X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=49e35431f060805faf6fc6dc0a056b30ce3da8e3;hb=c766c1829042b039ea2ff56fc05f4a0100c2a73d;hp=af10e1d180a37114726ace7c78888867c4f25d5c;hpb=c3c305755d392741176209a0274a47897ac4d8a8;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index af10e1d..49e3543 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -49,7 +49,7 @@ public class BinarySequence extends Sequence
     public void encode()
     {
         // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
+        dbinary = new double[getSequence().length * 21];
 
         int nores = 21;
 
@@ -58,13 +58,13 @@ public class BinarySequence extends Sequence
             dbinary[i] = 0.0;
         }
 
-        for (int i = 0; i < getSequence().length(); i++)
+        for (int i = 0; i < getSequence().length; i++)
         {
             int aanum = 20;
 
             try
             {
-                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];
             }
             catch (NullPointerException e)
             {
@@ -86,20 +86,20 @@ public class BinarySequence extends Sequence
     public void blosumEncode()
     {
         // Set all matrix to 0
-        dbinary = new double[getSequence().length() * 21];
+        dbinary = new double[getSequence().length * 21];
 
         int nores = 21;
 
         //for (int i = 0; i < dbinary.length; i++) {
         //  dbinary[i] = 0.0;
         //}
-        for (int i = 0; i < getSequence().length(); i++)
+        for (int i = 0; i < getSequence().length; i++)
         {
             int aanum = 20;
 
             try
             {
-                aanum = ResidueProperties.aaIndex[getSequence().charAt(i)];
+                aanum = ResidueProperties.aaIndex[getCharAt(i)];
             }
             catch (NullPointerException e)
             {