X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fmath%2FSparseMatrixTest.java;h=321286caf1f309755f3c9586017e573877daafc1;hb=e9a1c2c372f4bbf6cf658de3dba73ef326b20c20;hp=5e32e18b8fdffa958c13ae3db72a9b38850ef7de;hpb=8fea25daa8f1f1cc564497ddf4e3c9e15a64596c;p=jalview.git

diff --git a/test/jalview/math/SparseMatrixTest.java b/test/jalview/math/SparseMatrixTest.java
index 5e32e18..321286c 100644
--- a/test/jalview/math/SparseMatrixTest.java
+++ b/test/jalview/math/SparseMatrixTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.math;
 
 import static org.testng.Assert.assertEquals;
@@ -20,7 +40,8 @@ public class SparseMatrixTest
   public void testConstructor()
   {
     MatrixI m1 = new SparseMatrix(
-            new double[][] { { 2, 0, 4 }, { 0, 6, 0 } });
+            new double[][]
+            { { 2, 0, 4 }, { 0, 6, 0 } });
     assertEquals(m1.getValue(0, 0), 2d);
     assertEquals(m1.getValue(0, 1), 0d);
     assertEquals(m1.getValue(0, 2), 4d);
@@ -33,7 +54,8 @@ public class SparseMatrixTest
   public void testTranspose()
   {
     MatrixI m1 = new SparseMatrix(
-            new double[][] { { 2, 0, 4 }, { 5, 6, 0 } });
+            new double[][]
+            { { 2, 0, 4 }, { 5, 6, 0 } });
     MatrixI m2 = m1.transpose();
     assertTrue(m2 instanceof SparseMatrix);
     assertEquals(m2.height(), 3);
@@ -45,6 +67,7 @@ public class SparseMatrixTest
     assertEquals(m2.getValue(2, 0), 4d);
     assertEquals(m2.getValue(2, 1), 0d);
   }
+
   @Test(groups = "Functional")
   public void testPreMultiply()
   {
@@ -80,11 +103,13 @@ public class SparseMatrixTest
 
   @Test(
     groups = "Functional",
-    expectedExceptions = { IllegalArgumentException.class })
+    expectedExceptions =
+    { IllegalArgumentException.class })
   public void testPreMultiply_tooManyColumns()
   {
     Matrix m1 = new SparseMatrix(
-            new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
+            new double[][]
+            { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
 
     /*
      * 2x3 times 2x3 invalid operation - 
@@ -96,11 +121,13 @@ public class SparseMatrixTest
 
   @Test(
     groups = "Functional",
-    expectedExceptions = { IllegalArgumentException.class })
+    expectedExceptions =
+    { IllegalArgumentException.class })
   public void testPreMultiply_tooFewColumns()
   {
     Matrix m1 = new SparseMatrix(
-            new double[][] { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
+            new double[][]
+            { { 2, 3, 4 }, { 3, 4, 5 } }); // 2x3
 
     /*
      * 3x2 times 3x2 invalid operation - 
@@ -109,7 +136,7 @@ public class SparseMatrixTest
     m1.preMultiply(m1);
     fail("Expected exception");
   }
-  
+
   @Test(groups = "Functional")
   public void testPostMultiply()
   {
@@ -122,8 +149,9 @@ public class SparseMatrixTest
      * (5040 50400)
      */
     MatrixI m1 = new SparseMatrix(new double[][] { { 2, 3 }, { 4, 5 } });
-    MatrixI m2 = new SparseMatrix(new double[][] { { 10, 100 },
-        { 1000, 10000 } });
+    MatrixI m2 = new SparseMatrix(
+            new double[][]
+            { { 10, 100 }, { 1000, 10000 } });
     MatrixI m3 = m1.postMultiply(m2);
     assertEquals(m3.getValue(0, 0), 3020d);
     assertEquals(m3.getValue(0, 1), 30200d);
@@ -134,7 +162,7 @@ public class SparseMatrixTest
      * also check m2.preMultiply(m1) - should be same as m1.postMultiply(m2) 
      */
     MatrixI m4 = m2.preMultiply(m1);
-    assertMatricesMatch(m3, m4);
+    assertMatricesMatch(m3, m4, 0.00001d);
 
     /*
      * m1 has more rows than columns
@@ -154,7 +182,7 @@ public class SparseMatrixTest
     assertEquals(m3.getValue(1, 2), 3000d);
 
     m4 = m2.preMultiply(m1);
-    assertMatricesMatch(m3, m4);
+    assertMatricesMatch(m3, m4, 0.00001d);
 
