Formatting changes

[jalview.git] / src / jalview / analysis / PCA.java

diff --git a/src/jalview/analysis/PCA.java b/src/jalview/analysis/PCA.java
index ecbe4ab..2e37e6a 100755 (executable)
--- a/src/jalview/analysis/PCA.java
+++ b/src/jalview/analysis/PCA.java
@@ -24,29 +24,37 @@ import jalview.math.*;
 \r
 import jalview.util.*;\r
 \r
-import java.awt.*;\r
-\r
 import java.io.*;\r
 \r
 \r
-public class PCA implements Runnable {\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
-    public PCA(Matrix m) {\r
-        this.m = m;\r
-    }\r
 \r
-    public PCA(SequenceI[] s) {\r
-        Runtime rt = Runtime.getRuntime();\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
+        while ((ii < s.length) && (s[ii] != null))\r
+        {\r
             bs[ii] = new BinarySequence(s[ii]);\r
             bs[ii].encode();\r
             ii++;\r
@@ -55,7 +63,8 @@ public class PCA implements Runnable {
         BinarySequence[] bs2 = new BinarySequence[s.length];\r
         ii = 0;\r
 \r
-        while ((ii < s.length) && (s[ii] != null)) {\r
+        while ((ii < s.length) && (s[ii] != null))\r
+        {\r
             bs2[ii] = new BinarySequence(s[ii]);\r
             bs2[ii].blosumEncode();\r
             ii++;\r
@@ -65,7 +74,8 @@ public class PCA implements Runnable {
         //printMemory(rt);\r
         int count = 0;\r
 \r
-        while ((count < bs.length) && (bs[count] != null)) {\r
+        while ((count < bs.length) && (bs[count] != null))\r
+        {\r
             count++;\r
         }\r
 \r
@@ -73,7 +83,8 @@ public class PCA implements Runnable {
         double[][] seqmat2 = new double[count][bs2[0].getDBinary().length];\r
         int i = 0;\r
 \r
-        while (i < count) {\r
+        while (i < count)\r
+        {\r
             seqmat[i] = bs[i].getDBinary();\r
             seqmat2[i] = bs2[i].getDBinary();\r
             i++;\r
@@ -85,34 +96,47 @@ public class PCA implements Runnable {
         m = new Matrix(seqmat, count, bs[0].getDBinary().length);\r
         m2 = new Matrix(seqmat2, count, bs2[0].getDBinary().length);\r
 \r
-        //System.out.println("Created matrix");\r
-        printMemory(rt);\r
-    }\r
+      }\r
 \r
-    public static void printMemory(Runtime rt) {\r
-        System.out.println("PCA:Free memory = " + rt.freeMemory());\r
-    }\r
+      /**\r
+       * Returns the matrix used in PCA calculation\r
+       *\r
+       * @return java.math.Matrix object\r
+       */\r
 \r
-    public Matrix getM() {\r
+      public Matrix getM()\r
+      {\r
         return m;\r
-    }\r
-\r
-    public double[] getEigenvector(int i) {\r
-        return eigenvector.getColumn(i);\r
-    }\r
-\r
-    public double getEigenvalue(int i) {\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
-    public float[][] getComponents(int l, int n, int mm) {\r
-        return getComponents(l, n, mm, 1);\r
-    }\r
-\r
-    public float[][] getComponents(int l, int n, int mm, float factor) {\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
+        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
@@ -121,51 +145,52 @@ public class PCA implements Runnable {
         return out;\r
     }\r
 \r
-    public double[] component(int n) {\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
+        for (int i = 0; i < m.rows; i++)\r
+        {\r
             out[i] = component(i, n);\r
         }\r
 \r
         return out;\r
     }\r
 \r
-    public double component(int row, int n) {\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
+        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
-    public void checkEigenvector(int n, PrintStream ps) {\r
-        ps.println(" --- Eigenvector " + n + " --- ");\r
-\r
-        double[] eigenv = eigenvector.getColumn(n);\r
-\r
-        for (int i = 0; i < eigenv.length; i++) {\r
-            Format.print(ps, "%15.4f", eigenv[i]);\r
-        }\r
-\r
-        System.out.println();\r
-\r
-        double[] neigenv = symm.vectorPostMultiply(eigenv);\r
-        System.out.println(" --- symmat * eigenv / lambda --- ");\r
-\r
-        if (eigenvector.d[n] > 1e-4) {\r
-            for (int i = 0; i < neigenv.length; i++) {\r
-                Format.print(System.out, "%15.4f", neigenv[i] / eigenvector.d[n]);\r
-            }\r
-        }\r
-\r
-        System.out.println();\r
-    }\r
 \r
-    public void run() {\r
+    /**\r
+     * DOCUMENT ME!\r
+     */\r
+    public void run()\r
+    {\r
         Matrix mt = m.transpose();\r
 \r
         //    System.out.println(" --- OrigT * Orig ---- ");\r