X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FScoreMatrixTest.java;h=99af6015f271dbc3418c71442f18e351fabf893e;hb=35679161e01fac267b1a58bec4244baae94d7fd2;hp=0ae7375ecea6298d3b1bb99aa4a66833162f2ed7;hpb=07394c1c2d9d4ae05c85cd6d9644e4d17f2818a2;p=jalview.git

diff --git a/test/jalview/schemes/ScoreMatrixTest.java b/test/jalview/schemes/ScoreMatrixTest.java
index 0ae7375..99af601 100644
--- a/test/jalview/schemes/ScoreMatrixTest.java
+++ b/test/jalview/schemes/ScoreMatrixTest.java
@@ -2,6 +2,8 @@ package jalview.schemes;
 
 import static org.testng.Assert.assertEquals;
 
+import jalview.math.MatrixI;
+
 import org.testng.annotations.Test;
 
 public class ScoreMatrixTest
@@ -23,13 +25,6 @@ public class ScoreMatrixTest
       assertEquals(m[row].length, rows);
       for (int col = 0; col < rows; col++)
       {
-        // if (m[row][col] != m[col][row])
-        // {
-        // System.out.println(String.format("%s [%d, %d] [%s, %s]",
-        // sm.getName(), m[row][col], m[col][row],
-        // ResidueProperties.aa[row],
-        // ResidueProperties.aa[col]));
-        // }
         assertEquals(m[row][col], m[col][row], String.format("%s [%s, %s]",
                 sm.getName(), ResidueProperties.aa[row],
                 ResidueProperties.aa[col]));
@@ -43,4 +38,132 @@ public class ScoreMatrixTest
     assertEquals(rows, (sm.isDNA() ? ResidueProperties.maxNucleotideIndex
             : ResidueProperties.maxProteinIndex) + 1);
   }
+
+  /**
+   * A test that just asserts the expected values in the Blosum62 score matrix
+   */
+  @Test(groups = "Functional")
+  public void testBlosum62_values()
+  {
+    ScoreMatrix sm = ResidueProperties.getScoreMatrix("BLOSUM62");
+
+    /*
+     * verify expected scores against ARNDCQEGHILKMFPSTWYVBZX
+     * scraped from https://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt
+     */
+    verifyValues(sm, 'A', new int[] { 4, -1, -2, -2, 0, -1, -1, 0, -2, -1,
+        -1, -1, -1, -2, -1, 1, 0, -3, -2, 0, -2, -1, 0 });
+    verifyValues(sm, 'R', new int[] { -1, 5, 0, -2, -3, 1, 0, -2, 0, -3,
+        -2, 2, -1, -3, -2, -1, -1, -3, -2, -3, -1, 0, -1 });
+    verifyValues(sm, 'N', new int[] { -2, 0, 6, 1, -3, 0, 0, 0, 1, -3, -3,
+        0, -2, -3, -2, 1, 0, -4, -2, -3, 3, 0, -1 });
+    verifyValues(sm, 'D', new int[] { -2, -2, 1, 6, -3, 0, 2, -1, -1, -3,
+        -4, -1, -3, -3, -1, 0, -1, -4, -3, -3, 4, 1, -1 });
+    verifyValues(sm, 'C', new int[] { 0, -3, -3, -3, 9, -3, -4, -3, -3, -1,
+        -1, -3, -1, -2, -3, -1, -1, -2, -2, -1, -3, -3, -2 });
+    verifyValues(sm, 'Q', new int[] { -1, 1, 0, 0, -3, 5, 2, -2, 0, -3, -2,
+        1, 0, -3, -1, 0, -1, -2, -1, -2, 0, 3, -1 });
+    verifyValues(sm, 'E', new int[] { -1, 0, 0, 2, -4, 2, 5, -2, 0, -3, -3,
+        1, -2, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 });
+    verifyValues(sm, 'G', new int[] { 0, -2, 0, -1, -3, -2, -2, 6, -2, -4,
+        -4, -2, -3, -3, -2, 0, -2, -2, -3, -3, -1, -2, -1 });
+    verifyValues(sm, 'H', new int[] { -2, 0, 1, -1, -3, 0, 0, -2, 8, -3,
+        -3, -1, -2, -1, -2, -1, -2, -2, 2, -3, 0, 0, -1 });
+    verifyValues(sm, 'I', new int[] { -1, -3, -3, -3, -1, -3, -3, -4, -3,
+        4, 2, -3, 1, 0, -3, -2, -1, -3, -1, 3, -3, -3, -1 });
+    verifyValues(sm, 'L', new int[] { -1, -2, -3, -4, -1, -2, -3, -4, -3,
+        2, 4, -2, 2, 0, -3, -2, -1, -2, -1, 1, -4, -3, -1 });
