-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
-*\r
-* This program is free software; you can redistribute it and/or\r
-* modify it under the terms of the GNU General Public License\r
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.analysis;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.math.*;\r
-\r
-import jalview.util.*;\r
-\r
-import java.io.*;\r
-\r
-\r
-/**\r
- * Performs Principal Component Analysis on given sequences\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class PCA implements Runnable\r
-{\r
- Matrix m;\r
- Matrix symm;\r
- Matrix m2;\r
- double[] eigenvalue;\r
- Matrix eigenvector;\r
-\r
-\r
- /**\r
- * Creates a new PCA object.\r
- *\r
- * @param s Set of sequences to perform PCA on\r
- */\r
- public PCA(SequenceI[] s)\r
- {\r
-\r
- BinarySequence[] bs = new BinarySequence[s.length];\r
- int ii = 0;\r
-\r
- while ((ii < s.length) && (s[ii] != null))\r
- {\r
- bs[ii] = new BinarySequence(s[ii]);\r
- bs[ii].encode();\r
- ii++;\r
- }\r
-\r
- BinarySequence[] bs2 = new BinarySequence[s.length];\r
- ii = 0;\r
-\r
- while ((ii < s.length) && (s[ii] != null))\r
- {\r
- bs2[ii] = new BinarySequence(s[ii]);\r
- bs2[ii].blosumEncode();\r
- ii++;\r
- }\r
-\r
- //System.out.println("Created binary encoding");\r
- //printMemory(rt);\r
- int count = 0;\r
-\r
- while ((count < bs.length) && (bs[count] != null))\r
- {\r
- count++;\r
- }\r
-\r
- double[][] seqmat = new double[count][bs[0].getDBinary().length];\r
- double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];\r
- int i = 0;\r
-\r
- while (i < count)\r
- {\r
- seqmat[i] = bs[i].getDBinary();\r
- seqmat2[i] = bs2[i].getDBinary();\r
- i++;\r
- }\r
-\r
- //System.out.println("Created array");\r
- //printMemory(rt);\r
- // System.out.println(" --- Original matrix ---- ");\r
- m = new Matrix(seqmat, count, bs[0].getDBinary().length);\r
- m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);\r
-\r
- }\r
-\r
- /**\r
- * Returns the matrix used in PCA calculation\r
- *\r
- * @return java.math.Matrix object\r
- */\r
-\r
- public Matrix getM()\r
- {\r
- return m;\r
- }\r
-\r
- /**\r
- * Returns Eigenvalue\r
- *\r
- * @param i Index of diagonal within matrix\r
- *\r
- * @return Returns value of diagonal from matrix\r
- */\r
- public double getEigenvalue(int i)\r
- {\r
- return eigenvector.d[i];\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param l DOCUMENT ME!\r
- * @param n DOCUMENT ME!\r
- * @param mm DOCUMENT ME!\r
- * @param factor DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public float[][] getComponents(int l, int n, int mm, float factor)\r
- {\r
- float[][] out = new float[m.rows][3];\r
-\r
- for (int i = 0; i < m.rows; i++)\r
- {\r
- out[i][0] = (float) component(i, l) * factor;\r
- out[i][1] = (float) component(i, n) * factor;\r
- out[i][2] = (float) component(i, mm) * factor;\r
- }\r
-\r
- return out;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public double[] component(int n)\r
- {\r
- // n = index of eigenvector\r
- double[] out = new double[m.rows];\r
-\r
- for (int i = 0; i < m.rows; i++)\r
- {\r
- out[i] = component(i, n);\r
- }\r
-\r
- return out;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param row DOCUMENT ME!\r
- * @param n DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- double component(int row, int n)\r
- {\r
- double out = 0.0;\r
-\r
- for (int i = 0; i < symm.cols; i++)\r
- {\r
- out += (symm.value[row][i] * eigenvector.value[i][n]);\r
- }\r
-\r
- return out / eigenvector.d[n];\r
- }\r
-\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public void run()\r
- {\r
- Matrix mt = m.transpose();\r
-\r
- // System.out.println(" --- OrigT * Orig ---- ");\r
- eigenvector = mt.preMultiply(m2);\r
-\r
- // eigenvector.print(System.out);\r
- symm = eigenvector.copy();\r
-\r
- //TextArea ta = new TextArea(25,72);\r
- //TextAreaPrintStream taps = new TextAreaPrintStream(System.out,ta);\r
- //Frame f = new Frame("PCA output");\r
- //f.resize(500,500);\r
- //f.setLayout(new BorderLayout());\r
- //f.add("Center",ta);\r
- //f.show();\r
- //symm.print(taps);\r
- long tstart = System.currentTimeMillis();\r
- eigenvector.tred();\r
-\r
- long tend = System.currentTimeMillis();\r
-\r
- //taps.println("Time take for tred = " + (tend-tstart) + "ms");\r
- //taps.println(" ---Tridiag transform matrix ---");\r
- //taps.println(" --- D vector ---");\r
- //eigenvector.printD(taps);\r
- //taps.println();\r
- //taps.println(" --- E vector ---");\r
- // eigenvector.printE(taps);\r
- //taps.println();\r
- // Now produce the diagonalization matrix\r
- tstart = System.currentTimeMillis();\r
- eigenvector.tqli();\r
- tend = System.currentTimeMillis();\r
-\r
- //System.out.println("Time take for tqli = " + (tend-tstart) + " ms");\r
- //System.out.println(" --- New diagonalization matrix ---");\r
- //System.out.println(" --- Eigenvalues ---");\r
- //eigenvector.printD(taps);\r
- //System.out.println();\r
- // for (int i=0; i < eigenvector.cols; i++) {\r
- // checkEigenvector(i,taps);\r
- // taps.println();\r
- // }\r
- // taps.println();\r
- // taps.println("Transformed sequences = ");\r
- // Matrix trans = m.preMultiply(eigenvector);\r
- // trans.print(System.out);\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 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 <http://www.gnu.org/licenses/>.
+ */
+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<symm.rows;seq++) { ps.print("\"Seq"+seq+"\""); for
+ * (int ev=0;ev<symm.rows; ev++) {
+ *
+ * ps.print(","+component(seq, ev)); } ps.println(); }
+ */
+ }
+}
git://source.jalview.org / jalview.git / blobdiff