X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fdatamodel%2FBinarySequence.java;h=062f6bab49f33ac6635aba28d6a03dcb4f205048;hb=aeb173dd7daa4559e760548d955ee83aac6828d8;hp=63c8d860a8c4dda9c002b3d2b2ecafba2a7b3237;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/datamodel/BinarySequence.java b/src/jalview/datamodel/BinarySequence.java
index 63c8d86..062f6ba 100755
--- a/src/jalview/datamodel/BinarySequence.java
+++ b/src/jalview/datamodel/BinarySequence.java
@@ -1,111 +1,192 @@
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 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.io.*;
-import jalview.analysis.PCA;
-import jalview.jbgui.*;
-import jalview.schemes.*;
-
-import java.awt.*;
-
-public class BinarySequence extends Sequence {
- int[] binary;
- double[] dbinary;
-
- public BinarySequence(SequenceI s) {
- super(s.getName(),s.getSequence(),s.getStart(),s.getEnd());
- }
-
- public BinarySequence(String name, String sequence, int start, int end) {
- super(name,sequence,start,end);
- }
-
- 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 = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();
- } catch (NullPointerException e) {
- aanum = 20;
- }
- if (aanum > 20) {
- aanum = 20;
- }
-
- dbinary[i* nores + aanum] = 1.0;
-
- }
- }
-
- public void blosumEncode() {
-
- // 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 = ((Integer)ResidueProperties.getAAHash().get(getSequence().substring(i,i+1))).intValue();
- } 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] = ResidueProperties.getBLOSUM62()[aanum][j];
- }
-
- }
- }
-
- 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;
- }
-
- public double[] getDBinary() {
- return dbinary;
- }
-
- public static void printMemory(Runtime rt) {
- System.out.println("DEBUG: Free memory = " + rt.freeMemory()); // log.
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 .
+ */
+package jalview.datamodel;
+
+import jalview.schemes.*;
+
+/**
+ * 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;
+ // Set all matrix to 0
+ 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 = 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 matrix
+ */
+ public void matrixEncode(final ScoreMatrix matrix) throws InvalidSequenceTypeException
+ {
+ 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(final int[] aaIndex, final int[][] matrix)
+ {
+ // Set all matrix to 0
+ // dbinary = new double[getSequence().length * 21];
+
+ int nores = initMatrixGetNoRes();
+
+ // for (int i = 0; i < dbinary.length; i++) {
+ // dbinary[i] = 0.0;
+ // }
+ for (int i = 0,iSize=getSequence().length; i=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 += (new Integer(binary[i])).toString();
+
+ if (i < (binary.length - 1))
+ {
+ out += " ";
+ }
+ }
+
+ return out;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public double[] getDBinary()
+ {
+ return dbinary;
+ }
+
+}