JAL-2379 use SparseMatrix for encoded sequences, tidy unneeded code

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

diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index fccd84c..62ee974 100755 (executable)
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -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;
   }
 
@@ -134,14 +130,8 @@ public class BinarySequence extends Sequence
 
   private void matrixEncode(final int[] aaIndex, final int[][] 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;