X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FRotatableCanvas.java;h=a2463e87d7a44c80e61fb26a8f884c5f8c3cc2d1;hb=10c2447aefb29bddf48799fb5a1631932a5940a8;hp=370de5f9cdbc95c8fb2b7021fa67e671520cfa1e;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/appletgui/RotatableCanvas.java b/src/jalview/appletgui/RotatableCanvas.java
index 370de5f..a2463e8 100755
--- a/src/jalview/appletgui/RotatableCanvas.java
+++ b/src/jalview/appletgui/RotatableCanvas.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
  *
  * This program is free software; you can redistribute it and/or
  * modify it under the terms of the GNU General Public License
@@ -99,7 +99,7 @@ public class RotatableCanvas
   {
     this.points = points;
     this.npoint = npoint;
-    PaintRefresher.Register(this, av.alignment);
+    PaintRefresher.Register(this, av.getSequenceSetId());
 
     prefsize = getPreferredSize();
     orig = new float[npoint][3];
@@ -297,6 +297,7 @@ public class RotatableCanvas
   {
     paint(g);
   }
+
   public void paint(Graphics g)
   {
     if (points == null)
@@ -329,7 +330,7 @@ public class RotatableCanvas
         drawAxes(ig);
       }
 
-      if(tooltip!=null)
+      if (tooltip != null)
       {
         ig.setColor(Color.red);
         ig.drawString(tooltip, toolx, tooly);
@@ -371,18 +372,19 @@ public class RotatableCanvas
       int y = (int) ( (float) (sp.coord[1] - centre[1]) * scale) + halfheight;
       float z = sp.coord[1] - centre[2];
 
-      if (sp.sequence.getColor() == Color.black)
+      if (av.getSequenceColour(sp.sequence) == Color.black)
       {
         g.setColor(Color.white);
       }
       else
       {
-        g.setColor(sp.sequence.getColor());
+        g.setColor(av.getSequenceColour(sp.sequence));
       }
 
       if (av.getSelectionGroup() != null)
       {
-        if (av.getSelectionGroup().sequences.contains( ( (SequencePoint) points.
+        if (av.getSelectionGroup().getSequences(null).contains( ( (
+            SequencePoint) points.
             elementAt(i)).sequence))
         {
           g.setColor(Color.gray);
@@ -497,33 +499,34 @@ public class RotatableCanvas
       if (av.getSelectionGroup() != null)
       {
         av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
-        PaintRefresher.Refresh(this, av.alignment);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+        PaintRefresher.Refresh(this, av.getSequenceSetId());
       }
       else
       {
         av.setSelectionGroup(new SequenceGroup());
         av.getSelectionGroup().addOrRemove(found, true);
-        av.getSelectionGroup().setEndRes(av.alignment.getWidth()-1);
+        av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
 
       }
     }
     repaint();
   }
 
-
   public void mouseMoved(MouseEvent evt)
   {
-     SequenceI found = findPoint(evt.getX(), evt.getY());
-     if(found==null)
-       tooltip = null;
-     else
-     {
-       tooltip = found.getName();
-       toolx = evt.getX();
-       tooly = evt.getY();
-     }
-     repaint();
+    SequenceI found = findPoint(evt.getX(), evt.getY());
+    if (found == null)
+    {
+      tooltip = null;
+    }
+    else
+    {
+      tooltip = found.getName();
+      toolx = evt.getX();
+      tooly = evt.getY();
+    }
+    repaint();
   }
 
   public void mouseDragged(MouseEvent evt)
@@ -531,35 +534,35 @@ public class RotatableCanvas
     mx = evt.getX();
     my = evt.getY();
 
-      rotmat.setIdentity();
+    rotmat.setIdentity();
 
-      rotmat.rotate( (float) (my - omy), 'x');
-      rotmat.rotate( (float) (mx - omx), 'y');
+    rotmat.rotate( (float) (my - omy), 'x');
+    rotmat.rotate( (float) (mx - omx), 'y');
 
-      for (int i = 0; i < npoint; i++)
-      {
-        SequencePoint sp = (SequencePoint) points.elementAt(i);
-        sp.coord[0] -= centre[0];
-        sp.coord[1] -= centre[1];
-        sp.coord[2] -= centre[2];
-
-        //Now apply the rotation matrix
-        sp.coord = rotmat.vectorMultiply(sp.coord);
-
-        //Now translate back again
-        sp.coord[0] += centre[0];
-        sp.coord[1] += centre[1];
-        sp.coord[2] += centre[2];
-      }
+    for (int i = 0; i < npoint; i++)
+    {
+      SequencePoint sp = (SequencePoint) points.elementAt(i);
+      sp.coord[0] -= centre[0];
+      sp.coord[1] -= centre[1];
+      sp.coord[2] -= centre[2];
 
-      for (int i = 0; i < 3; i++)
-      {
-        axes[i] = rotmat.vectorMultiply(axes[i]);
-      }
-      omx = mx;
-      omy = my;
+      //Now apply the rotation matrix
+      sp.coord = rotmat.vectorMultiply(sp.coord);
+
+      //Now translate back again
+      sp.coord[0] += centre[0];
+      sp.coord[1] += centre[1];
+      sp.coord[2] += centre[2];
+    }
+
+    for (int i = 0; i < 3; i++)
+    {
+      axes[i] = rotmat.vectorMultiply(axes[i]);
+    }
+    omx = mx;
+    omy = my;
 
-      paint(this.getGraphics());
+    paint(this.getGraphics());
   }
 
   public void rectSelect(int x1, int y1, int x2, int y2)
@@ -577,7 +580,7 @@ public class RotatableCanvas
       {
         if (av != null)
         {
-          if (!av.getSelectionGroup().sequences.contains(sp.sequence))
+          if (!av.getSelectionGroup().getSequences(null).contains(sp.sequence))
           {
             av.getSelectionGroup().addSequence(sp.sequence, true);
           }