Sequence is char []

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

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