Sequence is char []

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

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index fb2047e..05ba166 100755 (executable)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -317,7 +317,7 @@ public class AlignViewport
             cons.findQuality();
           }
 
-          String sequence = cons.getConsSequence().getSequence();
+          char [] sequence = cons.getConsSequence().getSequence();
           float minR;
           float minG;
           float minB;
@@ -352,7 +352,7 @@ public class AlignViewport
           {
             float value = 0;
 
-            c = sequence.charAt(i);
+            c = sequence[i];
 
             if (Character.isDigit(c))
               value = (int) (c - '0');
@@ -1513,7 +1513,7 @@ public class AlignViewport
       } else {
         for(i=0; i<iSize; i++)
         {
-          selection[i] = seqs[i].getSequence(start, end);
+          selection[i] = seqs[i].getSequenceAsString(start, end);
         }
 
       }