Merge branch 'Release_2_8_0b1_Branch' into try_r20b1_merge

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

diff --git a/src/jalview/workers/ConsensusThread.java b/src/jalview/workers/ConsensusThread.java
index b36f367..97d1236 100644 (file)
--- a/src/jalview/workers/ConsensusThread.java
+++ b/src/jalview/workers/ConsensusThread.java
@@ -25,6 +25,7 @@ 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;
@@ -32,6 +33,8 @@ import java.util.Hashtable;
 public class ConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
 {
+  private long nseq=-1;
+
   public ConsensusThread(AlignViewportI alignViewport,
           AlignmentViewPanel alignPanel)
   {
@@ -95,7 +98,9 @@ public class ConsensusThread extends AlignCalcWorker implements
       hconsensus = new Hashtable[aWidth];
       try
       {
-        AAFrequency.calculate(alignment.getSequencesArray(), 0,
+        SequenceI aseqs[] = alignment.getSequencesArray();
+        nseq = aseqs.length;
+        AAFrequency.calculate(aseqs, 0,
                 alignment.getWidth(), hconsensus, true);
       } catch (ArrayIndexOutOfBoundsException x)
       {
@@ -151,7 +156,7 @@ public class ConsensusThread extends AlignCalcWorker implements
     {
       AAFrequency.completeConsensus(consensus, hconsensus, 0,
               hconsensus.length, alignViewport.getIgnoreGapsConsensus(),
-              alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }
 }