X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fmath%2FMatrix.java;h=b22bf4e1d27558fc09c6e59e64a45733f12d75cf;hb=187269da0130408d24901c88acb10c217f6284f9;hp=0f93eb5a4a3d4f1bba87115983fcc530c2d532cd;hpb=ab7ccf4373a27d71bca31bd6356c1390d9a0054c;p=jalview.git

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index 0f93eb5..b22bf4e 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -24,53 +24,53 @@ import jalview.util.Format;
 import jalview.util.MessageManager;
 
 import java.io.PrintStream;
+import java.util.Arrays;
 
 /**
- * DOCUMENT ME!
- * 
- * @author $author$
- * @version $Revision$
+ * A class to model rectangular matrices of double values and operations on them
  */
 public class Matrix implements MatrixI
 {
   /*
-   * the [row][column] values in the matrix
+   * maximum number of iterations for tqli
    */
-  private double[][] value;
+  private static final int MAX_ITER = 45;
+  // fudge - add 15 iterations, just in case
 
   /*
    * the number of rows
    */
-  protected int rows;
+  final protected int rows;
 
   /*
    * the number of columns
    */
-  protected int cols;
+  final protected int cols;
+
+  /*
+   * the cell values in row-major order
+   */
+  private double[][] value;
 
-  /** DOCUMENT ME!! */
   protected double[] d; // Diagonal
 
-  /** DOCUMENT ME!! */
   protected double[] e; // off diagonal
 
   /**
-   * maximum number of iterations for tqli
+   * Constructor given number of rows and columns
    * 
+   * @param colCount
+   * @param rowCount
    */
-  private static final int maxIter = 45; // fudge - add 15 iterations, just in
-                                         // case
-
-  /**
-   * Default constructor
-   */
-  public Matrix()
+  protected Matrix(int rowCount, int colCount)
   {
-
+    rows = rowCount;
+    cols = colCount;
   }
-  
+
   /**
-   * Creates a new Matrix object. For example
+   * Creates a new Matrix object containing a copy of the supplied array values.
+   * For example
    * 
    * <pre>
    *   new Matrix(new double[][] {{2, 3, 4}, {5, 6, 7})
@@ -89,18 +89,24 @@ public class Matrix implements MatrixI
   public Matrix(double[][] values)
   {
     this.rows = values.length;
-    if (rows > 0)
+    this.cols = this.rows == 0 ? 0 : values[0].length;
+
+    /*
+     * make a copy of the values array, for immutability
+     */
+    this.value = new double[rows][];
+    int i = 0;
+    for (double[] row : values)
     {
-      this.cols = values[0].length;
+      if (row != null)
+      {
+        value[i] = new double[row.length];
+        System.arraycopy(row, 0, value[i], 0, row.length);
+      }
+      i++;
     }
-    this.value = values;
   }
 
-  /**
-   * Returns a new matrix which is the transpose of this one
-   * 
-   * @return DOCUMENT ME!
-   */
   @Override
   public MatrixI transpose()
   {
@@ -138,18 +144,6 @@ public class Matrix implements MatrixI
     }
   }
 
-  /**
-   * Returns a new matrix which is the result of premultiplying this matrix by
-   * the supplied argument. If this of size AxB (A rows and B columns), and the
-   * argument is CxA (C rows and A columns), the result is of size CxB.
-   * 
-   * @param in
-   * 
-   * @return
-   * @throws IllegalArgumentException
-   *           if the number of columns in the pre-multiplier is not equal to
-   *           the number of rows in the multiplicand (this)
-   */
   @Override
   public MatrixI preMultiply(MatrixI in)
   {
@@ -201,21 +195,6 @@ public class Matrix implements MatrixI
     return out;
   }
 
-  /**
-   * Returns a new matrix which is the result of postmultiplying this matrix by
-   * the supplied argument. If this of size AxB (A rows and B columns), and the
-   * argument is BxC (B rows and C columns), the result is of size AxC.
-   * <p>
-   * This method simply returns the result of in.preMultiply(this)
-   * 
-   * @param in
-   * 
-   * @return
-   * @throws IllegalArgumentException
-   *           if the number of rows in the post-multiplier is not equal to the
-   *           number of columns in the multiplicand (this)
-   * @see #preMultiply(Matrix)
-   */
   @Override
   public MatrixI postMultiply(MatrixI in)
   {
@@ -227,11 +206,6 @@ public class Matrix implements MatrixI
     return in.preMultiply(this);
   }
 
-  /**
-   * Answers a new matrix with a copy of the values in this one
-   * 
-   * @return
-   */
   @Override
   public MatrixI copy()
   {
@@ -242,7 +216,17 @@ public class Matrix implements MatrixI
       System.arraycopy(value[i], 0, newmat[i], 0, value[i].length);
     }
 
