JAL-2416 seqspace.scm and PIDDistanceModel replaced by PIDModel

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

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 510df94..7040c42 100755 (executable)
--- 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();
 
@@ -672,13 +672,13 @@ public class TreeCanvas extends Panel implements MouseListener,
       // instead we set it manually - recalc called after updateAnnotation
       sg.setColourScheme(cs);
       sg.getGroupColourScheme().setThreshold(
-              av.getViewportColourScheme().getThreshold(),
+              av.getResidueShading().getThreshold(),
               av.isIgnoreGapsConsensus());
 
       sg.setName("JTreeGroup:" + sg.hashCode());
       sg.setIdColour(col);
       if (av.getGlobalColourScheme() != null
-              && av.getViewportColourScheme().conservationApplied())
+              && av.getResidueShading().conservationApplied())
       {
         Conservation c = new Conservation("Group", sg.getSequences(null),
                 sg.getStartRes(), sg.getEndRes());