X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=9be0e3ced5135a4077ae6707d2ab0b4f8a33b11d;hb=9e3e20c98eae9498a68bb0a770359564797a12ef;hp=c11610a28bc9e5f0fdc76aab450510827b7b6ba0;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index c11610a..9be0e3c 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -1,239 +1,255 @@
-/*
- * 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 java.io.*;
-
-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;
- 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[] 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];
- }
-
- public String getDetails()
- {
- return details.toString();
- }
-
- /**
- * DOCUMENT ME!
- */
- public void run()
- {
- 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);
-
- 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);
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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.analysis;
+
+import java.io.*;
+
+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;
+
+ 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[] 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];
+ }
+
+ public String getDetails()
+ {
+ return details.toString();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public void run()
+ {
+ Matrix mt = m.transpose();
+
+ details.append(" --- OrigT * Orig ---- \n");
+ // eigenvector = mt.preMultiply(m); // standard seqspace comparison matrix
+ eigenvector = mt.preMultiply(m2); // jalview variation on seqsmace method
+
+ PrintStream ps = new PrintStream(System.out)
+ {
+ public void print(String x)
+ {
+ details.append(x);
+ }
+
+ 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");
+ eigenvector.print(ps);
+ details.append(" --- Eigenvalues ---\n");
+ eigenvector.printD(ps);
+ ps.println();
+ /*
+ * for (int seq=0;seq