-    return new Matrix(newmat);
+    Matrix m = new Matrix(newmat);
+    if (this.d != null)
+    {
+      m.d = Arrays.copyOf(this.d, this.d.length);
+    }
+    if (this.e != null)
+    {
+      m.e = Arrays.copyOf(this.e, this.e.length);
+    }
+
+    return m;
   }
 
   /**
@@ -275,27 +259,22 @@ public class Matrix implements MatrixI
       {
         for (k = 1; k <= l; k++)
         {
-          // double v = Math.abs(value[i - 1][k - 1]);
           double v = Math.abs(getValue(i - 1, k - 1));
           scale += v;
         }
 
         if (scale == 0.0)
         {
-          // e[i - 1] = value[i - 1][l - 1];
           e[i - 1] = getValue(i - 1, l - 1);
         }
         else
         {
           for (k = 1; k <= l; k++)
           {
-            // value[i - 1][k - 1] /= scale;
-            // h += (value[i - 1][k - 1] * value[i - 1][k - 1]);
             double v = divideValue(i - 1, k - 1, scale);
             h += v * v;
           }
 
-          // f = value[i - 1][l - 1];
           f = getValue(i - 1, l - 1);
 
           if (f > 0)
@@ -309,34 +288,26 @@ public class Matrix implements MatrixI
 
           e[i - 1] = scale * g;
           h -= (f * g);
-          // value[i - 1][l - 1] = f - g;
           setValue(i - 1, l - 1, f - g);
-          // System.out.println(String.format("%d %d %f %f %f %f %f %.5e", i,
-          // l,
-          // scale, f, g, h, getValue(i - 1, l - 1), checksum()));
           f = 0.0;
 
           for (j = 1; j <= l; j++)
           {
-            // value[j - 1][i - 1] = value[i - 1][j - 1] / h;
             double val = getValue(i - 1, j - 1) / h;
             setValue(j - 1, i - 1, val);
             g = 0.0;
 
             for (k = 1; k <= j; k++)
             {
-              // g += (value[j - 1][k - 1] * value[i - 1][k - 1]);
               g += (getValue(j - 1, k - 1) * getValue(i - 1, k - 1));
             }
 
             for (k = j + 1; k <= l; k++)
             {
-              // g += (value[k - 1][j - 1] * value[i - 1][k - 1]);
               g += (getValue(k - 1, j - 1) * getValue(i - 1, k - 1));
             }
 
             e[j - 1] = g / h;
-            // f += (e[j - 1] * value[i - 1][j - 1]);
             f += (e[j - 1] * getValue(i - 1, j - 1));
           }
 
@@ -344,15 +315,12 @@ public class Matrix implements MatrixI
 
           for (j = 1; j <= l; j++)
           {
-            // f = value[i - 1][j - 1];
             f = getValue(i - 1, j - 1);
             g = e[j - 1] - (hh * f);
             e[j - 1] = g;
 
             for (k = 1; k <= j; k++)
             {
-              // value[j - 1][k - 1] -= ((f * e[k - 1]) + (g * value[i - 1][k -
-              // 1]));
               double val = (f * e[k - 1]) + (g * getValue(i - 1, k - 1));
               addValue(j - 1, k - 1, -val);
             }
@@ -361,7 +329,6 @@ public class Matrix implements MatrixI
       }
       else
       {
-        // e[i - 1] = value[i - 1][l - 1];
         e[i - 1] = getValue(i - 1, l - 1);
       }
 
@@ -383,27 +350,21 @@ public class Matrix implements MatrixI
 
           for (k = 1; k <= l; k++)
           {
-            // g += (value[i - 1][k - 1] * value[k - 1][j - 1]);
             g += (getValue(i - 1, k - 1) * getValue(k - 1, j - 1));
           }
 
           for (k = 1; k <= l; k++)
           {
-            // value[k - 1][j - 1] -= (g * value[k - 1][i - 1]);
             addValue(k - 1, j - 1, -(g * getValue(k - 1, i - 1)));
           }
         }
       }
 
-      // d[i - 1] = value[i - 1][i - 1];
-      // value[i - 1][i - 1] = 1.0;
       d[i - 1] = getValue(i - 1, i - 1);
       setValue(i - 1, i - 1, 1.0);
 
       for (j = 1; j <= l; j++)
       {
-        // value[j - 1][i - 1] = 0.0;
-        // value[i - 1][j - 1] = 0.0;
         setValue(j - 1, i - 1, 0.0);
         setValue(i - 1, j - 1, 0.0);
       }
@@ -495,11 +456,11 @@ public class Matrix implements MatrixI
         {
           iter++;
 
