X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FScoreMatrixFileTest.java;h=254feaa625523aa68249d2a622ccaeaf7eb4fd72;hb=3da878124135ff033f42d19d8733891b09e953cd;hp=a98b2d66a6129c348526671282c9a08604eeb26e;hpb=e0f478e7dd73384609bd596f7edf6106dc7d9330;p=jalview.git

diff --git a/test/jalview/io/ScoreMatrixFileTest.java b/test/jalview/io/ScoreMatrixFileTest.java
index a98b2d6..254feaa 100644
--- a/test/jalview/io/ScoreMatrixFileTest.java
+++ b/test/jalview/io/ScoreMatrixFileTest.java
@@ -13,11 +13,18 @@ import jalview.analysis.scoremodels.ScoreModels;
 import java.io.IOException;
 import java.net.MalformedURLException;
 
+import org.testng.annotations.AfterMethod;
 import org.testng.annotations.Test;
 
 public class ScoreMatrixFileTest
 {
 
+  @AfterMethod(alwaysRun=true)
+  public void tearDownAfterTest()
+  {
+    ScoreModels.getInstance().reset();
+  }
+
   /**
    * Test a successful parse of a (small) score matrix file
    * 
@@ -310,7 +317,6 @@ 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);
@@ -342,7 +348,6 @@ 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);
@@ -486,7 +491,7 @@ 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"
@@ -496,8 +501,8 @@ 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");