X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FScoreMatrixFileTest.java;h=97349b5b9fafed4457144463baa9d135c10d3b40;hb=783c351b9a8aed11ea41c9db193e8ae3be20b017;hp=52ad735beae91dff1ea82fd9fa9488c9d1e14416;hpb=a862a922bf20918fc3f5066ac92e4c69da07e105;p=jalview.git

diff --git a/test/jalview/io/ScoreMatrixFileTest.java b/test/jalview/io/ScoreMatrixFileTest.java
index 52ad735..97349b5 100644
--- 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
   }
@@ -308,7 +310,6 @@ public class ScoreMatrixFileTest
     assertFalse(sm.isDNA());
     assertTrue(sm.isProtein());
     assertEquals(20, sm.getSize());
-    assertEquals(sm.getGapIndex(), -1);
 
     assertEquals(sm.getPairwiseScore('A', 'A'), 7f);
     assertEquals(sm.getPairwiseScore('A', 'R'), -3f);
@@ -340,7 +341,6 @@ public class ScoreMatrixFileTest
   
     assertNotNull(sm);
     assertEquals(sm.getSize(), 3);
-    assertEquals(sm.getGapIndex(), -1);
     assertEquals(sm.getName(), "MyTest");
     assertEquals(sm.getDescription(), "My description");
     assertEquals(sm.getPairwiseScore('A', 'A'), 1.0f);
@@ -484,7 +484,7 @@ public class ScoreMatrixFileTest
   public void testParse_ncbiFormat() throws MalformedURLException,
           IOException
   {
-    assertNull(ScoreModels.getInstance().forName("MyNewTest"));
+    assertNull(ScoreModels.getInstance().getScoreModel("MyNewTest", null));
 
     String data = "ScoreMatrix MyNewTest\n" + "\tA\tB\tC\n"
             + "A\t1.0\t2.0\t3.0\n" + "B\t4.0\t5.0\t6.0\n"
@@ -494,8 +494,8 @@ public class ScoreMatrixFileTest
 
     parser.parse();
   
-    ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance().forName(
-            "MyNewTest");
+    ScoreMatrix sm = (ScoreMatrix) ScoreModels.getInstance().getScoreModel(
+            "MyNewTest", null);
     assertNotNull(sm);
     assertEquals(sm.getName(), "MyNewTest");
     assertEquals(parser.getMatrixName(), "MyNewTest");