X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=62ee97443a37ab68b37bb10665d2058781934b84;hb=532f84b54e9039d831af69f394d72dd6ffbcee15;hp=456b8b05c8f0e39ff2a05d93a9ee3f22cf706fe2;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 456b8b0..62ee974 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,24 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.datamodel;
-import jalview.schemes.*;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.ScoreMatrix;
/**
* Encode a sequence as a numeric vector using either classic residue binary
@@ -66,13 +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;
}
@@ -131,14 +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;