X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=cea9de7ecec5c0095a40a0ccc7388f63067d525a;hb=34cd990de2acbfc60802d2ab0c869481749a2406;hp=b7e15a6ba5fd9c51f3658092cacd348c49b55983;hpb=f46c404585087d8937c48504bfcff716440d5186;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index b7e15a6..cea9de7 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;
 
@@ -119,10 +119,10 @@ public class BinarySequence extends Sequence
   {
     if (isNa != smtrx.isDNA())
     {
-      throw new InvalidSequenceTypeException("matrix "
-              + smtrx.getClass().getCanonicalName()
-              + " is not a valid matrix for "
-              + (isNa ? "nucleotide" : "protein") + "sequences");
+      throw new InvalidSequenceTypeException(
+              "matrix " + smtrx.getClass().getCanonicalName()
+                      + " is not a valid matrix for "
+                      + (isNa ? "nucleotide" : "protein") + "sequences");
     }
     matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
             : ResidueProperties.aaIndex, smtrx.getMatrix());
@@ -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;
 
@@ -169,7 +169,7 @@ public class BinarySequence extends Sequence
 
     for (int i = 0; i < binary.length; i++)
     {
-      out += (new Integer(binary[i])).toString();
+      out += (Integer.valueOf(binary[i])).toString();
 
       if (i < (binary.length - 1))
       {