JAL-728 offer choice of substitution matrix for Quality calculation

[jalview.git] / src / jalview / viewmodel / AlignmentViewport.java

diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 3547757..7d152ce 100644 (file)
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -20,17 +20,6 @@
  */
 package jalview.viewmodel;
 
-import java.awt.Color;
-import java.beans.PropertyChangeSupport;
-import java.util.ArrayDeque;
-import java.util.ArrayList;
-import java.util.BitSet;
-import java.util.Deque;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Map;
-
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.analysis.Conservation;
 import jalview.api.AlignCalcManagerI;
@@ -62,12 +51,24 @@ import jalview.structure.VamsasSource;
 import jalview.util.Comparison;
 import jalview.util.MapList;
 import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
 import jalview.viewmodel.styles.ViewStyle;
 import jalview.workers.AlignCalcManager;
 import jalview.workers.ComplementConsensusThread;
 import jalview.workers.ConsensusThread;
 import jalview.workers.StrucConsensusThread;
 
+import java.awt.Color;
+import java.beans.PropertyChangeSupport;
+import java.util.ArrayDeque;
+import java.util.ArrayList;
+import java.util.BitSet;
+import java.util.Deque;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Map;
+
 /**
  * base class holding visualization and analysis attributes and common logic for
  * an active alignment view displayed in the GUI
@@ -1859,7 +1860,7 @@ public abstract class AlignmentViewport implements AlignViewportI,
       {
         rs.setConservation(Conservation.calculateConservation("All",
                 alignment.getSequences(), 0, alignment.getWidth(), false,
-                getConsPercGaps(), false));
+                getConsPercGaps(), false, null));
       }
     }
 
@@ -1988,8 +1989,9 @@ public abstract class AlignmentViewport implements AlignViewportI,
       if (quality == null)
       {
         quality = new AlignmentAnnotation("Quality",
-                "Alignment Quality based on Blosum62 scores",
-                new Annotation[1], 0f, 11f, AlignmentAnnotation.BAR_GRAPH);
+                MessageManager.formatMessage("label.quality_label",
+                        "Blosum62"), new Annotation[1], 0f, 11f,
+                AlignmentAnnotation.BAR_GRAPH);
         quality.hasText = true;
         quality.autoCalculated = true;
         alignment.addAnnotation(quality);