-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-\r
-package jalview.datamodel;\r
-\r
-import jalview.io.*;\r
-import jalview.analysis.PCA;\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-\r
-import java.awt.*;\r
-\r
-public class BinarySequence extends Sequence {\r
- int[] binary;\r
- double[] dbinary;\r
-\r
- public BinarySequence(SequenceI s) {\r
- super(s.getName(),s.getSequence(),s.getStart(),s.getEnd());\r
- }\r
-\r
- public BinarySequence(String name, String sequence, int start, int end) {\r
- super(name,sequence,start,end);\r
- }\r
-\r
- public void encode() {\r
- // Set all matrix to 0\r
- dbinary = new double[getSequence().length() * 21];\r
- int nores = 21;\r
- for (int i = 0; i < dbinary.length; i++) {\r
- dbinary[i] = 0.0;\r
- }\r
-\r
- for (int i=0; i < getSequence().length(); i++ ) {\r
- int aanum = 20;\r
- try {\r
- aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
- } catch (NullPointerException e) {\r
- aanum = 20;\r
- }\r
- if (aanum > 20) {\r
- aanum = 20;\r
- }\r
-\r
- dbinary[i* nores + aanum] = 1.0;\r
-\r
- }\r
- }\r
-\r
- public void blosumEncode() {\r
-\r
- // Set all matrix to 0\r
- dbinary = new double[getSequence().length() * 21];\r
- int nores = 21;\r
- //for (int i = 0; i < dbinary.length; i++) {\r
- // dbinary[i] = 0.0;\r
- //}\r
-\r
- for (int i=0; i < getSequence().length(); i++ ) {\r
- int aanum = 20;\r
- try {\r
- aanum = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();\r
- } catch (NullPointerException e) {\r
- aanum = 20;\r
- }\r
- if (aanum > 20) {\r
- aanum = 20;\r
- }\r
-\r
- // Do the blosum thing\r
- for (int j = 0;j < 20;j++) {\r
- dbinary[i * nores + j] = ResidueProperties.getBLOSUM62()[aanum][j];\r
- }\r
-\r
- }\r
- }\r
-\r
- public String toBinaryString() {\r
- String out = "";\r
- for (int i=0; i < binary.length;i++) {\r
- out += (new Integer(binary[i])).toString();\r
- if (i < binary.length-1) {\r
- out += " ";\r
- }\r
- }\r
- return out;\r
- }\r
-\r
- public double[] getDBinary() {\r
- return dbinary;\r
- }\r
-\r
- public static void printMemory(Runtime rt) {\r
- System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.\r
- }\r
-}\r
+/*
+* 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
+*/
+package jalview.datamodel;
+
+import jalview.schemes.*;
+
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class BinarySequence extends Sequence
+{
+ 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++)
+ {
+ 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());
+ }
+ /**
+ * 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++)
+ {
+ 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()
+ {
+ String out = "";
+
+ for (int i = 0; i < binary.length; i++)
+ {
+ out += (new Integer(binary[i])).toString();
+
+ if (i < (binary.length - 1))
+ {
+ out += " ";
+ }
+ }
+
+ return out;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double[] getDBinary()
+ {
+ return dbinary;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff