/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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.*;
/**
- * DOCUMENT ME!
- *
+ * Encode a sequence as a numeric vector using either classic residue binary
+ * encoding or convolved with residue substitution matrix.
+ *
* @author $author$
* @version $Revision$
*/
-public class BinarySequence
- extends Sequence
+public class BinarySequence extends Sequence
{
+ public class InvalidSequenceTypeException extends Exception
+ {
+
+ public InvalidSequenceTypeException(String string)
+ {
+ super(string);
+ }
+
+ }
+
int[] binary;
+
double[] dbinary;
+ boolean isNa = false;
+
/**
* Creates a new BinarySequence object.
- *
- * @param s DOCUMENT ME!
+ *
+ * @param s
+ * DOCUMENT ME!
*/
- public BinarySequence(String s)
+ public BinarySequence(String s, boolean isNa)
{
super("", s, 0, s.length());
+ this.isNa = isNa;
}
/**
- * DOCUMENT ME!
+ * clear the dbinary matrix
+ *
+ * @return nores - dimension of sequence symbol encoding for this sequence
*/
- public void encode()
+ private int initMatrixGetNoRes()
{
+ int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+ : ResidueProperties.maxProteinIndex;
// Set all matrix to 0
- dbinary = new double[getSequence().length * 21];
-
- int nores = 21;
+ dbinary = new double[getSequence().length * nores];
for (int i = 0; i < dbinary.length; i++)
{
dbinary[i] = 0.0;
}
+ return nores;
+ }
+
+ private int[] getSymbolmatrix()
+ {
+ 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 aanum = 20;
+ int aanum = nores - 1;
try
{
- aanum = ResidueProperties.aaIndex[getCharAt(i)];
- }
- catch (NullPointerException e)
+ aanum = sindex[getCharAt(i)];
+ } catch (NullPointerException e)
{
- aanum = 20;
+ aanum = nores - 1;
}
- if (aanum > 20)
+ if (aanum >= nores)
{
- aanum = 20;
+ aanum = nores - 1;
}
- dbinary[ (i * nores) + aanum] = 1.0;
+ dbinary[(i * nores) + aanum] = 1.0;
}
}
/**
* ancode using substitution matrix given in matrix
+ *
* @param matrix
*/
- public void matrixEncode(ScoreMatrix matrix)
- {
- matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex :
- ResidueProperties.aaIndex, matrix.getMatrix());
- }
-
- /**
- * DOCUMENT ME!
- */
- public void blosumEncode()
+ public void matrixEncode(final ScoreMatrix matrix)
+ throws InvalidSequenceTypeException
{
- matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
+ if (isNa != matrix.isDNA())
+ {
+ throw new InvalidSequenceTypeException("matrix "
+ + matrix.getClass().getCanonicalName()
+ + " is not a valid matrix for "
+ + (isNa ? "nucleotide" : "protein") + "sequences");
+ }
+ matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex, matrix.getMatrix());
}
- private void matrixEncode(int[] aaIndex, int[][] matrix)
+ private void matrixEncode(final int[] aaIndex, final int[][] matrix)
{
// Set all matrix to 0
- dbinary = new double[getSequence().length * 21];
+ // dbinary = new double[getSequence().length * 21];
- int nores = 21;
+ int nores = initMatrixGetNoRes();
- //for (int i = 0; i < dbinary.length; i++) {
- // dbinary[i] = 0.0;
- //}
- for (int i = 0; i < getSequence().length; i++)
+ // for (int i = 0; i < dbinary.length; i++) {
+ // dbinary[i] = 0.0;
+ // }
+ for (int i = 0, iSize = getSequence().length; i < iSize; i++)
{
- int aanum = 20;
+ int aanum = nores - 1;
try
{
aanum = aaIndex[getCharAt(i)];
- }
- catch (NullPointerException e)
+ } catch (NullPointerException e)
{
- aanum = 20;
+ aanum = nores - 1;
}
- if (aanum > 20)
+ if (aanum >= nores)
{
- aanum = 20;
+ aanum = nores - 1;
}
- // Do the blosum thing
+ // Do the blosum^H^H^H^H^H score matrix summation thing
- for (int j = 0; j < 20; j++)
+ for (int j = 0; j < nores; j++)
{
- dbinary[ (i * nores) + j] = matrix[aanum][j];
+ dbinary[(i * nores) + j] = matrix[aanum][j];
}
}
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public String toBinaryString()
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public double[] getDBinary()
git://source.jalview.org / jalview.git / blobdiff