X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=c11610a28bc9e5f0fdc76aab450510827b7b6ba0;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=500573223c98c967eede401eac7382c907c9b963;hpb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;p=jalview.git diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java index 5005732..c11610a 100755 --- a/src/jalview/analysis/PCA.java +++ b/src/jalview/analysis/PCA.java @@ -1,241 +1,239 @@ /* -* 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.analysis; -import jalview.datamodel.*; +import java.io.*; +import jalview.datamodel.*; import jalview.math.*; -import java.io.*; - /** * Performs Principal Component Analysis on given sequences * * @author $author$ * @version $Revision$ */ -public class PCA implements Runnable +public class PCA + implements Runnable { - Matrix m; - Matrix symm; - Matrix m2; - double[] eigenvalue; - Matrix eigenvector; - StringBuffer details = new StringBuffer(); - - - /** - * Creates a new PCA object. - * - * @param s Set of sequences to perform PCA on - */ - public PCA(String[] s) + Matrix m; + Matrix symm; + Matrix m2; + double[] eigenvalue; + Matrix eigenvector; + StringBuffer details = new StringBuffer(); + + /** + * Creates a new PCA object. + * + * @param s Set of sequences to perform PCA on + */ + public PCA(String[] s) + { + + BinarySequence[] bs = new BinarySequence[s.length]; + int ii = 0; + + while ( (ii < s.length) && (s[ii] != null)) { + bs[ii] = new BinarySequence(s[ii]); + bs[ii].encode(); + ii++; + } - BinarySequence[] bs = new BinarySequence[s.length]; - int ii = 0; - - while ((ii < s.length) && (s[ii] != null)) - { - bs[ii] = new BinarySequence(s[ii]); - bs[ii].encode(); - ii++; - } - - BinarySequence[] bs2 = new BinarySequence[s.length]; - ii = 0; - - while ((ii < s.length) && (s[ii] != null)) - { - bs2[ii] = new BinarySequence(s[ii]); - bs2[ii].blosumEncode(); - ii++; - } - - //System.out.println("Created binary encoding"); - //printMemory(rt); - int count = 0; - - while ((count < bs.length) && (bs[count] != null)) - { - count++; - } - - double[][] seqmat = new double[count][bs[0].getDBinary().length]; - double[][] seqmat2 = new double[count][bs2[0].getDBinary().length]; - int i = 0; - - while (i < count) - { - seqmat[i] = bs[i].getDBinary(); - seqmat2[i] = bs2[i].getDBinary(); - i++; - } - - //System.out.println("Created array"); - //printMemory(rt); - // System.out.println(" --- Original matrix ---- "); - m = new Matrix(seqmat, count, bs[0].getDBinary().length); - m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length); - - } - - /** - * Returns the matrix used in PCA calculation - * - * @return java.math.Matrix object - */ + BinarySequence[] bs2 = new BinarySequence[s.length]; + ii = 0; - public Matrix getM() - { - return m; - } - - /** - * Returns Eigenvalue - * - * @param i Index of diagonal within matrix - * - * @return Returns value of diagonal from matrix - */ - public double getEigenvalue(int i) + while ( (ii < s.length) && (s[ii] != null)) { - return eigenvector.d[i]; + bs2[ii] = new BinarySequence(s[ii]); + bs2[ii].blosumEncode(); + ii++; } - /** - * DOCUMENT ME! - * - * @param l DOCUMENT ME! - * @param n DOCUMENT ME! - * @param mm DOCUMENT ME! - * @param factor DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public float[][] getComponents(int l, int n, int mm, float factor) - { - float[][] out = new float[m.rows][3]; - - for (int i = 0; i < m.rows; i++) - { - out[i][0] = (float) component(i, l) * factor; - out[i][1] = (float) component(i, n) * factor; - out[i][2] = (float) component(i, mm) * factor; - } + //System.out.println("Created binary encoding"); + //printMemory(rt); + int count = 0; - return out; - } - - /** - * DOCUMENT ME! - * - * @param n DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public double[] component(int n) + while ( (count < bs.length) && (bs[count] != null)) { - // n = index of eigenvector - double[] out = new double[m.rows]; + count++; + } - for (int i = 0; i < m.rows; i++) - { - out[i] = component(i, n); - } + double[][] seqmat = new double[count][bs[0].getDBinary().length]; + double[][] seqmat2 = new double[count][bs2[0].getDBinary().length]; + int i = 0; - return out; + while (i < count) + { + seqmat[i] = bs[i].getDBinary(); + seqmat2[i] = bs2[i].getDBinary(); + i++; } - /** - * DOCUMENT ME! - * - * @param row DOCUMENT ME! - * @param n DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - double component(int row, int n) + //System.out.println("Created array"); + //printMemory(rt); + // System.out.println(" --- Original matrix ---- "); + m = new Matrix(seqmat, count, bs[0].getDBinary().length); + m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length); + + } + + /** + * Returns the matrix used in PCA calculation + * + * @return java.math.Matrix object + */ + + public Matrix getM() + { + return m; + } + + /** + * Returns Eigenvalue + * + * @param i Index of diagonal within matrix + * + * @return Returns value of diagonal from matrix + */ + public double getEigenvalue(int i) + { + return eigenvector.d[i]; + } + + /** + * DOCUMENT ME! + * + * @param l DOCUMENT ME! + * @param n DOCUMENT ME! + * @param mm DOCUMENT ME! + * @param factor DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public float[][] getComponents(int l, int n, int mm, float factor) + { + float[][] out = new float[m.rows][3]; + + for (int i = 0; i < m.rows; i++) { - double out = 0.0; - - for (int i = 0; i < symm.cols; i++) - { - out += (symm.value[row][i] * eigenvector.value[i][n]); - } - - return out / eigenvector.d[n]; + out[i][0] = (float) component(i, l) * factor; + out[i][1] = (float) component(i, n) * factor; + out[i][2] = (float) component(i, mm) * factor; } - public String getDetails() + return out; + } + + /** + * DOCUMENT ME! + * + * @param n DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public double[] component(int n) + { + // n = index of eigenvector + double[] out = new double[m.rows]; + + for (int i = 0; i < m.rows; i++) { - return details.toString(); + out[i] = component(i, n); } - - /** - * DOCUMENT ME! - */ - public void run() + return out; + } + + /** + * DOCUMENT ME! + * + * @param row DOCUMENT ME! + * @param n DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + double component(int row, int n) + { + double out = 0.0; + + for (int i = 0; i < symm.cols; i++) { - Matrix mt = m.transpose(); - - details.append(" --- OrigT * Orig ---- \n"); - eigenvector = mt.preMultiply(m2); - - PrintStream ps = new PrintStream(System.out) - { - public void print(String x) { - details.append(x); - } - public void println() - { - details.append("\n"); - } - }; - - - eigenvector.print( ps ); + out += (symm.value[row][i] * eigenvector.value[i][n]); + } - symm = eigenvector.copy(); + return out / eigenvector.d[n]; + } - eigenvector.tred(); + public String getDetails() + { + return details.toString(); + } - details.append(" ---Tridiag transform matrix ---\n"); - details.append(" --- D vector ---\n"); - eigenvector.printD(ps); - ps.println(); - details.append("--- E vector ---\n"); - eigenvector.printE(ps); - ps.println(); + /** + * DOCUMENT ME! + */ + public void run() + { + Matrix mt = m.transpose(); - // Now produce the diagonalization matrix - eigenvector.tqli(); + details.append(" --- OrigT * Orig ---- \n"); + eigenvector = mt.preMultiply(m2); + PrintStream ps = new PrintStream(System.out) + { + public void print(String x) + { + details.append(x); + } - details.append(" --- New diagonalization matrix ---\n"); - details.append(" --- Eigenvalues ---\n"); - eigenvector.printD(ps); - ps.println(); - // taps.println(); - // taps.println("Transformed sequences = "); - // Matrix trans = m.preMultiply(eigenvector); - // trans.print(System.out); - } + public void println() + { + details.append("\n"); + } + }; + + eigenvector.print(ps); + + symm = eigenvector.copy(); + + eigenvector.tred(); + + details.append(" ---Tridiag transform matrix ---\n"); + details.append(" --- D vector ---\n"); + eigenvector.printD(ps); + ps.println(); + details.append("--- E vector ---\n"); + eigenvector.printE(ps); + ps.println(); + + // Now produce the diagonalization matrix + eigenvector.tqli(); + + details.append(" --- New diagonalization matrix ---\n"); + details.append(" --- Eigenvalues ---\n"); + eigenvector.printD(ps); + ps.println(); + // taps.println(); + // taps.println("Transformed sequences = "); + // Matrix trans = m.preMultiply(eigenvector); + // trans.print(System.out); + } }