From d6a30c6516e8e2f923c8c2f6dce7592cb3b7d974 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 23 Feb 2017 15:39:01 +0000
Subject: [PATCH] JAL-2403 additional methods to support distance/similarity
 score conversion

---
 src/jalview/math/Matrix.java      |   47 +++++++++++++++++++++++++++++++
 src/jalview/math/MatrixI.java     |   17 +++++++++++
 test/jalview/math/MatrixTest.java |   56 +++++++++++++++++++++++++++++++++++--
 3 files changed, 118 insertions(+), 2 deletions(-)

diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java
index de0bf77..3f0bae4 100755
--- a/src/jalview/math/Matrix.java
+++ b/src/jalview/math/Matrix.java
@@ -532,6 +532,7 @@ public class Matrix implements MatrixI
     return value[i][j];
   }
 
+  @Override
   public void setValue(int i, int j, double val)
   {
     value[i][j] = val;
@@ -889,4 +890,50 @@ public class Matrix implements MatrixI
     System.arraycopy(value[i], 0, row, 0, cols);
     return row;
   }
+
+  @Override
+  public double getMaxValue()
+  {
+    if (value == null)
+    {
+      return 0;
+    }
+    double max = -Double.MAX_VALUE;
+    for (double[] row : value)
+    {
+      if (row != null)
+      {
+        for (double x : row)
+        {
+          if (x > max)
+          {
+            max = x;
+          }
+        }
+      }
+    }
+    return max;
+  }
+
+  @Override
+  public void subtractAllFrom(double val)
+  {
+    if (value == null)
+    {
+      return;
+    }
+
+    for (double[] row : value)
+    {
+      if (row != null)
+      {
+        int j = 0;
+        for (double x : row)
+        {
+          row[j] = val - x;
+          j++;
+        }
+      }
+    }
+  }
 }
diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java
index d74a98b..05fe22f 100644
--- a/src/jalview/math/MatrixI.java
+++ b/src/jalview/math/MatrixI.java
@@ -28,6 +28,15 @@ public interface MatrixI
   double getValue(int i, int j);
 
   /**
+   * Sets the value at row i, colum j
+   * 
+   * @param i
+   * @param j
+   * @param d
+   */
+  void setValue(int i, int j, double d);
+
+  /**
    * Answers a copy of the values in the i'th row
    * 
    * @return
@@ -56,4 +65,12 @@ public interface MatrixI
 
   void tred();
 
+  double getMaxValue();
+
+  /**
+   * Update each value in the matrix by subtracting it from the given value
+   * 
+   * @param val
+   */
+  void subtractAllFrom(double val);
 }
diff --git a/test/jalview/math/MatrixTest.java b/test/jalview/math/MatrixTest.java
index 961602d..0d066dd 100644
--- a/test/jalview/math/MatrixTest.java
+++ b/test/jalview/math/MatrixTest.java
@@ -17,8 +17,8 @@ public class MatrixTest
   @Test(groups = "Timing")
   public void testPreMultiply_timing()
   {
-    int rows = 500;
-    int cols = 1000;
+    int rows = 50; // increase to stress test timing
+    int cols = 100;
     double[][] d1 = new double[rows][cols];
     double[][] d2 = new double[cols][rows];
     Matrix m1 = new Matrix(d1);
@@ -378,4 +378,56 @@ public class MatrixTest
     ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
     ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
   }
+
+  @Test(groups = "Functional")
+  public void testGetMaxValue() {
+    double[][] vals = new double[2][];
+    vals[0] = new double[] {7d, 1d, -2.3d};
+    vals[1] = new double[] {-12d, 94.3d, -102.34d};
+    MatrixI m = new Matrix(vals);
+    assertEquals(m.getMaxValue(), 94.3d);
+  }
+
+  @Test(groups = { "Functional", "Timing" })
+  public void testGetMaxValue_timing()
+  {
+    Random r = new Random();
+    int size = 1000; // increase to stress test timing
+    double[][] vals = new double[size][size];
+    double max = -Double.MAX_VALUE;
+    for (int i = 0; i < size; i++)
+    {
+      vals[i] = new double[size];
+      for (int j = 0; j < size; j++)
+      {
+        double d = r.nextDouble();
+        if (d > max)
+        {
+          max = d;
+        }
+        vals[i][j] = d;
+      }
+      i++;
+    }
+    MatrixI m = new Matrix(vals);
+    long now = System.currentTimeMillis();
+    double theMax = m.getMaxValue();
+    System.out.println(String.format("getMaxValue for %d x %d took %dms",
+            size, size, (System.currentTimeMillis() - now)));
+    assertEquals(theMax, max);
+  }
+
+  @Test(groups = "Functional")
+  public void testSubtractAllFrom()
+  {
+    Matrix m1 = new Matrix(new double[][] { { 2, 3, 4 }, { -3, 4, 15 } });
+    m1.subtractAllFrom(12.5);
+    assertEquals(m1.getValue(0, 0), 10.5d);
+    assertEquals(m1.getValue(0, 1), 9.5d);
+    assertEquals(m1.getValue(0, 2), 8.5d);
+    assertEquals(m1.getValue(1, 0), 15.5d);
+    assertEquals(m1.getValue(1, 1), 8.5d);
+    assertEquals(m1.getValue(1, 2), -2.5d);
+  }
+
 }
-- 
1.7.10.2