-          if (iter == maxIter)
+          if (iter == MAX_ITER)
           {
             throw new Exception(MessageManager.formatMessage(
-                    "exception.matrix_too_many_iteration", new String[] {
-                        "tqli", Integer.valueOf(maxIter).toString() }));
+                    "exception.matrix_too_many_iteration", new String[]
+                    { "tqli", Integer.valueOf(MAX_ITER).toString() }));
           }
           else
           {
@@ -543,12 +504,10 @@ public class Matrix implements MatrixI
 
             for (k = 1; k <= n; k++)
             {
-              // f = value[k - 1][i];
-              // value[k - 1][i] = (s * value[k - 1][i - 1]) + (c * f);
-              // value[k - 1][i - 1] = (c * value[k - 1][i - 1]) - (s * f);
               f = getValue(k - 1, i);
               setValue(k - 1, i, (s * getValue(k - 1, i - 1)) + (c * f));
-              setValue(k - 1, i - 1, (c * getValue(k - 1, i - 1)) - (s * f));
+              setValue(k - 1, i - 1,
+                      (c * getValue(k - 1, i - 1)) - (s * f));
             }
           }
 
@@ -566,6 +525,7 @@ public class Matrix implements MatrixI
     return value[i][j];
   }
 
+  @Override
   public void setValue(int i, int j, double val)
   {
     value[i][j] = val;
@@ -760,11 +720,11 @@ public class Matrix implements MatrixI
         {
           iter++;
 
-          if (iter == maxIter)
+          if (iter == MAX_ITER)
           {
             throw new Exception(MessageManager.formatMessage(
-                    "exception.matrix_too_many_iteration", new String[] {
-                        "tqli2", Integer.valueOf(maxIter).toString() }));
+                    "exception.matrix_too_many_iteration", new String[]
+                    { "tqli2", Integer.valueOf(MAX_ITER).toString() }));
           }
           else
           {
@@ -882,7 +842,8 @@ public class Matrix implements MatrixI
    * 
    * @param ps
    *          DOCUMENT ME!
-   * @param format TODO
+   * @param format
+   *          TODO
    */
   @Override
   public void printE(PrintStream ps, String format)
@@ -904,9 +865,10 @@ public class Matrix implements MatrixI
   {
     return e;
   }
-  
+
   @Override
-  public int height() {
+  public int height()
+  {
     return rows;
   }
 
@@ -923,4 +885,141 @@ public class Matrix implements MatrixI
     System.arraycopy(value[i], 0, row, 0, cols);
     return row;
   }
+
+  /**
+   * Returns a length 2 array of {minValue, maxValue} of all values in the
+   * matrix. Returns null if the matrix is null or empty.
+   * 
+   * @return
+   */
+  double[] findMinMax()
+  {
+    if (value == null)
+    {
+      return null;
+    }
+    double min = Double.MAX_VALUE;
+    double max = -Double.MAX_VALUE;
+    boolean empty = true;
+    for (double[] row : value)
+    {
+      if (row != null)
+      {
+        for (double x : row)
+        {
+          empty = false;
+          if (x > max)
+          {
+            max = x;
+          }
+          if (x < min)
+          {
+            min = x;
+          }
+        }
+      }
+    }
+    return empty ? null : new double[] { min, max };
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public void reverseRange(boolean maxToZero)
+  {
+    if (value == null)
+    {
+      return;
+    }
+    double[] minMax = findMinMax();
+    if (minMax == null)
+    {
+      return; // empty matrix
+    }
+    double subtractFrom = maxToZero ? minMax[1] : minMax[0] + minMax[1];
+
+    for (double[] row : value)
+    {
+      if (row != null)
+      {
+        int j = 0;
+        for (double x : row)
+        {
+          row[j] = subtractFrom - x;
+          j++;
+        }
+      }
+    }
+  }
+
+  /**
+   * Multiplies every entry in the matrix by the given value.
+   * 
+   * @param
+   */
+  @Override
+  public void multiply(double by)
+  {
+    for (double[] row : value)
+    {
+      if (row != null)
+      {
+        for (int i = 0; i < row.length; i++)
+        {
+          row[i] *= by;
+        }
+      }
+    }
+  }
+
+  @Override
+  public void setD(double[] v)
+  {
+    d = v;
+  }
+
+  @Override
+  public void setE(double[] v)
+  {
+    e = v;
+  }
+
+  public double getTotal()
+  {
+    double d = 0d;
+    for (int i = 0; i < this.height(); i++)
+    {
+      for (int j = 0; j < this.width(); j++)
+      {
+        d += value[i][j];
+      }
+    }
+    return d;
+  }
+
+  /**
+   * {@inheritDoc}
+   */
+  @Override
+  public boolean equals(MatrixI m2, double delta)
+  {
+    if (m2 == null || this.height() != m2.height()
+            || this.width() != m2.width())
+    {
+      return false;
+    }
+    for (int i = 0; i < this.height(); i++)
+    {
+      for (int j = 0; j < this.width(); j++)
+      {
+        double diff = this.getValue(i, j) - m2.getValue(i, j);
+        if (Math.abs(diff) > delta)
+        {
+          return false;
+        }
+      }
+    }
+    return true;
+  }
 }