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 5ff2d7b..f4ec05b 100644 (file)
--- a/test/jalview/datamodel/features/SequenceFeaturesTest.java
+++ b/test/jalview/datamodel/features/SequenceFeaturesTest.java
@@ -689,8 +689,14 @@ public class SequenceFeaturesTest
     features = store.getAllFeatures();
     assertEquals(features.size(), 5);
     assertTrue(features.contains(sf5));
+
+    /*
+     * select by type does not apply to non-positional features
+     */
     features = store.getAllFeatures("Cath");
-    assertTrue(features.isEmpty());
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf3));
+
     features = store.getAllFeatures("Pfam", "Cath", "Metal");
     assertEquals(features.size(), 3);
     assertTrue(features.contains(sf1));
@@ -890,14 +896,14 @@ public class SequenceFeaturesTest
     assertFalse(iterator.hasNext());
 
     /*
-     * two types specified
+     * two types specified - get sorted alphabetically
      */
     types = sf.varargToTypes("Metal", "Helix");
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
-    assertTrue(iterator.hasNext());
     assertEquals(iterator.next(), "Helix");
+    assertTrue(iterator.hasNext());
+    assertEquals(iterator.next(), "Metal");
     assertFalse(iterator.hasNext());
 
     /*
@@ -906,9 +912,9 @@ public class SequenceFeaturesTest
     types = sf.varargToTypes("Metal", null, "Helix");
     iterator = types.iterator();
     assertTrue(iterator.hasNext());
-    assertEquals(iterator.next(), "Metal");
-    assertTrue(iterator.hasNext());
     assertEquals(iterator.next(), "Helix");
+    assertTrue(iterator.hasNext());
+    assertEquals(iterator.next(), "Metal");
     assertFalse(iterator.hasNext());
   }
 
@@ -1012,4 +1018,149 @@ public class SequenceFeaturesTest
     assertSame(sfs.get(1), sf2);
     assertSame(sfs.get(2), sf3);
   }
+
+  @Test(groups = "Functional")
+  public void testGetFeaturesForGroup()
+  {
+    SequenceFeaturesI store = new SequenceFeatures();
+
+    List<SequenceFeature> features = store.getFeaturesForGroup(true, null);
+    assertTrue(features.isEmpty());
+    assertTrue(store.getFeaturesForGroup(false, null).isEmpty());
+    assertTrue(store.getFeaturesForGroup(true, "Uniprot").isEmpty());
+    assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
+
+    SequenceFeature sf1 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+            null);
+    SequenceFeature sf2 = new SequenceFeature("Pfam", "desc", 0, 0, 0f,
+            null);
+    SequenceFeature sf3 = new SequenceFeature("Pfam", "desc", 4, 10, 0f,
+            "Uniprot");
+    SequenceFeature sf4 = new SequenceFeature("Metal", "desc", 0, 0, 0f,
+            "Rfam");
+    SequenceFeature sf5 = new SequenceFeature("Cath", "desc", 5, 15, 0f,
+            null);
+    store.add(sf1);
+    store.add(sf2);
+    store.add(sf3);
+    store.add(sf4);
+    store.add(sf5);
+
+    // positional features for null group, any type
+    features = store.getFeaturesForGroup(true, null);
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf5));
+
+    // positional features for null group, specified type
+    features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
+        "Xfam" });
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf1));
+    features = store.getFeaturesForGroup(true, null, new String[] { "Pfam",
+        "Xfam", "Cath" });
+    assertEquals(features.size(), 2);
+    assertTrue(features.contains(sf1));
+    assertTrue(features.contains(sf5));
+
+    // positional features for non-null group, any type
+    features = store.getFeaturesForGroup(true, "Uniprot");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf3));
+    assertTrue(store.getFeaturesForGroup(true, "Rfam").isEmpty());
+
+    // positional features for non-null group, specified type
+    features = store.getFeaturesForGroup(true, "Uniprot", "Pfam", "Xfam",
+            "Rfam");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf3));
+    assertTrue(store.getFeaturesForGroup(true, "Uniprot", "Cath").isEmpty());
+
+    // non-positional features for null group, any type
+    features = store.getFeaturesForGroup(false, null);
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+
+    // non-positional features for null group, specified type
+    features = store.getFeaturesForGroup(false, null, "Pfam", "Xfam");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf2));
+    assertTrue(store.getFeaturesForGroup(false, null, "Cath").isEmpty());
+
+    // non-positional features for non-null group, any type
+    features = store.getFeaturesForGroup(false, "Rfam");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf4));
+    assertTrue(store.getFeaturesForGroup(false, "Uniprot").isEmpty());
+
+    // non-positional features for non-null group, specified type
+    features = store.getFeaturesForGroup(false, "Rfam", "Pfam", "Metal");
+    assertEquals(features.size(), 1);
+    assertTrue(features.contains(sf4));
+    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");
+  }
 }