X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=b7e15a6ba5fd9c51f3658092cacd348c49b55983;hb=f46c404585087d8937c48504bfcff716440d5186;hp=a959cc7fadebe68bcbcc5b4677164826cc062231;hpb=1750b2f1dcdb6e7de41d0ef7beda88dc3400afba;p=jalview.git

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index a959cc7..b7e15a6 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -69,13 +69,9 @@ public class BinarySequence extends Sequence
   {
     int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
             : ResidueProperties.maxProteinIndex;
-    // Set all matrix to 0
+
     dbinary = new double[getSequence().length * nores];
 
-    for (int i = 0; i < dbinary.length; i++)
-    {
-      dbinary[i] = 0.0;
-    }
     return nores;
   }
 
@@ -116,32 +112,26 @@ public class BinarySequence extends Sequence
   /**
    * ancode using substitution matrix given in matrix
    * 
-   * @param matrix
+   * @param smtrx
    */
-  public void matrixEncode(final ScoreMatrix matrix)
+  public void matrixEncode(final ScoreMatrix smtrx)
           throws InvalidSequenceTypeException
   {
-    if (isNa != matrix.isDNA())
+    if (isNa != smtrx.isDNA())
     {
       throw new InvalidSequenceTypeException("matrix "
-              + matrix.getClass().getCanonicalName()
+              + smtrx.getClass().getCanonicalName()
               + " is not a valid matrix for "
               + (isNa ? "nucleotide" : "protein") + "sequences");
     }
-    matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
-            : ResidueProperties.aaIndex, matrix.getMatrix());
+    matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
+            : ResidueProperties.aaIndex, smtrx.getMatrix());
   }
 
-  private void matrixEncode(final int[] aaIndex, final int[][] matrix)
+  private void matrixEncode(final int[] aaIndex, final float[][] matrix)
   {
-    // Set all matrix to 0
-    // dbinary = new double[getSequence().length * 21];
-
     int nores = initMatrixGetNoRes();
 
-    // for (int i = 0; i < dbinary.length; i++) {
-    // dbinary[i] = 0.0;
-    // }
     for (int i = 0, iSize = getSequence().length; i < iSize; i++)
     {
       int aanum = nores - 1;