JAL-2505 JAL-2542 SequenceFeatures.shift() to shift all positional

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

diff --git a/test/jalview/datamodel/features/SequenceFeaturesTest.java b/test/jalview/datamodel/features/SequenceFeaturesTest.java
index e3d587f..f4ec05b 100644 (file)
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -1100,4 +1100,67 @@ public class SequenceFeaturesTest
     assertTrue(store.getFeaturesForGroup(false, "Rfam", "Cath", "Pfam")
             .isEmpty());
   }
+
+  @Test(groups = "Functional")
+  public void testShiftFeatures()
+  {
+    SequenceFeatures store = new SequenceFeatures();
+    assertFalse(store.shiftFeatures(1));
+
+    SequenceFeature sf1 = new SequenceFeature("Cath", "", 2, 5, 0f, null);
+    store.add(sf1);
+    // nested feature:
+    SequenceFeature sf2 = new SequenceFeature("Metal", "", 8, 14, 0f, null);
+    store.add(sf2);
+    // contact feature:
+    SequenceFeature sf3 = new SequenceFeature("Disulfide bond", "", 23, 32,
+            0f, null);
+    store.add(sf3);
+    // non-positional feature:
+    SequenceFeature sf4 = new SequenceFeature("Pfam", "", 0, 0, 0f, null);
+    store.add(sf4);
+  
+    /*
+     * shift features right by 5
+     */
+    assertTrue(store.shiftFeatures(5));
+  
+    // non-positional features untouched:
+    List<SequenceFeature> nonPos = store.getNonPositionalFeatures();
+    assertEquals(nonPos.size(), 1);
+    assertTrue(nonPos.contains(sf4));
+  
+    // positional features are replaced
+    List<SequenceFeature> pos = store.getPositionalFeatures();
+    assertEquals(pos.size(), 3);
+    assertFalse(pos.contains(sf1));
+    assertFalse(pos.contains(sf2));
+    assertFalse(pos.contains(sf3));
+    SequenceFeatures.sortFeatures(pos, true); // ascending start pos
+    assertEquals(pos.get(0).getBegin(), 7);
+    assertEquals(pos.get(0).getEnd(), 10);
+    assertEquals(pos.get(0).getType(), "Cath");
+    assertEquals(pos.get(1).getBegin(), 13);
+    assertEquals(pos.get(1).getEnd(), 19);
+    assertEquals(pos.get(1).getType(), "Metal");
+    assertEquals(pos.get(2).getBegin(), 28);
+    assertEquals(pos.get(2).getEnd(), 37);
+    assertEquals(pos.get(2).getType(), "Disulfide bond");
+  
+    /*
+     * now shift left by 15
+     * feature at [7-10] should be removed
+     * feature at [13-19] should become [1-4] 
+     */
+    assertTrue(store.shiftFeatures(-15));
+    pos = store.getPositionalFeatures();
+    assertEquals(pos.size(), 2);
+    SequenceFeatures.sortFeatures(pos, true);
+    assertEquals(pos.get(0).getBegin(), 1);
+    assertEquals(pos.get(0).getEnd(), 4);
+    assertEquals(pos.get(0).getType(), "Metal");
+    assertEquals(pos.get(1).getBegin(), 13);
+    assertEquals(pos.get(1).getEnd(), 22);
+    assertEquals(pos.get(1).getType(), "Disulfide bond");
+  }
 }