after merge

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index c413588..c68e85c 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -44,11 +44,24 @@ public class SequenceRenderer
     renderGaps = b;\r
   }\r
 \r
-  public Color getResidueBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
+  public Color getResidueBoxColour(SequenceI seq, int i)\r
   {\r
-    getBoxColour(cs, seq, i);\r
+    allGroups = av.alignment.findAllGroups(seq);\r
+\r
+    if (inCurrentSequenceGroup(i))\r
+    {\r
+      if (currentSequenceGroup.getDisplayBoxes())\r
+      {\r
+        getBoxColour(currentSequenceGroup.cs, seq, i);\r
+      }\r
+    }\r
+    else if (av.getShowBoxes())\r
+    {\r
+        getBoxColour(av.globalColourScheme, seq, i);\r
+    }\r
+\r
     return resBoxColour;\r
-  }\r
+    }\r
 \r
   void getBoxColour(ColourSchemeI cs, SequenceI seq, int i)\r
   {\r
@@ -62,6 +75,14 @@ public class SequenceRenderer
     }\r
   }\r
 \r
+  Image offscreen;\r
+  public Color findSequenceColour(SequenceI seq, int i)\r
+  {\r
+    allGroups = av.alignment.findAllGroups(seq);\r
+    drawBoxes(seq, i,i, 0, 0, 1,1);\r
+    return resBoxColour;\r
+  }\r
+\r
   public void drawSequence(Graphics g, SequenceI seq, SequenceGroup[] sg,\r
                            int start, int end, int x1, int y1, int width,\r
                            int height)\r