X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=cea9de7ecec5c0095a40a0ccc7388f63067d525a;hb=747167089ecf8d6afc70d417f5a20352e029bd95;hp=2b4ce6b47376754c363adc67df37fd374fe20b96;hpb=b2824493add6517beee16bf7dc9066642c9bd26e;p=jalview.git
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 2b4ce6b..cea9de7 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, 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
@@ -42,7 +46,8 @@ public class BinarySequence extends Sequence
double[] dbinary;
- boolean isNa=false;
+ boolean isNa = false;
+
/**
* Creates a new BinarySequence object.
*
@@ -52,51 +57,52 @@ public class BinarySequence extends Sequence
public BinarySequence(String s, boolean isNa)
{
super("", s, 0, s.length());
- this.isNa=isNa;
+ this.isNa = isNa;
}
/**
- * clear the dbinary matrix
+ * clear the dbinary matrix
+ *
* @return nores - dimension of sequence symbol encoding for this sequence
*/
private int initMatrixGetNoRes()
{
- int nores=(isNa) ? ResidueProperties.maxNucleotideIndex : ResidueProperties.maxProteinIndex;
- // Set all matrix to 0
- dbinary = new double[getSequence().length * nores];
+ int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+ : ResidueProperties.maxProteinIndex;
+
+ dbinary = new double[getLength() * nores];
- for (int i = 0; i < dbinary.length; i++)
- {
- dbinary[i] = 0.0;
- }
return nores;
}
+
private int[] getSymbolmatrix()
{
- return (isNa) ? ResidueProperties.nucleotideIndex : ResidueProperties.aaIndex;
+ return (isNa) ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex;
}
+
/**
* DOCUMENT ME!
*/
public void encode()
{
- int nores=initMatrixGetNoRes();
- final int[] sindex=getSymbolmatrix();
- for (int i = 0; i < getSequence().length; i++)
+ int nores = initMatrixGetNoRes();
+ final int[] sindex = getSymbolmatrix();
+ for (int i = 0; i < getLength(); i++)
{
- int aanum = nores-1;
+ int aanum = nores - 1;
try
{
aanum = sindex[getCharAt(i)];
} catch (NullPointerException e)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
if (aanum >= nores)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
dbinary[(i * nores) + aanum] = 1.0;
@@ -106,46 +112,41 @@ public class BinarySequence extends Sequence
/**
* ancode using substitution matrix given in matrix
*
- * @param matrix
+ * @param smtrx
*/
- public void matrixEncode(final ScoreMatrix matrix) throws InvalidSequenceTypeException
+ 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=nores)
+ if (aanum >= nores)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
// Do the blosum^H^H^H^H^H score matrix summation thing
@@ -168,7 +169,7 @@ public class BinarySequence extends Sequence
for (int i = 0; i < binary.length; i++)
{
- out += (new Integer(binary[i])).toString();
+ out += (Integer.valueOf(binary[i])).toString();
if (i < (binary.length - 1))
{