Looks to viewportfor global settings

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 4264c64..5c3ee12 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -54,22 +54,20 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;\r
     int curWidth = width;\r
 \r
-    if(currentSequenceGroup!=null && currentSequenceGroup.getDisplayBoxes())\r
-    {\r
-      curStart = currentSequenceGroup.getStartRes();\r
-      curWidth = currentSequenceGroup.getEndRes();\r
-    }\r
-\r
   //  int threshold = 80;\r
 \r
     while (i <= end && i < length)\r
     {\r
+      color = color.white;\r
+\r
       if(inCurrentSequenceGroup(i))\r
       {\r
-        color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);\r
+        if( currentSequenceGroup.getDisplayBoxes())\r
+             color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);\r
       }\r
-      else\r
-        color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);\r
+      else if(av.getShowBoxes())\r
+           color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);\r
+\r
 \r
     //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);\r
     //  String    s     = (String)hash.get("maxResidue");\r
@@ -135,6 +133,7 @@ public class SequenceRenderer implements RendererI
         if(!renderGaps && (s=='-' || s=='.' || s==' '))\r
           continue;\r
 \r
+        g.setColor(Color.black);\r
 \r
         if (inCurrentSequenceGroup(i))\r
         {\r
@@ -145,7 +144,13 @@ public class SequenceRenderer implements RendererI
             g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());\r
         }\r
         else\r
-          g.setColor(Color.black);\r
+        {\r
+          if(!av.getShowText())\r
+            continue;\r
+\r
+          if(av.getColourText())\r
+            g.setColor(getResidueBoxColour(av.getGlobalColourScheme(), seq, i).darker());\r
+        }\r
 \r
       charOffset =  (width - fm.charWidth(s))/2;\r
       g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);\r