X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FPCA.java;h=4d691c0f01264683c52e9a5ea59fa4c1851dc35e;hb=f932cb5bb08dce9d7441c788d6996efaef53d15a;hp=ecbe4ab45d75930e4118305b31f3733acf2feab1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index ecbe4ab..4d691c0 100755
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -22,31 +22,35 @@ import jalview.datamodel.*;
 
 import jalview.math.*;
 
-import jalview.util.*;
 
-import java.awt.*;
-
-import java.io.*;
-
-
-public class PCA implements Runnable {
+/**
+ * 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;
 
-    public PCA(Matrix m) {
-        this.m = m;
-    }
 
-    public PCA(SequenceI[] s) {
-        Runtime rt = Runtime.getRuntime();
+    /**
+     * 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)) {
+        while ((ii < s.length) && (s[ii] != null))
+        {
             bs[ii] = new BinarySequence(s[ii]);
             bs[ii].encode();
             ii++;
@@ -55,7 +59,8 @@ public class PCA implements Runnable {
         BinarySequence[] bs2 = new BinarySequence[s.length];
         ii = 0;
 
-        while ((ii < s.length) && (s[ii] != null)) {
+        while ((ii < s.length) && (s[ii] != null))
+        {
             bs2[ii] = new BinarySequence(s[ii]);
             bs2[ii].blosumEncode();
             ii++;
@@ -65,7 +70,8 @@ public class PCA implements Runnable {
         //printMemory(rt);
         int count = 0;
 
-        while ((count < bs.length) && (bs[count] != null)) {
+        while ((count < bs.length) && (bs[count] != null))
+        {
             count++;
         }
 
@@ -73,7 +79,8 @@ public class PCA implements Runnable {
         double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];
         int i = 0;
 
-        while (i < count) {
+        while (i < count)
+        {
             seqmat[i] = bs[i].getDBinary();
             seqmat2[i] = bs2[i].getDBinary();
             i++;
@@ -85,34 +92,47 @@ public class PCA implements Runnable {
         m = new Matrix(seqmat, count, bs[0].getDBinary().length);
         m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);
 
-        //System.out.println("Created matrix");
-        printMemory(rt);
-    }
+      }
 
-    public static void printMemory(Runtime rt) {
-        System.out.println("PCA:Free memory = " + rt.freeMemory());
-    }
+      /**
+       * Returns the matrix used in PCA calculation
+       *
+       * @return java.math.Matrix object
+       */
 
-    public Matrix getM() {
+      public Matrix getM()
+      {
         return m;
-    }
-
-    public double[] getEigenvector(int i) {
-        return eigenvector.getColumn(i);
-    }
-
-    public double getEigenvalue(int i) {
+      }
+
+    /**
+     * 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];
     }
 
-    public float[][] getComponents(int l, int n, int mm) {
-        return getComponents(l, n, mm, 1);
-    }
-
-    public float[][] getComponents(int l, int n, int mm, float factor) {
+     /**
+     * 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++) {
+        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;
@@ -121,51 +141,52 @@ public class PCA implements Runnable {
         return out;
     }
 
-    public double[] component(int n) {
+    /**
+     * 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++) {
+        for (int i = 0; i < m.rows; i++)
+        {
             out[i] = component(i, n);
         }
 
         return out;
     }
 
-    public double component(int row, int n) {
+    /**
+     * 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++) {
+        for (int i = 0; i < symm.cols; i++)
+        {
             out += (symm.value[row][i] * eigenvector.value[i][n]);
         }
 
         return out / eigenvector.d[n];
     }
 
-    public void checkEigenvector(int n, PrintStream ps) {
-        ps.println(" --- Eigenvector " + n + " --- ");
-
-        double[] eigenv = eigenvector.getColumn(n);
-
-        for (int i = 0; i < eigenv.length; i++) {
-            Format.print(ps, "%15.4f", eigenv[i]);
-        }
-
-        System.out.println();
-
-        double[] neigenv = symm.vectorPostMultiply(eigenv);
-        System.out.println(" --- symmat * eigenv / lambda --- ");
-
-        if (eigenvector.d[n] > 1e-4) {
-            for (int i = 0; i < neigenv.length; i++) {
-                Format.print(System.out, "%15.4f", neigenv[i] / eigenvector.d[n]);
-            }
-        }
-
-        System.out.println();
-    }
 
-    public void run() {
+    /**
+     * DOCUMENT ME!
+     */
+    public void run()
+    {
         Matrix mt = m.transpose();
 
         //    System.out.println(" --- OrigT * Orig ---- ");