JAL-2416 revert to '*' not '-' in score matrix, handle gaps explicitly

[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 16d9504..da17000 100644 (file)
--- a/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreMatrixTest.java
@@ -46,8 +46,6 @@ public class ScoreMatrixTest
     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
   }
 
   @Test(
@@ -166,8 +164,8 @@ public class ScoreMatrixTest
     assertEquals(sm.getMatrixIndex('D'), 3);
     assertEquals(sm.getMatrixIndex('X'), 22);
     assertEquals(sm.getMatrixIndex('x'), 22);
-    assertEquals(sm.getMatrixIndex('-'), 23);
-    assertEquals(sm.getMatrixIndex('*'), -1);
+    assertEquals(sm.getMatrixIndex('-'), -1);
+    assertEquals(sm.getMatrixIndex('*'), 23);
     assertEquals(sm.getMatrixIndex('.'), -1);
     assertEquals(sm.getMatrixIndex(' '), -1);
     assertEquals(sm.getMatrixIndex('?'), -1);
@@ -175,13 +173,6 @@ public class ScoreMatrixTest
   }
 
   @Test(groups = "Functional")
-  public void testGetGapIndex()
-  {
-    ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
-    assertEquals(sm.getGapIndex(), 23);
-  }
-
-  @Test(groups = "Functional")
   public void testGetSize()
   {
     ScoreMatrix sm = ScoreModels.getInstance().getBlosum62();
@@ -534,8 +525,6 @@ public class ScoreMatrixTest
     assertEquals(sm.getMatrixIndex('-'), 1);
     assertEquals(sm.getMatrixIndex(' '), -1);
     assertEquals(sm.getMatrixIndex('.'), -1);
-  
-    assertEquals(sm.getGapIndex(), 1);
   }
 
   @Test(groups = "Functional")