Merge branch 'bug/JAL-2682parseId' into develop

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index fce5869..c0cb09c 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1358,6 +1358,10 @@ public class SequenceTest
     SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
             "desc", 13, 14, 2f, null);
     sq.addSequenceFeature(sfContactFG);
+    // add single position feature at [I]
+    SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
+            "desc", 16, 16, null);
+    sq.addSequenceFeature(sfI);
 
     // no features in columns 1-2 (-A)
     List<SequenceFeature> found = sq.findFeatures(1, 2);
@@ -1384,6 +1388,11 @@ public class SequenceTest
     // columns 10-11 (--) should find nothing
     found = sq.findFeatures(10, 11);
     assertEquals(0, found.size());
+
+    // columns 14-14 (I) should find variant feature
+    found = sq.findFeatures(14, 14);
+    assertEquals(1, found.size());
+    assertTrue(found.contains(sfI));
   }
 
   @Test(groups = { "Functional" })
@@ -1665,6 +1674,38 @@ public class SequenceTest
   }
 
   @Test(groups = { "Functional" })
+  public void testFindFeatures_largeEndPos()
+  {
+    /*
+     * imitate a PDB sequence where end is larger than end position
+     */
+    SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
+    sq.createDatasetSequence();
+  
+    assertTrue(sq.findFeatures(1, 9).isEmpty());
+    // should be no array bounds exception - JAL-2772
+    assertTrue(sq.findFeatures(1, 15).isEmpty());
+  
+    // add feature on BCD
+    SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
+            null);
+    sq.addSequenceFeature(sfBCD);
+  
+    // no features in columns 1-2 (-A)
+    List<SequenceFeature> found = sq.findFeatures(1, 2);
+    assertTrue(found.isEmpty());
+  
+    // columns 1-6 (-ABC--) includes BCD
+    found = sq.findFeatures(1, 6);
+    assertEquals(1, found.size());
+    assertTrue(found.contains(sfBCD));
+
+    // columns 10-11 (--) should find nothing
+    found = sq.findFeatures(10, 11);
+    assertEquals(0, found.size());
+  }
+
+  @Test(groups = { "Functional" })
   public void testSetName()
   {
     SequenceI sq = new Sequence("test", "-ABC---DE-F--");