X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FTreeCanvas.java;h=7040c42f26aaf554723f5e4508233b44944194f3;hb=6666fd8b18b395d444e7f4c76016231f5a4d3669;hp=ca9f2d847447c65ffe713a35d97a518ed0b58835;hpb=320c96aed11f5c396a9efd9ea83b0e35f05e21e4;p=jalview.git

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index ca9f2d8..7040c42 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -146,7 +146,7 @@ public class TreeCanvas extends Panel implements MouseListener,
   }
 
   public void drawNode(Graphics g, SequenceNode node, float chunk,
-          float scale, int width, int offx, int offy)
+          double scale, int width, int offx, int offy)
   {
     if (node == null)
     {
@@ -157,8 +157,8 @@ public class TreeCanvas extends Panel implements MouseListener,
     {
       // Drawing leaf node
 
-      float height = node.height;
-      float dist = node.dist;
+      double height = node.height;
+      double dist = node.dist;
 
       int xstart = (int) ((height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
@@ -240,8 +240,8 @@ public class TreeCanvas extends Panel implements MouseListener,
       drawNode(g, (SequenceNode) node.right(), chunk, scale, width, offx,
               offy);
 
-      float height = node.height;
-      float dist = node.dist;
+      double height = node.height;
+      double dist = node.dist;
 
       int xstart = (int) ((height - dist) * scale) + offx;
       int xend = (int) (height * scale) + offx;
@@ -338,7 +338,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
     SequenceNode top = tree.getTopNode();
 
-    float wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
+    double wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
     if (top.count == 0)
     {
       top.count = ((SequenceNode) top.left()).count
@@ -350,7 +350,7 @@ public class TreeCanvas extends Panel implements MouseListener,
   }
 
   public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
-          float scale, int width, int offx, int offy)
+          double scale, int width, int offx, int offy)
   {
     if (node == null)
     {
@@ -359,7 +359,7 @@ public class TreeCanvas extends Panel implements MouseListener,
 
     if (node.left() == null && node.right() == null)
     {
-      float height = node.height;
+      double height = node.height;
       // float dist = node.dist;
 
       // int xstart = (int) ( (height - dist) * scale) + offx;
@@ -465,7 +465,7 @@ public class TreeCanvas extends Panel implements MouseListener,
     // for
     // scrollbar
 
-    float wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
+    double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
 
     SequenceNode top = tree.getTopNode();
 
@@ -661,31 +661,33 @@ public class TreeCanvas extends Panel implements MouseListener,
                           .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.getResidueShading().getThreshold(),
+              av.isIgnoreGapsConsensus());
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
       if (av.getGlobalColourScheme() != null
-              && av.getGlobalColourScheme().conservationApplied())
+              && av.getResidueShading().conservationApplied())
       {
         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);