-/* Jalview - a java multiple alignment editor\r
- * Copyright (C) 1998 Michele Clamp\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., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.\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("Free memory = " + rt.freeMemory());\r
- }\r
-}\r
+/*
+ * 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.
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.datamodel;
+
+import jalview.analysis.scoremodels.ScoreMatrix;
+import jalview.schemes.ResidueProperties;
+
+/**
+ * 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 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!
+ */
+ public BinarySequence(String s, boolean isNa)
+ {
+ super("", s, 0, s.length());
+ this.isNa = isNa;
+ }
+
+ /**
+ * clear the dbinary matrix
+ *
+ * @return nores - dimension of sequence symbol encoding for this sequence
+ */
+ private int initMatrixGetNoRes()
+ {
+ int nores = (isNa) ? ResidueProperties.maxNucleotideIndex
+ : ResidueProperties.maxProteinIndex;
+
+ dbinary = new double[getLength() * nores];
+
+ 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 < getLength(); i++)
+ {
+ int aanum = nores - 1;
+
+ try
+ {
+ aanum = sindex[getCharAt(i)];
+ } catch (NullPointerException e)
+ {
+ aanum = nores - 1;
+ }
+
+ if (aanum >= nores)
+ {
+ aanum = nores - 1;
+ }
+
+ dbinary[(i * nores) + aanum] = 1.0;
+ }
+ }
+
+ /**
+ * ancode using substitution matrix given in matrix
+ *
+ * @param smtrx
+ */
+ public void matrixEncode(final ScoreMatrix smtrx)
+ throws InvalidSequenceTypeException
+ {
+ if (isNa != smtrx.isDNA())
+ {
+ throw new InvalidSequenceTypeException(
+ "matrix " + smtrx.getClass().getCanonicalName()
+ + " is not a valid matrix for "
+ + (isNa ? "nucleotide" : "protein") + "sequences");
+ }
+ matrixEncode(smtrx.isDNA() ? ResidueProperties.nucleotideIndex
+ : ResidueProperties.aaIndex, smtrx.getMatrix());
+ }
+
+ private void matrixEncode(final int[] aaIndex, final float[][] matrix)
+ {
+ int nores = initMatrixGetNoRes();
+
+ for (int i = 0, iSize = getLength(); i < iSize; i++)
+ {
+ int aanum = nores - 1;
+
+ try
+ {
+ aanum = aaIndex[getCharAt(i)];
+ } catch (NullPointerException e)
+ {
+ aanum = nores - 1;
+ }
+
+ if (aanum >= nores)
+ {
+ aanum = nores - 1;
+ }
+
+ // Do the blosum^H^H^H^H^H score matrix summation thing
+
+ for (int j = 0; j < nores; 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 += (Integer.valueOf(binary[i])).toString();
+
+ if (i < (binary.length - 1))
+ {
+ out += " ";
+ }
+ }
+
+ return out;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double[] getDBinary()
+ {
+ return dbinary;
+ }
+
+}