/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2006 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
-* 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.
-*
-* 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
-*/
+ * 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
+ * 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.
+ *
+ * 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
+ */
package jalview.datamodel;
import jalview.schemes.*;
-
-
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
-public class BinarySequence extends Sequence
+public class BinarySequence
+ extends Sequence
{
- int[] binary;
- double[] dbinary;
-
- /**
- * Creates a new BinarySequence object.
- *
- * @param s DOCUMENT ME!
- */
- public BinarySequence(String s)
+ int[] binary;
+ double[] dbinary;
+
+ /**
+ * Creates a new BinarySequence object.
+ *
+ * @param s DOCUMENT ME!
+ */
+ public BinarySequence(String s)
+ {
+ super("", s, 0, s.length());
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void encode()
+ {
+ // Set all matrix to 0
+ dbinary = new double[getSequence().length * 21];
+
+ int nores = 21;
+
+ for (int i = 0; i < dbinary.length; i++)
{
- super("", s, 0, s.length());
+ dbinary[i] = 0.0;
}
- /**
- * DOCUMENT ME!
- */
- public void encode()
+ for (int i = 0; i < getSequence().length; i++)
{
- // Set all matrix to 0
- dbinary = new double[getSequence().length * 21];
-
- int nores = 21;
-
- for (int i = 0; i < dbinary.length; i++)
- {
- dbinary[i] = 0.0;
- }
-
- for (int i = 0; i < getSequence().length; i++)
- {
- int aanum = 20;
-
- try
- {
- aanum = ResidueProperties.aaIndex[getCharAt(i)];
- }
- catch (NullPointerException e)
- {
- aanum = 20;
- }
-
- if (aanum > 20)
- {
- aanum = 20;
- }
-
- 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());
+ int aanum = 20;
+
+ try
+ {
+ aanum = ResidueProperties.aaIndex[getCharAt(i)];
+ }
+ catch (NullPointerException e)
+ {
+ aanum = 20;
+ }
+
+ if (aanum > 20)
+ {
+ aanum = 20;
+ }
+
+ dbinary[ (i * nores) + aanum] = 1.0;
}
- /**
- * DOCUMENT ME!
- */
- public void blosumEncode()
+ }
+
+ /**
+ * 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()
+ {
+ matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
+ }
+
+ private void matrixEncode(int[] aaIndex, int[][] matrix)
+ {
+ // Set all matrix to 0
+ dbinary = new double[getSequence().length * 21];
+
+ int nores = 21;
+
+ //for (int i = 0; i < dbinary.length; i++) {
+ // dbinary[i] = 0.0;
+ //}
+ for (int i = 0; i < getSequence().length; i++)
{
- matrixEncode(ResidueProperties.aaIndex, ResidueProperties.getBLOSUM62());
+ int aanum = 20;
+
+ try
+ {
+ aanum = aaIndex[getCharAt(i)];
+ }
+ catch (NullPointerException e)
+ {
+ aanum = 20;
+ }
+
+ if (aanum > 20)
+ {
+ aanum = 20;
+ }
+
+ // Do the blosum thing
+
+ for (int j = 0; j < 20; j++)
+ {
+ dbinary[ (i * nores) + j] = matrix[aanum][j];
+ }
}
- private void matrixEncode(int[] aaIndex, int[][] matrix) {
- // Set all matrix to 0
- dbinary = new double[getSequence().length * 21];
-
- int nores = 21;
-
- //for (int i = 0; i < dbinary.length; i++) {
- // dbinary[i] = 0.0;
- //}
- for (int i = 0; i < getSequence().length; i++)
- {
- int aanum = 20;
-
- try
- {
- aanum = aaIndex[getCharAt(i)];
- }
- catch (NullPointerException e)
- {
- aanum = 20;
- }
-
- if (aanum > 20)
- {
- aanum = 20;
- }
-
- // Do the blosum thing
-
- for (int j = 0; j < 20; j++)
- {
- dbinary[(i * nores) + j] = matrix[aanum][j];
- }
- }
- }
-
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public String toBinaryString()
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String toBinaryString()
+ {
+ String out = "";
+
+ for (int i = 0; i < binary.length; i++)
{
- String out = "";
-
- for (int i = 0; i < binary.length; i++)
- {
- out += (new Integer(binary[i])).toString();
+ out += (new Integer(binary[i])).toString();
- if (i < (binary.length - 1))
- {
- out += " ";
- }
- }
-
- return out;
+ if (i < (binary.length - 1))
+ {
+ out += " ";
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- public double[] getDBinary()
- {
- return dbinary;
- }
+ return out;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double[] getDBinary()
+ {
+ return dbinary;
+ }
}
git://source.jalview.org / jalview.git / blobdiff