sequence is char []

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

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 40d67b0..ad7113a 100755 (executable)
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -296,7 +296,7 @@ public class AlignViewport
           cons.findQuality();\r
         }\r
 \r
-        String sequence = cons.getConsSequence().getSequence();\r
+        char [] sequence = cons.getConsSequence().getSequence();\r
         float minR;\r
         float minG;\r
         float minB;\r
@@ -331,7 +331,7 @@ public class AlignViewport
         {\r
           float value = 0;\r
 \r
-          c = sequence.charAt(i);\r
+          c = sequence[i];\r
 \r
           if (Character.isDigit(c))\r
             value = (int) (c - '0');\r
@@ -1201,7 +1201,7 @@ public class AlignViewport
       }\r
       else\r
       {\r
-        selection[i] = seqs[i].getSequence(start, end);\r
+        selection[i] = seqs[i].getSequenceAsString(start, end);\r
       }\r
     }\r
 \r