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

[jalview.git] / test / jalview / io / ScoreMatrixFileTest.java

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
   }