X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=39ed19484aefc3cc9ef982b921ab78595381b1f4;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=4d691c0f01264683c52e9a5ea59fa4c1851dc35e;hpb=12db79ae5127e57cb0e5c1e7805592e5a3e17d8f;p=jalview.git diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java index 4d691c0..39ed194 100755 --- a/src/jalview/analysis/PCA.java +++ b/src/jalview/analysis/PCA.java @@ -1,238 +1,331 @@ -/* -* 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.analysis; - -import jalview.datamodel.*; - -import jalview.math.*; - - -/** - * Performs Principal Component Analysis on given sequences - * - * @author $author$ - * @version $Revision$ - */ -public class PCA implements Runnable -{ - Matrix m; - Matrix symm; - Matrix m2; - double[] eigenvalue; - Matrix eigenvector; - - - /** - * Creates a new PCA object. - * - * @param s Set of sequences to perform PCA on - */ - public PCA(SequenceI[] 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[] 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 - */ - - 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++) - { - out[i][0] = (float) component(i, l) * factor; - out[i][1] = (float) component(i, n) * factor; - out[i][2] = (float) component(i, mm) * factor; - } - - 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++) - { - out[i] = component(i, n); - } - - 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++) - { - out += (symm.value[row][i] * eigenvector.value[i][n]); - } - - return out / eigenvector.d[n]; - } - - - /** - * DOCUMENT ME! - */ - public void run() - { - Matrix mt = m.transpose(); - - // System.out.println(" --- OrigT * Orig ---- "); - eigenvector = mt.preMultiply(m2); - - // eigenvector.print(System.out); - symm = eigenvector.copy(); - - //TextArea ta = new TextArea(25,72); - //TextAreaPrintStream taps = new TextAreaPrintStream(System.out,ta); - //Frame f = new Frame("PCA output"); - //f.resize(500,500); - //f.setLayout(new BorderLayout()); - //f.add("Center",ta); - //f.show(); - //symm.print(taps); - long tstart = System.currentTimeMillis(); - eigenvector.tred(); - - long tend = System.currentTimeMillis(); - - //taps.println("Time take for tred = " + (tend-tstart) + "ms"); - //taps.println(" ---Tridiag transform matrix ---"); - //taps.println(" --- D vector ---"); - //eigenvector.printD(taps); - //taps.println(); - //taps.println(" --- E vector ---"); - // eigenvector.printE(taps); - //taps.println(); - // Now produce the diagonalization matrix - tstart = System.currentTimeMillis(); - eigenvector.tqli(); - tend = System.currentTimeMillis(); - - //System.out.println("Time take for tqli = " + (tend-tstart) + " ms"); - //System.out.println(" --- New diagonalization matrix ---"); - //System.out.println(" --- Eigenvalues ---"); - //eigenvector.printD(taps); - //System.out.println(); - // for (int i=0; i < eigenvector.cols; i++) { - // checkEigenvector(i,taps); - // taps.println(); - // } - // taps.println(); - // taps.println("Transformed sequences = "); - // Matrix trans = m.preMultiply(eigenvector); - // trans.print(System.out); - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) + * Copyright (C) 2014 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.analysis; + +import java.io.*; + +import jalview.datamodel.*; +import jalview.datamodel.BinarySequence.InvalidSequenceTypeException; +import jalview.math.*; +import jalview.schemes.ResidueProperties; +import jalview.schemes.ScoreMatrix; + +/** + * Performs Principal Component Analysis on given sequences + * + * @author $author$ + * @version $Revision$ + */ +public class PCA implements Runnable +{ + Matrix m; + + Matrix symm; + + Matrix m2; + + double[] eigenvalue; + + Matrix eigenvector; + + StringBuffer details = new StringBuffer(); + + /** + * Creates a new PCA object. By default, uses blosum62 matrix to generate + * sequence similarity matrices + * + * @param s + * Set of amino acid sequences to perform PCA on + */ + public PCA(String[] s) + { + this(s, false); + } + + /** + * Creates a new PCA object. By default, uses blosum62 matrix to generate + * sequence similarity matrices + * + * @param s + * Set of sequences to perform PCA on + * @param nucleotides + * if true, uses standard DNA/RNA matrix for sequence similarity + * calculation. + */ + public PCA(String[] s, boolean nucleotides) + { + this(s, nucleotides, null); + } + + public PCA(String[] s, boolean nucleotides, String s_m) + { + + BinarySequence[] bs = new BinarySequence[s.length]; + int ii = 0; + + while ((ii < s.length) && (s[ii] != null)) + { + bs[ii] = new BinarySequence(s[ii], nucleotides); + bs[ii].encode(); + ii++; + } + + BinarySequence[] bs2 = new BinarySequence[s.length]; + ii = 0; + ScoreMatrix smtrx = null; + String sm = s_m; + if (sm != null) + { + smtrx = ResidueProperties.getScoreMatrix(sm); + } + if (smtrx == null) + { + // either we were given a non-existent score matrix or a scoremodel that + // isn't based on a pairwise symbol score matrix + smtrx = ResidueProperties.getScoreMatrix(sm = (nucleotides ? "DNA" + : "BLOSUM62")); + } + details.append("PCA calculation using " + sm + + " sequence similarity matrix\n========\n\n"); + while ((ii < s.length) && (s[ii] != null)) + { + bs2[ii] = new BinarySequence(s[ii], nucleotides); + if (smtrx != null) + { + try + { + bs2[ii].matrixEncode(smtrx); + } catch (InvalidSequenceTypeException x) + { + details.append("Unexpected mismatch of sequence type and score matrix. Calculation will not be valid!\n\n"); + } + } + 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 + */ + + 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++) + { + out[i][0] = (float) component(i, l) * factor; + out[i][1] = (float) component(i, n) * factor; + out[i][2] = (float) component(i, mm) * factor; + } + + 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++) + { + out[i] = component(i, n); + } + + 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++) + { + out += (symm.value[row][i] * eigenvector.value[i][n]); + } + + return out / eigenvector.d[n]; + } + + public String getDetails() + { + return details.toString(); + } + + /** + * DOCUMENT ME! + */ + public void run() + { + PrintStream ps = new PrintStream(System.out) + { + public void print(String x) + { + details.append(x); + } + + public void println() + { + details.append("\n"); + } + }; + + try + { + details.append("PCA Calculation Mode is " + + (jvCalcMode ? "Jalview variant" : "Original SeqSpace") + + "\n"); + Matrix mt = m.transpose(); + + details.append(" --- OrigT * Orig ---- \n"); + if (!jvCalcMode) + { + eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix + } + else + { + eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace + // method + } + + 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(); + } catch (Exception q) + { + q.printStackTrace(); + details.append("\n*** Unexpected exception when performing PCA ***\n" + + q.getLocalizedMessage()); + details.append("*** Matrices below may not be fully diagonalised. ***\n"); + } + + details.append(" --- New diagonalization matrix ---\n"); + eigenvector.print(ps); + details.append(" --- Eigenvalues ---\n"); + eigenvector.printD(ps); + ps.println(); + /* + * for (int seq=0;seq