X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=6c7fb37cd615f5a85e52eab5f2be52076f20c43d;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=8d7755cf2d96da99f89c053de76d0233ee334653;hpb=2f96585f0cd39dc5cac42011d602b08740148518;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 8d7755c..6c7fb37 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -104,7 +104,7 @@ public class SequenceRenderer
     {
         if (cs != null)
         {
-            resBoxColour = cs.findColour(seq.getSequence(i, i + 1), i);
+            resBoxColour = cs.findColour(seq.getCharAt(i), i);
         }
         else if(forOverview && !jalview.util.Comparison.isGap(seq.getCharAt(i)))
         {
@@ -236,12 +236,12 @@ public class SequenceRenderer
            && !av.getColourText()
            && av.thresholdTextColour==0)
         {
-          if(av.renderGaps)
-          graphics.drawString(seq.getSequence(start, end + 1), 0, y1);
-         else
+          if (av.renderGaps)
+            graphics.drawString(seq.getSequenceAsString(start, end + 1), 0, y1);
+          else
          {
            char gap = av.getGapCharacter();
-           graphics.drawString( seq.getSequence(start, end+1).replace(gap, ' '), 0, y1);
+           graphics.drawString( seq.getSequenceAsString(start, end+1).replace(gap, ' '), 0, y1);
          }
         }
         else
@@ -387,7 +387,7 @@ public class SequenceRenderer
           {
             if (i < seq.getLength())
             {
-              s = seq.getSequence().charAt(i);
+              s = seq.getCharAt(i);
             }
 
             charOffset = (av.charWidth - fm.charWidth(s)) / 2;