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Merge branch 'develop' into features/JAL-2393customMatrices
[jalview.git]
/
src
/
jalview
/
datamodel
/
BinarySequence.java
diff --git
a/src/jalview/datamodel/BinarySequence.java
b/src/jalview/datamodel/BinarySequence.java
index
fccd84c
..
b7e15a6
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.
*
*
* This file is part of Jalview.
*
@@
-20,8
+20,8
@@
*/
package jalview.datamodel;
*/
package jalview.datamodel;
+import jalview.analysis.scoremodels.ScoreMatrix;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ResidueProperties;
-import jalview.schemes.ScoreMatrix;
/**
* Encode a sequence as a numeric vector using either classic residue binary
/**
* Encode a sequence as a numeric vector using either classic residue binary
@@
-69,13
+69,9
@@
public class BinarySequence extends Sequence
{
int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
: ResidueProperties.maxProteinIndex;
{
int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
: ResidueProperties.maxProteinIndex;
- // Set all matrix to 0
+
dbinary = new double[getSequence().length * nores];
dbinary = new double[getSequence().length * nores];
- for (int i = 0; i < dbinary.length; i++)
- {
- dbinary[i] = 0.0;
- }
return nores;
}
return nores;
}
@@
-116,32
+112,26
@@
public class BinarySequence extends Sequence
/**
* ancode using substitution matrix given in matrix
*
/**
* 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
{
throws InvalidSequenceTypeException
{
- if (isNa != matrix.isDNA())
+ if (isNa != smtrx.isDNA())
{
throw new InvalidSequenceTypeException("matrix "
{
throw new InvalidSequenceTypeException("matrix "
- + matrix.getClass().getCanonicalName()
+ + smtrx.getClass().getCanonicalName()
+ " is not a valid matrix for "
+ (isNa ? "nucleotide" : "protein") + "sequences");
}
+ " 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();
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;
for (int i = 0, iSize = getSequence().length; i < iSize; i++)
{
int aanum = nores - 1;