/*
- * 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * 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
double[] dbinary;
- boolean isNa=false;
+ boolean isNa = false;
+
/**
* Creates a new BinarySequence object.
*
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;
+ int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+ : ResidueProperties.maxProteinIndex;
// Set all matrix to 0
dbinary = new double[getSequence().length * nores];
}
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();
+ int nores = initMatrixGetNoRes();
+ final int[] sindex = getSymbolmatrix();
for (int i = 0; i < getSequence().length; 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;
*
* @param matrix
*/
- public void matrixEncode(final ScoreMatrix matrix) throws InvalidSequenceTypeException
+ public void matrixEncode(final ScoreMatrix matrix)
+ throws InvalidSequenceTypeException
{
- if (isNa!=matrix.isDNA())
+ if (isNa != matrix.isDNA())
{
throw new InvalidSequenceTypeException("matrix "
+ matrix.getClass().getCanonicalName()
// 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 = getSequence().length; i < iSize; i++)
{
- int aanum = nores-1;
+ int aanum = nores - 1;
try
{
aanum = aaIndex[getCharAt(i)];
} catch (NullPointerException e)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
- if (aanum >=nores)
+ if (aanum >= nores)
{
- aanum = nores-1;
+ aanum = nores - 1;
}
// Do the blosum^H^H^H^H^H score matrix summation thing