X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=c8f526ceedd611ef60a43684fedc4e98ac4c6c6a;hb=3f12f4932226512316ec113e600695150431fd0a;hp=7d457d4129bcac4ccda243d4e6823baddb0b3882;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 7d457d4..c8f526c 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,15 +20,36 @@
  */
 package jalview.appletgui;
 
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.schemes.*;
-import jalview.util.*;
+import jalview.analysis.Conservation;
+import jalview.analysis.NJTree;
+import jalview.api.AlignViewportI;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+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;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Point;
+import java.awt.Rectangle;
+import java.awt.ScrollPane;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
 
 public class TreeCanvas extends Panel implements MouseListener,
         MouseMotionListener
@@ -101,13 +122,13 @@ 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())
       {
@@ -504,12 +525,11 @@ 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))
+          SequenceI seq = (SequenceI) leaves.elementAt(i)
                   .element();
           treeSelectionChanged(seq);
         }
@@ -582,6 +602,13 @@ public class TreeCanvas extends Panel implements MouseListener,
         av.setSelectionGroup(null);
         av.getAlignment().deleteAllGroups();
         av.clearSequenceColours();
+        final AlignViewportI codingComplement = av.getCodingComplement();
+        if (codingComplement != null)
+        {
+          codingComplement.setSelectionGroup(null);
+          codingComplement.getAlignment().deleteAllGroups();
+          codingComplement.clearSequenceColours();
+        }
 
         colourGroups();
 
@@ -602,13 +629,13 @@ public class TreeCanvas extends Panel implements MouseListener,
               (int) (Math.random() * 255), (int) (Math.random() * 255));
       setColor((SequenceNode) tree.getGroups().elementAt(i), col.brighter());
 
-      Vector l = tree.findLeaves(
-              (SequenceNode) tree.getGroups().elementAt(i), new Vector());
+      Vector<SequenceNode> l = tree.findLeaves((SequenceNode) 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))
+        SequenceI s1 = (SequenceI) l.elementAt(j)
                 .element();
         if (!sequences.contains(s1))
         {
@@ -639,7 +666,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         if (cs != null)
         {
           cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.getIgnoreGapsConsensus());
+                  av.isIgnoreGapsConsensus());
         }
       }
       // TODO: cs used to be initialized with a sequence collection and
@@ -666,9 +693,31 @@ public class TreeCanvas extends Panel implements MouseListener,
 
       av.getAlignment().addGroup(sg);
 
+      // TODO this is duplicated with gui TreeCanvas - refactor
+      av.getAlignment().addGroup(sg);
+      final AlignViewportI codingComplement = av.getCodingComplement();
+      if (codingComplement != null)
+      {
+        SequenceGroup mappedGroup = MappingUtils.mapSequenceGroup(sg, av,
+                codingComplement);
+        if (mappedGroup.getSequences().size() > 0)
+        {
+          codingComplement.getAlignment().addGroup(mappedGroup);
+          for (SequenceI seq : mappedGroup.getSequences())
+          {
+            // TODO why does gui require col.brighter() here??
+            codingComplement.setSequenceColour(seq, col);
+          }
+        }
+      }
+
     }
     ap.updateAnnotation();
-
+    if (av.getCodingComplement() != null)
+    {
+      ((AlignmentViewport) av.getCodingComplement()).firePropertyChange(
+              "alignment", null, ap.av.getAlignment().getSequences());
+    }
   }
 
   public void setShowDistances(boolean state)