X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqCanvas.java;h=42424d9dc8a4a30b95cd7f93905ec5d9e0385ec5;hb=32ce9ddb7ce1a68add53dd81785ae428ca136a83;hp=fd19721cd6055a48894f7ed1235e561fff547811;hpb=783520af519c958e10a2af29f1d4242e1ab890a3;p=jalview.git

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index fd19721..42424d9 100755
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -48,8 +48,6 @@ public class SeqCanvas extends JComponent
     int LABEL_WEST;
     int LABEL_EAST;
 
-    boolean isOverview = false;
-
     /**
      * Creates a new SeqCanvas object.
      *
@@ -65,11 +63,28 @@ public class SeqCanvas extends JComponent
         setBackground(Color.white);
     }
 
+    MCview.PDBCanvas pdbCanvas;
+    public SequenceRenderer getSequenceRenderer()
+    {
+      return sr;
+    }
+
     public FeatureRenderer getFeatureRenderer()
     {
       return fr;
     }
 
+    public void setPDBCanvas(MCview.PDBCanvas pc)
+    {
+      pdbCanvas = pc;
+    }
+
+    public AlignViewport getViewport()
+    {
+      return av;
+    }
+
+
     /**
      * DOCUMENT ME!
      *
@@ -264,18 +279,20 @@ public class SeqCanvas extends JComponent
     // Set this to false to force a full panel paint
     public void paintComponent(Graphics g)
     {
+        super.paintComponent(g);
+
         sr.renderGaps(av.renderGaps);
 
-        if ((img != null) &&
-                (fastPaint || (getWidth() != g.getClipBounds().width) ||
-                (getHeight() != g.getClipBounds().height)))
+        if ( img != null && (fastPaint
+             || (getVisibleRect().width != g.getClipBounds().width)
+             || (getVisibleRect().height != g.getClipBounds().height)))
         {
             g.drawImage(img, 0, 0, this);
             fastPaint = false;
-
             return;
         }
 
+
         // this draws the whole of the alignment
         imgWidth = getWidth();
         imgHeight = getHeight();
@@ -288,7 +305,6 @@ public class SeqCanvas extends JComponent
             return;
         }
 
-
         img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);
         gg = (Graphics2D) img.getGraphics();
         gg.setFont(av.getFont());
@@ -310,6 +326,12 @@ public class SeqCanvas extends JComponent
         }
 
         g.drawImage(img, 0, 0, this);
+
+        if (pdbCanvas != null)
+        {
+         pdbCanvas.updateSeqColours();
+        }
+
     }
 
     /**
@@ -516,6 +538,7 @@ public class SeqCanvas extends JComponent
       repaint();
     }
 
+
     synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,
         int y2, int startx, int starty, int offset)
     {
@@ -577,7 +600,6 @@ public class SeqCanvas extends JComponent
                             offset + ( (i - starty) * av.charHeight), av.charWidth,
                             aaHeight);
 
-
          /*   if(av.getShowTranslation())
             {
               av.setGlobalColourScheme(new NucleotideColourScheme());
@@ -592,8 +614,7 @@ public class SeqCanvas extends JComponent
 
             if (av.showSequenceFeatures)
             {
-                fr.drawSequence(g, nextSeq,
-                    av.alignment.findAllGroups(nextSeq), x1, x2,
+                fr.drawSequence(g, nextSeq, x1, x2,
                     (x1 - startx) * av.charWidth,
                     offset + ((i - starty) * av.charHeight), av.charWidth,
                     av.charHeight);
@@ -617,7 +638,7 @@ public class SeqCanvas extends JComponent
             groupIndex = 0;
         }
 
-        if (group != null && !isOverview)
+        if (group != null)
         {
             do
             {