+    verifyValues(sm, 'K', new int[] { -1, 2, 0, -1, -3, 1, 1, -2, -1, -3,
+        -2, 5, -1, -3, -1, 0, -1, -3, -2, -2, 0, 1, -1 });
+    verifyValues(sm, 'M', new int[] { -1, -1, -2, -3, -1, 0, -2, -3, -2, 1,
+        2, -1, 5, 0, -2, -1, -1, -1, -1, 1, -3, -1, -1 });
+    verifyValues(sm, 'F', new int[] { -2, -3, -3, -3, -2, -3, -3, -3, -1,
+        0, 0, -3, 0, 6, -4, -2, -2, 1, 3, -1, -3, -3, -1 });
+    verifyValues(sm, 'P', new int[] { -1, -2, -2, -1, -3, -1, -1, -2, -2,
+        -3, -3, -1, -2, -4, 7, -1, -1, -4, -3, -2, -2, -1, -2 });
+    verifyValues(sm, 'S', new int[] { 1, -1, 1, 0, -1, 0, 0, 0, -1, -2, -2,
+        0, -1, -2, -1, 4, 1, -3, -2, -2, 0, 0, 0 });
+    verifyValues(sm, 'T', new int[] { 0, -1, 0, -1, -1, -1, -1, -2, -2, -1,
+        -1, -1, -1, -2, -1, 1, 5, -2, -2, 0, -1, -1, 0 });
+    verifyValues(sm, 'W', new int[] { -3, -3, -4, -4, -2, -2, -3, -2, -2,
+        -3, -2, -3, -1, 1, -4, -3, -2, 11, 2, -3, -4, -3, -2 });
+    verifyValues(sm, 'Y', new int[] { -2, -2, -2, -3, -2, -1, -2, -3, 2,
+        -1, -1, -2, -1, 3, -3, -2, -2, 2, 7, -1, -3, -2, -1 });
+    verifyValues(sm, 'V', new int[] { 0, -3, -3, -3, -1, -2, -2, -3, -3, 3,
+        1, -2, 1, -1, -2, -2, 0, -3, -1, 4, -3, -2, -1 });
+    verifyValues(sm, 'B', new int[] { -2, -1, 3, 4, -3, 0, 1, -1, 0, -3,
+        -4, 0, -3, -3, -2, 0, -1, -4, -3, -3, 4, 1, -1 });
+    verifyValues(sm, 'Z', new int[] { -1, 0, 0, 1, -3, 3, 4, -2, 0, -3, -3,
+        1, -1, -3, -1, 0, -1, -3, -2, -2, 1, 4, -1 });
+    verifyValues(sm, 'X', new int[] { 0, -1, -1, -1, -2, -1, -1, -1, -1,
+        -1, -1, -1, -1, -1, -2, 0, 0, -2, -1, -1, -1, -1, -1 });
+  }
+  /**
+   * Helper method to check pairwise scores for one residue
+   * 
+   * @param sm
+   * @param res
+   * @param expected
+   *          score values against 'res', in ResidueProperties.aaIndex order
+   */
+  private void verifyValues(ScoreMatrix sm, char res, int[] expected)
+  {
+    for (int j = 0; j < expected.length; j++)
+    {
+      char c2 = ResidueProperties.aa[j].charAt(0);
+      assertEquals(sm.getPairwiseScore(res, c2), expected[j],
+              String.format("%s->%s", res, c2));
+    }
+  }
+
+  @Test(groups = "Functional")
+  public void testComputePairwiseScores()
+  {
+    String[] seqs = new String[] { "FKL", "R-D", "QIA", "GWC" };
+    ScoreMatrix sm = ResidueProperties.getScoreMatrix("BLOSUM62");
+  
+    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 = 0; j < pairwise.width(); j++)
+      {
+        assertEquals(pairwise.getValue(i, j), pairwise.getValue(j, i),
+                "Not symmetric");
+      }
+    }
+    /*
+     * verify expected BLOSUM dot product scores
+     * Note: gap is treated like 'X' [22] in the matrix
+     */
+    // F.F + K.K + L.L = 6 + 5 + 4 = 15
+    assertEquals(pairwise.getValue(0, 0), 15d);
+    // R.R + X.X + D.D = 5 + -1 + 6 = 10
+    assertEquals(pairwise.getValue(1, 1), 10d);
+    // 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.X + L.D = -3 + -1 + -3 = -8
+    assertEquals(pairwise.getValue(0, 1), -8d);
+    // 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 + X.I + D.A = 1 + -1 + -2 = -2
+    assertEquals(pairwise.getValue(1, 2), -2d);
+    // R.G + X.W + D.C = -2 + -2 + -3 = -7
+    assertEquals(pairwise.getValue(1, 3), -7d);
+    // Q.G + I.W + A.C = -2 + -3 + 0 = -5
+    assertEquals(pairwise.getValue(2, 3), -5d);
+  }
 }