X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=c33abb33693a3171a198bf5d06448887b067908a;hb=be762d8d9c71a7aa3121e845c45911c7192b7827;hp=53bffa910c228450c072d82e8269e955de839b92;hpb=e327ac5df98f528afeb347ac9a79085ad0d0975b;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 53bffa9..c33abb3 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -70,7 +70,7 @@ public class BinarySequence extends Sequence
     int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
             : ResidueProperties.maxProteinIndex;
 
-    dbinary = new double[getSequence().length * nores];
+    dbinary = new double[getLength() * nores];
 
     return nores;
   }
@@ -88,7 +88,7 @@ public class BinarySequence extends Sequence
   {
     int nores = initMatrixGetNoRes();
     final int[] sindex = getSymbolmatrix();
-    for (int i = 0; i < getSequence().length; i++)
+    for (int i = 0; i < getLength(); i++)
     {
       int aanum = nores - 1;
 
@@ -132,7 +132,7 @@ public class BinarySequence extends Sequence
   {
     int nores = initMatrixGetNoRes();
 
-    for (int i = 0, iSize = getSequence().length; i < iSize; i++)
+    for (int i = 0, iSize = getLength(); i < iSize; i++)
     {
       int aanum = nores - 1;