From b2109d7b41871be692f88eb9e58c815eeed97be9 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Fri, 10 Dec 2004 14:37:55 +0000
Subject: [PATCH] Looks to viewportfor global settings

---
 src/jalview/gui/SequenceRenderer.java |   25 +++++++++++++++----------
 1 file changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 4264c64..5c3ee12 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -54,22 +54,20 @@ public class SequenceRenderer implements RendererI
     int curStart = x1;
     int curWidth = width;
 
-    if(currentSequenceGroup!=null && currentSequenceGroup.getDisplayBoxes())
-    {
-      curStart = currentSequenceGroup.getStartRes();
-      curWidth = currentSequenceGroup.getEndRes();
-    }
-
   //  int threshold = 80;
 
     while (i <= end && i < length)
     {
+      color = color.white;
+
       if(inCurrentSequenceGroup(i))
       {
-        color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);
+        if( currentSequenceGroup.getDisplayBoxes())
+             color = getResidueBoxColour(currentSequenceGroup.cs, seq, i);
       }
-      else
-        color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);
+      else if(av.getShowBoxes())
+           color = getResidueBoxColour(av.getGlobalColourScheme(), seq, i);
+
 
     //  Hashtable hash  = (Hashtable)freq.elementAt(i-start);
     //  String    s     = (String)hash.get("maxResidue");
@@ -135,6 +133,7 @@ public class SequenceRenderer implements RendererI
         if(!renderGaps && (s=='-' || s=='.' || s==' '))
           continue;
 
+        g.setColor(Color.black);
 
         if (inCurrentSequenceGroup(i))
         {
@@ -145,7 +144,13 @@ public class SequenceRenderer implements RendererI
             g.setColor(getResidueBoxColour(currentSequenceGroup.cs, seq, i).darker());
         }
         else
-          g.setColor(Color.black);
+        {
+          if(!av.getShowText())
+            continue;
+
+          if(av.getColourText())
+            g.setColor(getResidueBoxColour(av.getGlobalColourScheme(), seq, i).darker());
+        }
 
       charOffset =  (width - fm.charWidth(s))/2;
       g.drawString(String.valueOf(s), charOffset + x1 + width * (i - start), y1 + height - pady);
-- 
1.7.10.2