     /*
      * m1 has more columns than rows
@@ -176,7 +204,7 @@ public class SparseMatrixTest
      * and check premultiply equivalent
      */
     m4 = m2.preMultiply(m1);
-    assertMatricesMatch(m3, m4);
+    assertMatricesMatch(m3, m4, 0.00001d);
   }
 
   @Test(groups = "Timing")
@@ -201,8 +229,7 @@ public class SparseMatrixTest
     /*
      * make a pseudo-random symmetric matrix as required for tred/tqli
      */
-    // TODO why does this fail for rows > 9??
-    int rows = 9;
+    int rows = 10;
     int cols = rows;
     double[][] d = getSparseValues(rows, cols, 3);
 
@@ -220,13 +247,13 @@ public class SparseMatrixTest
     }
     Matrix m1 = new Matrix(d);
     Matrix m2 = new SparseMatrix(d1);
-    assertMatricesMatch(m1, m2); // sanity check
+    assertMatricesMatch(m1, m2, 0.00001d); // sanity check
     m1.tred();
     m2.tred();
-    assertMatricesMatch(m1, m2);
+    assertMatricesMatch(m1, m2, 0.00001d);
   }
 
-  private void assertMatricesMatch(MatrixI m1, MatrixI m2)
+  private void assertMatricesMatch(MatrixI m1, MatrixI m2, double delta)
   {
     if (m1.height() != m2.height())
     {
@@ -248,7 +275,7 @@ public class SparseMatrixTest
         }
       }
     }
-    ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), 0.00001d);
+    ArrayAsserts.assertArrayEquals(m1.getD(), m2.getD(), delta);
     ArrayAsserts.assertArrayEquals(m1.getE(), m2.getE(), 0.00001d);
   }
 
@@ -284,7 +311,7 @@ public class SparseMatrixTest
     int rows = 6;
     int cols = rows;
     double[][] d = getSparseValues(rows, cols, 3);
-  
+
     /*
      * make a copy of the values so m1, m2 are not
      * sharing arrays!
@@ -303,11 +330,11 @@ public class SparseMatrixTest
     // have to do tred() before doing tqli()
     m1.tred();
     m2.tred();
-    assertMatricesMatch(m1, m2);
+    assertMatricesMatch(m1, m2, 0.00001d);
 
     m1.tqli();
     m2.tqli();
-    assertMatricesMatch(m1, m2);
+    assertMatricesMatch(m1, m2, 0.00001d);
   }
 
   /**
@@ -353,10 +380,11 @@ public class SparseMatrixTest
   @Test(groups = "Functional")
   public void testPreMultiply_sparseProduct()
   {
-    MatrixI m1 = new SparseMatrix(new double[][] { { 1 }, { 0 }, { 0 },
-        { 0 }, { 0 } }); // 5x1
+    MatrixI m1 = new SparseMatrix(
+            new double[][]
+            { { 1 }, { 0 }, { 0 }, { 0 }, { 0 } }); // 5x1
     MatrixI m2 = new SparseMatrix(new double[][] { { 1, 1, 1, 1 } }); // 1x4
-  
+
     /*
      * m1.m2 makes a row of 4 1's, and 4 rows of zeros
      * 20% non-zero so not 'sparse'
@@ -376,8 +404,9 @@ public class SparseMatrixTest
   @Test(groups = "Functional")
   public void testFillRatio()
   {
-    SparseMatrix m1 = new SparseMatrix(new double[][] { { 2, 0, 4, 1, 0 },
-    { 0, 6, 0, 0, 0 } });
+    SparseMatrix m1 = new SparseMatrix(
+            new double[][]
+            { { 2, 0, 4, 1, 0 }, { 0, 6, 0, 0, 0 } });
     assertEquals(m1.getFillRatio(), 0.4f);
   }
 
@@ -394,7 +423,7 @@ public class SparseMatrixTest
     int rows = 10;
     int cols = rows;
     double[][] d = getSparseValues(rows, cols, 3);
-  
+
     /*
      * make a copy of the values so m1, m2 are not
      * sharing arrays!
@@ -409,9 +438,9 @@ public class SparseMatrixTest
     }
     Matrix m1 = new SparseMatrix(d);
     Matrix m2 = new SparseMatrix(d1);
-    assertMatricesMatch(m1, m2); // sanity check
+    assertMatricesMatch(m1, m2, 1.0e16); // sanity check
     m1.tred();
     m2.tred();
-    assertMatricesMatch(m1, m2);
+    assertMatricesMatch(m1, m2, 0.00001d);
   }
 }
\ No newline at end of file