fix for JAL-1398 - original colourscheme is enabled if colourscheme has a BaseColour...

[jalview.git] / src / jalview / datamodel / SequenceGroup.java

diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java
index c42a955..9ed3a53 100755 (executable)
--- a/src/jalview/datamodel/SequenceGroup.java
+++ b/src/jalview/datamodel/SequenceGroup.java
@@ -493,7 +493,7 @@ public class SequenceGroup implements AnnotatedCollectionI
               endRes + 1, showSequenceLogo);
       if (consensus != null)
       {
-        _updateConsensusRow(cnsns);
+        _updateConsensusRow(cnsns, sequences.size());
       }
       if (cs != null)
       {
@@ -552,7 +552,7 @@ public class SequenceGroup implements AnnotatedCollectionI
 
   public Hashtable[] consensusData = null;
 
-  private void _updateConsensusRow(Hashtable[] cnsns)
+  private void _updateConsensusRow(Hashtable[] cnsns, long nseq)
   {
     if (consensus == null)
     {
@@ -569,7 +569,7 @@ public class SequenceGroup implements AnnotatedCollectionI
     consensus.annotations = new Annotation[aWidth]; // should be alignment width
 
     AAFrequency.completeConsensus(consensus, cnsns, startRes, endRes + 1,
-            ignoreGapsInConsensus, showSequenceLogo); // TODO: setting container
+            ignoreGapsInConsensus, showSequenceLogo, nseq); // TODO: setting container
                                                       // for
                                                       // ignoreGapsInConsensusCalculation);
   }
@@ -612,9 +612,9 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * 
+   * @return the first column selected by this group. Runs from 0<=i<N_cols
    */
   public int getStartRes()
   {
@@ -622,9 +622,8 @@ public class SequenceGroup implements AnnotatedCollectionI
   }
 
   /**
-   * DOCUMENT ME!
    * 
-   * @return DOCUMENT ME!
+   * @return the groups last selected column. Runs from 0<=i<N_cols
    */
   public int getEndRes()
   {
@@ -1034,12 +1033,12 @@ public class SequenceGroup implements AnnotatedCollectionI
     {
       consensus = new AlignmentAnnotation("", "", new Annotation[1], 0f,
               100f, AlignmentAnnotation.BAR_GRAPH);
+      consensus.hasText = true;
+      consensus.autoCalculated = true;
+      consensus.groupRef = this;
+      consensus.label = "Consensus for " + getName();
+      consensus.description = "Percent Identity";
     }
-    consensus.hasText = true;
-    consensus.autoCalculated = true;
-    consensus.groupRef = this;
-    consensus.label = "Consensus for " + getName();
-    consensus.description = "Percent Identity";
     return consensus;
   }