Merge branch 'develop' into features/JAL-2393customMatrices

[jalview.git] / test / jalview / analysis / scoremodels / ScoreMatrixTest.java

diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 0a9dd25..97cb742 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -2,6 +2,8 @@ package jalview.analysis.scoremodels;
 import static org.testng.Assert.assertEquals;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.math.MatrixI;
+
 import org.testng.annotations.Test;
 
 public class ScoreMatrixTest
@@ -134,4 +136,58 @@ 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.computePairwiseScores(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);
+  }
 }