JAL-2403 JAL-2416 pairwise score unexpected symbols as minimum matrix

substitution score (or 1 for identity) (reproduces '*' score column)

diff --git a/src/jalview/analysis/scoremodels/ScoreMatrix.java b/src/jalview/analysis/scoremodels/ScoreMatrix.java
index 84e91ae..7e07b9f 100644 (file)
--- a/src/jalview/analysis/scoremodels/ScoreMatrix.java
+++ b/src/jalview/analysis/scoremodels/ScoreMatrix.java
@@ -289,8 +289,9 @@ public class ScoreMatrix implements SimilarityScoreModelI,
   }
 
   /**
-   * Returns the pairwise score for substituting c with d, or zero if c or d is
-   * an unscored or unexpected character
+   * Returns the pairwise score for substituting c with d. If either c or d is
+   * an unexpected character, returns 1 for identity (c == d), else the minimum
+   * score value in the matrix.
    */
   @Override
   public float getPairwiseScore(char c, char d)
@@ -315,10 +316,8 @@ public class ScoreMatrix implements SimilarityScoreModelI,
 
     /*
      * one or both symbols not found in the matrix
-     * note: a possible strategy here would be to return the minimum
-     * matrix value if c != d
      */
-    return 0;
+    return c == d ? 1 : getMinimumScore();
   }
 
   /**

diff --git a/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index 85f619b..b9e866d 100644 (file)
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -70,7 +70,7 @@ public class AlignSeqTest
   {
     AlignSeq as = new AlignSeq(new Sequence("s1", "PFY"), new Sequence(
             "s2", "RQW"), AlignSeq.PEP);
-    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, 24,
+    int[] expected = new int[] { 0, 0, 1, 1, 2, 2, 21, 21, 22, 22, -1, -1,
         -1, 23, -1 };
     String s = "aArRnNzZxX *.-?";
     assertArrayEquals(expected, as.indexEncode(s));

diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 9c9e917..16d9504 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -30,7 +30,7 @@ public class ScoreMatrixTest
     // note score matrix does not have to be symmetric (though it should be!)
     float[][] scores = new float[3][];
     scores[0] = new float[] { 1f, 2f, 3f };
-    scores[1] = new float[] { 4f, 5f, 6f };
+    scores[1] = new float[] { -4f, 5f, 6f };
     scores[2] = new float[] { 7f, 8f, 9f };
     ScoreMatrix sm = new ScoreMatrix("Test", "ABC".toCharArray(), scores);
     assertEquals(sm.getSize(), 3);
@@ -38,10 +38,15 @@ public class ScoreMatrixTest
     assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
     assertEquals(sm.getPairwiseScore('b', 'c'), 6f);
     assertEquals(sm.getPairwiseScore('c', 'b'), 8f);
-    assertEquals(sm.getPairwiseScore('A', 'D'), 0f);
     assertEquals(sm.getMatrixIndex('c'), 2);
     assertEquals(sm.getMatrixIndex(' '), -1);
 
+    // substitution to or from unknown symbol gets minimum score
+    assertEquals(sm.getPairwiseScore('A', 'D'), -4f);
+    assertEquals(sm.getPairwiseScore('D', 'A'), -4f);
+    // unknown-to-self gets a score of 1
+    assertEquals(sm.getPairwiseScore('D', 'D'), 1f);
+
     assertEquals(sm.getGapIndex(), -1); // no gap symbol
   }
 
@@ -538,21 +543,24 @@ public class ScoreMatrixTest
   {
     float[][] scores = new float[2][];
     scores[0] = new float[] { 1f, 2f };
-    scores[1] = new float[] { 4f, 5f };
+    scores[1] = new float[] { -4f, 5f };
     ScoreMatrix sm = new ScoreMatrix("Test", new char[] { 'A', 'B' },
             scores);
     assertEquals(sm.getPairwiseScore('A', 'A'), 1f);
     assertEquals(sm.getPairwiseScore('A', 'a'), 1f);
     assertEquals(sm.getPairwiseScore('A', 'B'), 2f);
-    assertEquals(sm.getPairwiseScore('b', 'a'), 4f);
+    assertEquals(sm.getPairwiseScore('b', 'a'), -4f);
     assertEquals(sm.getPairwiseScore('B', 'b'), 5f);
 
     /*
-     * unknown symbols currently score zero
+     * unknown symbols currently score minimum score
+     * or 1 for identity with self
      */
-    assertEquals(sm.getPairwiseScore('A', '-'), 0f);
-    assertEquals(sm.getPairwiseScore('-', '-'), 0f);
-    assertEquals(sm.getPairwiseScore('Q', 'W'), 0f);
+    assertEquals(sm.getPairwiseScore('A', '-'), -4f);
+    assertEquals(sm.getPairwiseScore('-', 'A'), -4f);
+    assertEquals(sm.getPairwiseScore('-', '-'), 1f);
+    assertEquals(sm.getPairwiseScore('Q', 'W'), -4f);
+    assertEquals(sm.getPairwiseScore('Q', 'Q'), 1f);
 
     /*
      * symbols not in basic ASCII set score zero

diff --git a/test/jalview/io/ScoreMatrixFileTest.java b/test/jalview/io/ScoreMatrixFileTest.java
index 52ad735..a98b2d6 100644 (file)
--- a/test/jalview/io/ScoreMatrixFileTest.java
+++ b/test/jalview/io/ScoreMatrixFileTest.java
@@ -51,6 +51,7 @@ public class ScoreMatrixFileTest
     assertNull(sm.getDescription());
     assertTrue(sm.isDNA());
     assertFalse(sm.isProtein());
+    assertEquals(sm.getMinimumScore(), 1.1f);
     assertEquals(sm.getPairwiseScore('A', 'A'), 1.1f);
     assertEquals(sm.getPairwiseScore('A', 'T'), 1.2f);
     assertEquals(sm.getPairwiseScore('a', 'T'), 1.2f); // A/a equivalent
@@ -58,8 +59,9 @@ public class ScoreMatrixFileTest
     assertEquals(sm.getPairwiseScore('a', 't'), 1.4f);
     assertEquals(sm.getPairwiseScore('U', 'x'), 3.5f);
     assertEquals(sm.getPairwiseScore('u', 'x'), 3.5f);
-    assertEquals(sm.getPairwiseScore('U', 'X'), 0f); // X (upper) unmapped
-    assertEquals(sm.getPairwiseScore('A', '.'), 0f); // . unmapped
+    // X (upper) and '.' unmapped - get minimum score
+    assertEquals(sm.getPairwiseScore('U', 'X'), 1.1f);
+    assertEquals(sm.getPairwiseScore('A', '.'), 1.1f);
     assertEquals(sm.getPairwiseScore('-', '-'), 7.6f);
     assertEquals(sm.getPairwiseScore('A', (char) 128), 0f); // out of range
   }