JAL-2557 removal of Sequence.sequenceFeatures

[jalview.git] / test / jalview / commands / EditCommandTest.java

diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 8781a93..155f00e 100644 (file)
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -31,10 +31,10 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.JvOptionPane;
 
-import java.util.Arrays;
-import java.util.Comparator;
+import java.util.List;
 import java.util.Map;
 
 import org.testng.Assert;
@@ -678,29 +678,23 @@ public class EditCommandTest
     Edit ec = testee.new Edit(Action.CUT, seqs, 3, 4, al); // cols 3-6 base 0
     EditCommand.cut(ec, new AlignmentI[] { al });
 
-    SequenceFeature[] sfs = seq0.getSequenceFeatures();
-    Arrays.sort(sfs, new Comparator<SequenceFeature>()
-    {
-      @Override
-      public int compare(SequenceFeature o1, SequenceFeature o2)
-      {
-        return Integer.compare(o1.getBegin(), o2.getBegin());
-      }
-    });
-    assertEquals(4, sfs.length); // feature internal to cut has been deleted
-    SequenceFeature sf = sfs[0];
+    List<SequenceFeature> sfs = seq0.getSequenceFeatures();
+    SequenceFeatures.sortFeatures(sfs, true);
+
+    assertEquals(4, sfs.size()); // feature internal to cut has been deleted
+    SequenceFeature sf = sfs.get(0);
     assertEquals("before", sf.getType());
     assertEquals(1, sf.getBegin());
     assertEquals(3, sf.getEnd());
-    sf = sfs[1];
+    sf = sfs.get(1);
     assertEquals("overlap left", sf.getType());
     assertEquals(2, sf.getBegin());
     assertEquals(3, sf.getEnd()); // truncated by cut
-    sf = sfs[2];
+    sf = sfs.get(2);
     assertEquals("overlap right", sf.getType());
     assertEquals(4, sf.getBegin()); // shifted left by cut
     assertEquals(5, sf.getEnd()); // truncated by cut
-    sf = sfs[3];
+    sf = sfs.get(3);
     assertEquals("after", sf.getType());
     assertEquals(4, sf.getBegin()); // shifted left by cut
     assertEquals(6, sf.getEnd()); // shifted left by cut
@@ -733,8 +727,8 @@ public class EditCommandTest
       }
     }
     // sanity check
-    SequenceFeature[] sfs = seq0.getSequenceFeatures();
-    assertEquals(func(5), sfs.length);
+    List<SequenceFeature> sfs = seq0.getSequenceFeatures();
+    assertEquals(func(5), sfs.size());
 
     /*
      * now perform all possible cuts of subranges of 1-5 (followed by Undo)
@@ -769,7 +763,7 @@ public class EditCommandTest
         else
         {
           assertEquals(msg + "wrong number of features left", func(5)
-                - func(to - from + 1), sfs.length);
+                  - func(to - from + 1), sfs.size());
         }
 
         /*
@@ -786,7 +780,7 @@ public class EditCommandTest
          * undo ready for next cut
          */
         testee.undoCommand(new AlignmentI[] { alignment });
-        assertEquals(func(5), seq0.getSequenceFeatures().length);
+        assertEquals(func(5), seq0.getSequenceFeatures().size());
       }
     }
   }
@@ -868,9 +862,9 @@ public class EditCommandTest
     /*
      * feature on CC(3-4) should now be on CC(1-2)
      */
-    SequenceFeature[] sfs = seq0.getSequenceFeatures();
-    assertEquals(1, sfs.length);
-    SequenceFeature sf = sfs[0];
+    List<SequenceFeature> sfs = seq0.getSequenceFeatures();
+    assertEquals(1, sfs.size());
+    SequenceFeature sf = sfs.get(0);
     assertEquals(1, sf.getBegin());
     assertEquals(2, sf.getEnd());