X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=8d0cc4290a1bd103a4550730c9710feb41df8940;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=ca78bdac0adb7e304535549d6f78fb762dcbe914;hpb=c78ae20a67370e2566d204e3f4c55749ad9bad27;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index ca78bda..8d0cc42 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -1,31 +1,55 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
  * This file is part of Jalview.
- *
+ * 
  * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
- * Jalview is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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
@@ -65,6 +89,7 @@ public class TreeCanvas extends Panel implements MouseListener,
   SequenceNode highlightNode;
 
   AlignmentPanel ap;
+
   public TreeCanvas(AlignmentPanel ap, ScrollPane scroller)
   {
     this.ap = ap;
@@ -199,8 +224,7 @@ public class TreeCanvas extends Panel implements MouseListener,
       // Colour selected leaves differently
       SequenceGroup selected = av.getSelectionGroup();
       if (selected != null
-              && selected.getSequences(null).contains(
-                      node.element()))
+              && selected.getSequences(null).contains(node.element()))
       {
         g.setColor(Color.gray);
 
@@ -442,8 +466,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     // for
     // scrollbar
 
-    float wscale = (width - labelLength - offx * 2)
-            / tree.getMaxHeight();
+    float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
@@ -467,8 +490,7 @@ public class TreeCanvas extends Panel implements MouseListener,
         g.setColor(Color.gray);
       }
 
-      int x = (int) (threshold
-              * (getSize().width - labelLength - 2 * offx) + offx);
+      int x = (int) (threshold * (getSize().width - labelLength - 2 * offx) + offx);
 
       g.drawLine(x, 0, x, getSize().height);
     }
@@ -580,7 +602,14 @@ public class TreeCanvas extends Panel implements MouseListener,
 
         av.setSelectionGroup(null);
         av.getAlignment().deleteAllGroups();
-        av.sequenceColours = null;
+        av.clearSequenceColours();
+        final AlignViewportI codingComplement = av.getCodingComplement();
+        if (codingComplement != null)
+        {
+          codingComplement.setSelectionGroup(null);
+          codingComplement.getAlignment().deleteAllGroups();
+          codingComplement.clearSequenceColours();
+        }
 
         colourGroups();
 
@@ -631,19 +660,20 @@ public class TreeCanvas extends Panel implements MouseListener,
         }
         else
         {
-          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty.getColourName(av
-                  .getGlobalColourScheme()));
+          cs = ColourSchemeProperty.getColour(sg, ColourSchemeProperty
+                  .getColourName(av.getGlobalColourScheme()));
         }
         // cs is null if shading is an annotationColourGradient
-        if (cs!=null)
+        if (cs != null)
         {
           cs.setThreshold(av.getGlobalColourScheme().getThreshold(),
-                  av.getIgnoreGapsConsensus());
+                  av.isIgnoreGapsConsensus());
         }
       }
-      // TODO: cs used to be initialized with a sequence collection and recalcConservation called automatically
+      // 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.cs = cs;
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
@@ -664,9 +694,31 @@ 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)