/*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
*/
package jalview.datamodel;
/**
* 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!
+ *
+ * @param s
+ * DOCUMENT ME!
*/
public BinarySequence(String s)
{
try
{
aanum = ResidueProperties.aaIndex[getCharAt(i)];
- }
- catch (NullPointerException e)
+ } catch (NullPointerException e)
{
aanum = 20;
}
aanum = 20;
}
- 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());
+ matrixEncode(matrix.isDNA() ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex, matrix.getMatrix());
}
/**
int nores = 21;
- //for (int i = 0; i < dbinary.length; i++) {
- // dbinary[i] = 0.0;
- //}
+ // 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)
+ } catch (NullPointerException e)
{
aanum = 20;
}
for (int j = 0; j < 20; 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()