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 7ba9977..510df94 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -29,10 +29,10 @@ 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;
+import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.Color;
 import java.awt.Dimension;
@@ -121,13 +121,13 @@ public class TreeCanvas extends Panel implements MouseListener,
     tree.findHeight(tree.getTopNode());
 
     // Now have to calculate longest name based on the leaves
-    Vector leaves = tree.findLeaves(tree.getTopNode(), new Vector());
+    Vector<SequenceNode> leaves = tree.findLeaves(tree.getTopNode());
     boolean has_placeholders = false;
     longestName = "";
 
     for (int i = 0; i < leaves.size(); i++)
     {
-      SequenceNode lf = (SequenceNode) leaves.elementAt(i);
+      SequenceNode lf = leaves.elementAt(i);
 
       if (lf.isPlaceholder())
       {
@@ -524,13 +524,11 @@ public class TreeCanvas extends Panel implements MouseListener,
       }
       else
       {
-        Vector leaves = new Vector();
-        tree.findLeaves(highlightNode, leaves);
+        Vector<SequenceNode> leaves = tree.findLeaves(highlightNode);
 
         for (int i = 0; i < leaves.size(); i++)
         {
-          SequenceI seq = (SequenceI) ((SequenceNode) 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 l = tree.findLeaves(
-              (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+      Vector<SequenceNode> l = tree.findLeaves(tree.getGroups()
+              .elementAt(i));
 
-      Vector sequences = new Vector();
+      Vector<SequenceI> sequences = new Vector<SequenceI>();
       for (int j = 0; j < l.size(); j++)
       {
-        SequenceI s1 = (SequenceI) ((SequenceNode) 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);
@@ -715,7 +714,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     ap.updateAnnotation();
     if (av.getCodingComplement() != null)
     {
-      ((AlignViewport) av.getCodingComplement()).firePropertyChange(
+      ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
               "alignment", null, ap.av.getAlignment().getSequences());
     }
   }