X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=c33abb33693a3171a198bf5d06448887b067908a;hb=refs%2Fheads%2FJAL-3437_load_project;hp=62171f7ec2c049f05a76eac31ea2a1a506272377;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 62171f7..c33abb3 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,23 +1,27 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 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.analysis.scoremodels.ScoreMatrix;
+import jalview.schemes.ResidueProperties;
/**
* Encode a sequence as a numeric vector using either classic residue binary
@@ -65,13 +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;
- }
+ 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;
@@ -112,33 +112,27 @@ 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()
- + " 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(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++)
+ for (int i = 0, iSize = getLength(); i < iSize; i++)
{
int aanum = nores - 1;