X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrixTest.java;fp=test%2Fjalview%2Fanalysis%2Fscoremodels%2FScoreMatrixTest.java;h=16d95049639a2deb9f9ef515f9f069e3b72d064e;hb=e0f478e7dd73384609bd596f7edf6106dc7d9330;hp=9c9e917ff1f50fd4860adb677e43f98f9eb609d6;hpb=7733b7433ee8771d85ccfe2ed32119feac8056e0;p=jalview.git

diff --git a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
index 9c9e917..16d9504 100644
--- 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