JAL-1889 ignore Clover instrumentation in test (second attempt)

[jalview.git] / test / jalview / datamodel / features / NCListTest.java

diff --git a/test/jalview/datamodel/features/NCListTest.java b/test/jalview/datamodel/features/NCListTest.java
index e874ce4..2c7f752 100644 (file)
--- a/test/jalview/datamodel/features/NCListTest.java
+++ b/test/jalview/datamodel/features/NCListTest.java
@@ -4,6 +4,8 @@ import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.Range;
 import jalview.datamodel.SequenceFeature;
 
 import java.util.ArrayList;
@@ -12,6 +14,8 @@ import java.util.Comparator;
 import java.util.List;
 import java.util.Random;
 
+import junit.extensions.PA;
+
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -202,30 +206,30 @@ public class NCListTest
    * @param ncl
    * @param features
    */
-  void testDelete_pseudoRandom(NCList<SequenceFeature> ncl,
+  protected void testDelete_pseudoRandom(NCList<SequenceFeature> ncl,
           List<SequenceFeature> features)
   {
     int deleted = 0;
 
     while (!features.isEmpty())
     {
-      assertEquals(ncl.getSize(), features.size());
+      assertEquals(ncl.size(), features.size());
       int toDelete = random.nextInt(features.size());
       SequenceFeature entry = features.get(toDelete);
-      String lastDeleted = "'" + entry.toString() + "'";
       assertTrue(ncl.contains(entry), String.format(
-              "NCList doesn't contain entry [%d] %s!", deleted,
-              lastDeleted));
+              "NCList doesn't contain entry [%d] '%s'!", deleted,
+              entry.toString()));
+
       ncl.delete(entry);
       assertFalse(ncl.contains(entry), String.format(
-              "NCList still contains deleted entry [%d] %s!", deleted,
-              lastDeleted));
+              "NCList still contains deleted entry [%d] '%s'!", deleted,
+              entry.toString()));
       features.remove(toDelete);
       deleted++;
 
       assertTrue(ncl.isValid(), String.format(
-              "NCList invalid after %d deletions, last deleted was %s",
-              deleted, lastDeleted));
+              "NCList invalid after %d deletions, last deleted was '%s'",
+              deleted, entry.toString()));
 
       /*
        * brute force check that deleting one entry didn't delete any others
@@ -234,11 +238,11 @@ public class NCListTest
       {
         SequenceFeature sf = features.get(i);
         assertTrue(ncl.contains(sf), String.format(
-                "NCList doesn't contain entry [%d] %s after deleting %s!",
-                i, sf.toString(), lastDeleted));
+                        "NCList doesn't contain entry [%d] %s after deleting '%s'!",
+                        i, sf.toString(), entry.toString()));
       }
     }
-    assertEquals(ncl.getSize(), 0); // all gone
+    assertEquals(ncl.size(), 0); // all gone
   }
 
   /**
@@ -250,7 +254,8 @@ public class NCListTest
    * @param ncl
    * @param features
    */
-  void testAdd_pseudoRandom(Integer scale, NCList<SequenceFeature> ncl,
+  protected void testAdd_pseudoRandom(Integer scale,
+          NCList<SequenceFeature> ncl,
           List<SequenceFeature> features)
   {
     int count = 0;
@@ -291,7 +296,7 @@ public class NCListTest
        */
       assertTrue(ncl.isValid(),
               String.format("Failed for scale = %d, i=%d", scale, i));
-      assertEquals(ncl.getSize(), count);
+      assertEquals(ncl.size(), count);
     }
     // System.out.println(ncl.prettyPrint());
   }
@@ -488,7 +493,7 @@ public class NCListTest
     assertSame(features.getEntries().get(1), sf1);
     assertTrue(features.delete(sf1)); // first match only is deleted
     assertTrue(features.contains(sf1));
-    assertEquals(features.getSize(), 1);
+    assertEquals(features.size(), 1);
     assertTrue(features.delete(sf1));
     assertTrue(features.getEntries().isEmpty());
   }
@@ -583,22 +588,22 @@ public class NCListTest
     assertEquals(ncl.toString(), "[40-50 [42-44 [43-43], 46-48]]");
     assertTrue(ncl.isValid());
 
-    r1.start = 43;
+    PA.setValue(r1, "start", 43);
     assertFalse(ncl.isValid()); // r2 not inside r1
-    r1.start = 40;
+    PA.setValue(r1, "start", 40);
     assertTrue(ncl.isValid());
 
-    r3.start = 41;
+    PA.setValue(r3, "start", 41);
     assertFalse(ncl.isValid()); // r3 should precede r2
-    r3.start = 46;
+    PA.setValue(r3, "start", 46);
     assertTrue(ncl.isValid());
 
-    r4.start = 41;
+    PA.setValue(r4, "start", 41);
     assertFalse(ncl.isValid()); // r4 not inside r2
-    r4.start = 43;
+    PA.setValue(r4, "start", 43);
     assertTrue(ncl.isValid());
 
-    r4.start = 44;
+    PA.setValue(r4, "start", 44);
     assertFalse(ncl.isValid()); // r4 has reverse range
   }