Merge branch 'features/JAL-2360colourSchemeApplicability' into features/JAL-2371colle...

[jalview.git] / src / jalview / appletgui / TreeCanvas.java

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index c8f526c..510df94 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -29,7 +29,6 @@ import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.util.Format;
 import jalview.util.MappingUtils;
@@ -529,8 +528,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
         for (int i = 0; i < leaves.size(); i++)
         {
-          SequenceI seq = (SequenceI) leaves.elementAt(i)
-                  .element();
+          SequenceI seq = (SequenceI) leaves.elementAt(i).element();
           treeSelectionChanged(seq);
         }
       }
@@ -627,16 +625,15 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       Color col = new Color((int) (Math.random() * 255),
               (int) (Math.random() * 255), (int) (Math.random() * 255));
-      setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
+      setColor(tree.getGroups().elementAt(i), col.brighter());
 
-      Vector<SequenceNode> l = tree.findLeaves((SequenceNode) tree
-              .getGroups().elementAt(i));
+      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+              .elementAt(i));
 
       Vector<SequenceI> sequences = new Vector<SequenceI>();
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) l.elementAt(j)
-                .element();
+        SequenceI s1 = (SequenceI) l.elementAt(j).element();
         if (!sequences.contains(s1))
         {
           sequences.addElement(s1);
@@ -659,36 +656,38 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
-                  .getColourName(av.getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColourScheme(sg,
+                  ColourSchemeProperty.getColourName(av
+                          .getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
-        if (cs != null)
-        {
-          cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.isIgnoreGapsConsensus());
-        }
+        // if (cs != null)
+        // {
+        // cs.setThreshold(av.getViewportColourScheme().getThreshold(),
+        // av.isIgnoreGapsConsensus());
+        // }
       }
       // TODO: cs used to be initialized with a sequence collection and
       // recalcConservation called automatically
       // instead we set it manually - recalc called after updateAnnotation
-      sg.cs = cs;
+      sg.setColourScheme(cs);
+      sg.getGroupColourScheme().setThreshold(
+              av.getViewportColourScheme().getThreshold(),
+              av.isIgnoreGapsConsensus());
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
       if (av.getGlobalColourScheme() != null
-              && av.getGlobalColourScheme().conservationApplied())
+              && av.getViewportColourScheme().conservationApplied())
       {
-        Conservation c = new Conservation("Group",
-                ResidueProperties.propHash, 3, sg.getSequences(null),
+        Conservation c = new Conservation("Group", sg.getSequences(null),
                 sg.getStartRes(), sg.getEndRes());
 
         c.calculate();
         c.verdict(false, av.getConsPercGaps());
-        cs.setConservation(c);
-
-        sg.cs = cs;
 
+        sg.setColourScheme(cs);
+        sg.getGroupColourScheme().setConservation(c);
       }
 
       av.getAlignment().addGroup(sg);