JAL-838 ScoreMatrix now respects SimilarityParams!

[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 1076d43..85be5b7 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -6,6 +6,7 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertTrue;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.api.analysis.SimilarityParamsI;
 import jalview.io.DataSourceType;
 import jalview.io.FileParse;
 import jalview.io.ScoreMatrixFile;
@@ -244,4 +245,134 @@ public class ScoreMatrixTest
     assertTrue(sm.equals(sm2));
     assertEquals(sm.hashCode(), sm2.hashCode());
   }
+
+  /**
+   * Tests for percentage identity variants where the longer length of two
+   * sequences is used
+   */
+  @Test(groups = "Functional")
+  public void testcomputeSimilarity_matchLongestSequence()
+  {
+    // TODO params.matchGaps() is not used for ScoreMatrix
+    // - includeGaps is sufficient (there is no denominator)
+    // ==> bespoke parameters only 3 booleans?
+    /*
+     * for now, using space for gap to match callers of
+     * AlignmentView.getSequenceStrings()
+     * may change this to '-' (with corresponding change to matrices)
+     */
+    String s1 = "FR K S";
+    String s2 = "FS  L";
+    ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62();
+  
+    /*
+     * score gap-gap and gap-char
+     * shorter sequence treated as if with trailing gaps
+     * score = F^F + R^S + -^- + K^- + -^L + S^-
+     * = 6 + -1 + 1 + -4 + -4 + -4 = -6
+     */
+    SimilarityParamsI params = new SimilarityParams(true, true, true, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -6d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(true, false, true, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -6d);
+  
+    /*
+     * score gap-char but not gap-gap
+     * score = F^F + R^S + 0 + K^- + -^L + S^-
+     * = 6 + -1 + 0 + -4 + -4 + -4 = -7
+     */
+    params = new SimilarityParams(false, true, true, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -7d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(false, false, true, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -7d);
+  
+    /*
+     * score gap-gap but not gap-char
+     * score = F^F + R^S + -^- + 0 + 0 + 0
+     * = 6 + -1 + 1 = 6
+     */
+    params = new SimilarityParams(true, false, false, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(true, true, false, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
+  
+    /*
+     * score neither gap-gap nor gap-char
+     * score = F^F + R^S + 0 + 0 + 0 + 0
+     * = 6 + -1  = 5
+     */
+    params = new SimilarityParams(false, false, false, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 5d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(false, true, false, false);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 5d);
+  }
+
+  /**
+   * Tests for percentage identity variants where only the shorter length of two
+   * sequences is used
+   */
+  @Test(groups = "Functional")
+  public void testcomputeSimilarity_matchShortestSequence()
+  {
+    // TODO params.matchGaps() is not used for ScoreMatrix
+    // - includeGaps is sufficient (there is no denominator)
+    // ==> bespoke parameters only 3 booleans?
+    /*
+     * for now, using space for gap to match callers of
+     * AlignmentView.getSequenceStrings()
+     * may change this to '-' (with corresponding change to matrices)
+     */
+    String s1 = "FR K S";
+    String s2 = "FS  L";
+    ScoreMatrix blosum = ScoreModels.getInstance().getBlosum62();
+
+    /*
+     * score gap-gap and gap-char
+     * shorter sequence treated as if with trailing gaps
+     * score = F^F + R^S + -^- + K^- + -^L
+     * = 6 + -1 + 1 + -4 + -4 = -2
+     */
+    SimilarityParamsI params = new SimilarityParams(true, true, true, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -2d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(true, false, true, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -2d);
+  
+    /*
+     * score gap-char but not gap-gap
+     * score = F^F + R^S + 0 + K^- + -^L
+     * = 6 + -1 + 0 + -4 + -4 = -3
+     */
+    params = new SimilarityParams(false, true, true, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -3d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(false, false, true, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), -3d);
+  
+    /*
+     * score gap-gap but not gap-char
+     * score = F^F + R^S + -^- + 0 + 0
+     * = 6 + -1 + 1 = 6
+     */
+    params = new SimilarityParams(true, false, false, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(true, true, false, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 6d);
+  
+    /*
+     * score neither gap-gap nor gap-char
+     * score = F^F + R^S + 0 + 0 + 0
+     * = 6 + -1  = 5
+     */
+    params = new SimilarityParams(false, false, false, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 5d);
+    // matchGap (arg2) is ignored:
+    params = new SimilarityParams(false, true, false, true);
+    assertEquals(blosum.computeSimilarity(s1, s2, params), 5d);
+  }
 }