spike branch updated from latest features/JAL-2446

[jalview.git] / src / jalview / datamodel / BinarySequence.java

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 5789b2b..477f4a7 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -69,6 +69,7 @@ public class BinarySequence extends Sequence
   {
     int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
             : ResidueProperties.maxProteinIndex;
+
     dbinary = new double[getLength() * nores];
 
     return nores;
@@ -131,7 +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;