after merge

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

diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 1de9418..5d02825 100755 (executable)
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -43,7 +43,6 @@ public class SeqCanvas
 \r
   boolean fastPaint = false;\r
 \r
-  boolean isOverview = false;\r
 \r
   public SeqCanvas(AlignViewport av)\r
   {\r
@@ -51,9 +50,30 @@ public class SeqCanvas
     fr = new FeatureRenderer(av);\r
     sr = new SequenceRenderer(av);\r
     PaintRefresher.Register(this, av.alignment);\r
+  }\r
 \r
+  public AlignViewport getViewport()\r
+  {\r
+    return av;\r
+  }\r
+\r
+  public FeatureRenderer getFeatureRenderer()\r
+  {\r
+    return fr;\r
   }\r
 \r
+  MCview.AppletPDBCanvas pdbCanvas;\r
+  public SequenceRenderer getSequenceRenderer()\r
+  {\r
+    return sr;\r
+  }\r
+\r
+  public void setPDBCanvas(MCview.AppletPDBCanvas pc)\r
+  {\r
+    pdbCanvas = pc;\r
+  }\r
+\r
+\r
   void drawNorthScale(Graphics g, int startx, int endx, int ypos)\r
   {\r
     int scalestartx = startx - startx % 10 + 10;\r
@@ -254,6 +274,10 @@ public class SeqCanvas
 \r
     g.drawImage(img, 0, 0, this);\r
 \r
+    if (pdbCanvas != null)\r
+    {\r
+      pdbCanvas.updateSeqColours();\r
+    }\r
   }\r
 \r
   int LABEL_WEST, LABEL_EAST;\r
@@ -368,12 +392,12 @@ public class SeqCanvas
 \r
         if(av.showAnnotation)\r
         {\r
-          g.translate(0, cHeight + ypos);\r
+          g.translate(0, cHeight + ypos+4);\r
           if(annotations==null)\r
             annotations = new AnnotationPanel(av);\r
 \r
           annotations.drawComponent( g, startRes, endx + 1);\r
-          g.translate(0, -cHeight - ypos);\r
+          g.translate(0, -cHeight - ypos-4);\r
         }\r
         g.translate(-LABEL_WEST, 0);\r
 \r
@@ -447,7 +471,7 @@ public class SeqCanvas
       group = (SequenceGroup) groups.elementAt(0);\r
       groupIndex = 0;\r
     }\r
-    if (group != null && !isOverview)\r
+    if (group != null)\r
     {\r
         do\r
         {\r
@@ -473,10 +497,12 @@ public class SeqCanvas
                         group.sequences.contains(av.alignment.getSequenceAt(\r
                                 i)))\r
                 {\r
-                    if ((bottom == -1) &&\r
-                            !group.sequences.contains(\r
-                                av.alignment.getSequenceAt(i + 1)))\r
-                    {\r
+\r
+                    if (bottom == -1)\r
+                   {\r
+                     if(i == y2-1 || // Dont check for i+1 if on the bottom row\r
+                      !group.sequences.contains(av.alignment.getSequenceAt(i+1 )))\r
+\r
                         bottom = sy + av.charHeight;\r
                     }\r
 \r