X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=f0b7f1644dedce27bb847c8efe292bd4df713eb6;hb=9c9bc24a6be8af1a97914b246b8ce2d0eaabf5fd;hp=f9a034334a2b78e0be9fd50b7c89ebc20de95a5c;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java index f9a0343..f0b7f16 100755 --- a/src/jalview/analysis/PCA.java +++ b/src/jalview/analysis/PCA.java @@ -1,27 +1,29 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * 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 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 file is part of Jalview. * - * 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. + * 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. * - * 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 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.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 @@ -44,20 +46,36 @@ public class PCA implements Runnable StringBuffer details = new StringBuffer(); /** - * Creates a new PCA object. + * Creates a new PCA object. By default, uses blosum62 matrix to generate + * sequence similarity matrices * * @param s - * Set of sequences to perform PCA on + * 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) + { BinarySequence[] bs = new BinarySequence[s.length]; int ii = 0; while ((ii < s.length) && (s[ii] != null)) { - bs[ii] = new BinarySequence(s[ii]); + bs[ii] = new BinarySequence(s[ii], nucleotides); bs[ii].encode(); ii++; } @@ -65,10 +83,23 @@ public class PCA implements Runnable BinarySequence[] bs2 = new BinarySequence[s.length]; ii = 0; + String sm = nucleotides ? "DNA" : "BLOSUM62"; + ScoreMatrix smtrx = ResidueProperties.getScoreMatrix(sm); + 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]); - bs2[ii].blosumEncode(); + 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++; } @@ -115,7 +146,7 @@ public class PCA implements Runnable * Returns Eigenvalue * * @param i - * Index of diagonal within matrix + * Index of diagonal within matrix * * @return Returns value of diagonal from matrix */ @@ -128,13 +159,13 @@ public class PCA implements Runnable * DOCUMENT ME! * * @param l - * DOCUMENT ME! + * DOCUMENT ME! * @param n - * DOCUMENT ME! + * DOCUMENT ME! * @param mm - * DOCUMENT ME! + * DOCUMENT ME! * @param factor - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -156,7 +187,7 @@ public class PCA implements Runnable * DOCUMENT ME! * * @param n - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -177,9 +208,9 @@ public class PCA implements Runnable * DOCUMENT ME! * * @param row - * DOCUMENT ME! + * DOCUMENT ME! * @param n - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -205,10 +236,18 @@ public class PCA implements Runnable */ public void run() { + details.append("PCA Calculation Mode is "+(jvCalcMode ? "Jalview variant" : "Original SeqSpace")+"\n"); Matrix mt = m.transpose(); details.append(" --- OrigT * Orig ---- \n"); - eigenvector = mt.preMultiply(m2); + if (!jvCalcMode) + { + eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix + } + else + { + eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method + } PrintStream ps = new PrintStream(System.out) { @@ -241,12 +280,22 @@ public class PCA implements Runnable eigenvector.tqli(); details.append(" --- New diagonalization matrix ---\n"); + eigenvector.print(ps); details.append(" --- Eigenvalues ---\n"); eigenvector.printD(ps); ps.println(); - // taps.println(); - // taps.println("Transformed sequences = "); - // Matrix trans = m.preMultiply(eigenvector); - // trans.print(System.out); + /* + * for (int seq=0;seq