (Profile[]) getViewportConsensus();
+    ProfileI[] hconsensus = (ProfileI[]) getViewportConsensus();
     if (immediate || !calcMan.isWorking(this) && consensus != null
             && hconsensus != null)
     {
@@ -195,7 +195,7 @@ public class ConsensusThread extends AlignCalcWorker
    *          the computed consensus data
    */
   protected void deriveConsensus(AlignmentAnnotation consensusAnnotation,
-          Profile[] hconsensus)
+          ProfileI[] hconsensus)
   {
     long nseq = getSequences().length;
     AAFrequency.completeConsensus(consensusAnnotation, hconsensus, 0,