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[jalview.git] / src / jalview / gui / SeqCanvas.java

diff --git a/src/jalview/gui/SeqCanvas.java b/src/jalview/gui/SeqCanvas.java
index fd19721..97b9f08 100755 (executable)
--- a/src/jalview/gui/SeqCanvas.java
+++ b/src/jalview/gui/SeqCanvas.java
@@ -65,11 +65,28 @@ public class SeqCanvas extends JComponent
         setBackground(Color.white);\r
     }\r
 \r
+    MCview.PDBCanvas pdbCanvas;\r
+    public SequenceRenderer getSequenceRenderer()\r
+    {\r
+      return sr;\r
+    }\r
+\r
     public FeatureRenderer getFeatureRenderer()\r
     {\r
       return fr;\r
     }\r
 \r
+    public void setPDBCanvas(MCview.PDBCanvas pc)\r
+    {\r
+      pdbCanvas = pc;\r
+    }\r
+\r
+    public AlignViewport getViewport()\r
+    {\r
+      return av;\r
+    }\r
+\r
+\r
     /**\r
      * DOCUMENT ME!\r
      *\r
@@ -267,15 +284,16 @@ public class SeqCanvas extends JComponent
         sr.renderGaps(av.renderGaps);\r
 \r
         if ((img != null) &&\r
-                (fastPaint || (getWidth() != g.getClipBounds().width) ||\r
-                (getHeight() != g.getClipBounds().height)))\r
+                (fastPaint && getVisibleRect() != g.getClipBounds()))\r
         {\r
             g.drawImage(img, 0, 0, this);\r
             fastPaint = false;\r
-\r
             return;\r
         }\r
 \r
+\r
+\r
+\r
         // this draws the whole of the alignment\r
         imgWidth = getWidth();\r
         imgHeight = getHeight();\r
@@ -288,7 +306,6 @@ public class SeqCanvas extends JComponent
             return;\r
         }\r
 \r
-\r
         img = new BufferedImage(imgWidth, imgHeight, BufferedImage.TYPE_INT_RGB);\r
         gg = (Graphics2D) img.getGraphics();\r
         gg.setFont(av.getFont());\r
@@ -310,6 +327,12 @@ public class SeqCanvas extends JComponent
         }\r
 \r
         g.drawImage(img, 0, 0, this);\r
+\r
+        if (pdbCanvas != null)\r
+        {\r
+          pdbCanvas.updateSeqColours();\r
+        }\r
+\r
     }\r
 \r
     /**\r
@@ -516,6 +539,7 @@ public class SeqCanvas extends JComponent
       repaint();\r
     }\r
 \r
+\r
     synchronized public void drawPanel(Graphics g1, int x1, int x2, int y1,\r
         int y2, int startx, int starty, int offset)\r
     {\r
@@ -577,7 +601,6 @@ public class SeqCanvas extends JComponent
                             offset + ( (i - starty) * av.charHeight), av.charWidth,\r
                             aaHeight);\r
 \r
-\r
          /*   if(av.getShowTranslation())\r
             {\r
               av.setGlobalColourScheme(new NucleotideColourScheme());\r
@@ -592,8 +615,7 @@ public class SeqCanvas extends JComponent
 \r
             if (av.showSequenceFeatures)\r
             {\r
-                fr.drawSequence(g, nextSeq,\r
-                    av.alignment.findAllGroups(nextSeq), x1, x2,\r
+                fr.drawSequence(g, nextSeq, x1, x2,\r
                     (x1 - startx) * av.charWidth,\r
                     offset + ((i - starty) * av.charHeight), av.charWidth,\r
                     av.charHeight);\r