Merge branch 'JAL-1373_precision' into Release_2_8_1_Branch

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

diff --git a/src/jalview/workers/StrucConsensusThread.java b/src/jalview/workers/StrucConsensusThread.java
index 86c3336..25e5cde 100644 (file)
--- a/src/jalview/workers/StrucConsensusThread.java
+++ b/src/jalview/workers/StrucConsensusThread.java
@@ -26,6 +26,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
 
 public class StrucConsensusThread extends AlignCalcWorker implements
         AlignCalcWorkerI
@@ -40,6 +41,8 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
   Hashtable[] hStrucConsensus;
 
+  private long nseq=-1;
+
   @Override
   public void run()
   {
@@ -107,8 +110,10 @@ public class StrucConsensusThread extends AlignCalcWorker implements
 
       try
       {
-        jalview.analysis.StructureFrequency.calculate(
-                alignment.getSequencesArray(), 0, alignment.getWidth(),
+        final SequenceI[] arr=
+                alignment.getSequencesArray();
+        nseq = arr.length;
+        jalview.analysis.StructureFrequency.calculate(arr, 0, alignment.getWidth(),
                 hStrucConsensus, true, rnaStruc);
       } catch (ArrayIndexOutOfBoundsException x)
       {
@@ -159,7 +164,7 @@ public class StrucConsensusThread extends AlignCalcWorker implements
       StructureFrequency.completeConsensus(strucConsensus, hStrucConsensus,
               0, hStrucConsensus.length,
               alignViewport.getIgnoreGapsConsensus(),
-              alignViewport.isShowSequenceLogo());
+              alignViewport.isShowSequenceLogo(), nseq);
     }
   }