X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrixTest.java;h=01de7415bd806e0c032b87af95c4bcaeec701d88;hb=7f5ab7d1f58d870622968e0e6a430f33403b8e4f;hp=0a9dd25668112998c583c97a4b362b70bb534833;hpb=7c5c70f4bbe69a722dd6e8bd269d7d01e1089034;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 0a9dd25..01de741 100644
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -1,7 +1,20 @@
 package jalview.analysis.scoremodels;
+
 import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
+import static org.testng.Assert.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.io.DataSourceType;
+import jalview.io.FileParse;
+import jalview.io.ScoreMatrixFile;
+import jalview.math.MatrixI;
+
+import java.io.IOException;
+import java.net.MalformedURLException;
+import java.util.Arrays;
+
 import org.testng.annotations.Test;
 
 public class ScoreMatrixTest
@@ -110,6 +123,19 @@ public class ScoreMatrixTest
   }
 
   @Test(groups = "Functional")
+  public void testGetMatrix()
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    float[][] m = sm.getMatrix();
+    assertEquals(m.length, sm.getSize());
+    assertEquals(m[2][4], -3f);
+    // verify a defensive copy is returned
+    float[][] m2 = sm.getMatrix();
+    assertNotSame(m, m2);
+    assertTrue(Arrays.deepEquals(m, m2));
+  }
+
+  @Test(groups = "Functional")
   public void testGetMatrixIndex()
   {
     ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
@@ -134,4 +160,88 @@ public class ScoreMatrixTest
     ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
     assertEquals(sm.getMatrix().length, sm.getSize());
   }
+
+  @Test(groups = "Functional")
+  public void testComputePairwiseScores()
+  {
+    /*
+     * NB score matrix assumes space for gap - Jalview converts
+     * space to gap before computing PCA or Tree
+     */
+    String[] seqs = new String[] { "FKL", "R D", "QIA", "GWC" };
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+
+    MatrixI pairwise = sm.findSimilarities(seqs);
+
+    /*
+     * should be NxN where N = number of sequences
+     */
+    assertEquals(pairwise.height(), 4);
+    assertEquals(pairwise.width(), 4);
+
+    /*
+     * should be symmetrical (because BLOSUM62 is)
+     */
+    for (int i = 0; i < pairwise.height(); i++)
+    {
+      for (int j = i + 1; j < pairwise.width(); j++)
+      {
+        assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i),
+                String.format("Not symmetric at [%d, %d]", i, j));
+      }
+    }
+    /*
+     * verify expected BLOSUM dot product scores
+     */
+    // F.F + K.K + L.L = 6 + 5 + 4 = 15
+    assertEquals(pairwise.getValue(0, 0), 15d);
+    // R.R + -.- + D.D = 5 + 1 + 6 = 12
+    assertEquals(pairwise.getValue(1, 1), 12d);
+    // Q.Q + I.I + A.A = 5 + 4 + 4 = 13
+    assertEquals(pairwise.getValue(2, 2), 13d);
+    // G.G + W.W + C.C = 6 + 11 + 9 = 26
+    assertEquals(pairwise.getValue(3, 3), 26d);
+    // F.R + K.- + L.D = -3 + -4 + -4 = -11
+    assertEquals(pairwise.getValue(0, 1), -11d);
+    // F.Q + K.I + L.A = -3 + -3 + -1 = -7
+    assertEquals(pairwise.getValue(0, 2), -7d);
+    // F.G + K.W + L.C = -3 + -3 + -1 = -7
+    assertEquals(pairwise.getValue(0, 3), -7d);
+    // R.Q + -.I + D.A = 1 + -4 + -2 = -5
+    assertEquals(pairwise.getValue(1, 2), -5d);
+    // R.G + -.W + D.C = -2 + -4 + -3 = -9
+    assertEquals(pairwise.getValue(1, 3), -9d);
+    // Q.G + I.W + A.C = -2 + -3 + 0 = -5
+    assertEquals(pairwise.getValue(2, 3), -5d);
+  }
+
+  /**
+   * Test that the result of outputMatrix can be reparsed to give an identical
+   * ScoreMatrix
+   * 
+   * @throws IOException
+   * @throws MalformedURLException
+   */
+  @Test(groups = "Functional")
+  public void testOutputMatrix_roundTrip() throws MalformedURLException,
+          IOException
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    String output = sm.outputMatrix(false);
+    FileParse fp = new FileParse(output, DataSourceType.PASTE);
+    ScoreMatrixFile parser = new ScoreMatrixFile(fp);
+    ScoreMatrix sm2 = parser.parseMatrix();
+    assertNotNull(sm2);
+    assertTrue(sm2.equals(sm));
+  }
+
+  @Test(groups = "Functional")
+  public void testEqualsAndHashCode()
+  {
+    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
+    ScoreMatrix sm2 = new ScoreMatrix(sm.getName(), sm.getSymbols()
+            .toCharArray(), sm.getMatrix());
+    assertTrue(sm.equals(sm2));
+    assertEquals(sm.hashCode(), sm2.hashCode());
+  }
 }