Merge branch 'bug/JAL-2784' 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..a084a8e 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--");
@@ -1762,4 +1803,82 @@ public class SequenceTest
     sq.checkValidRange();
     assertEquals(22, sq.getEnd());
   }
+
+  @Test(groups = { "Functional" })
+  public void testDeleteChars_withGaps()
+  {
+    /*
+     * delete gaps only
+     */
+    SequenceI sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+    sq.deleteChars(1, 2); // delete first gap
+    assertEquals("AB-C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(10, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues at start (no new dataset sequence)
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(0, 3); // delete A-B
+    assertEquals("-C", sq.getSequenceAsString());
+    assertEquals(10, sq.getStart());
+    assertEquals(10, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues at end (no new dataset sequence)
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(2, 5); // delete B-C
+    assertEquals("A-", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(8, sq.getEnd());
+    assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
+
+    /*
+     * delete gaps and residues internally (new dataset sequence)
+     * first delete from gap to residue
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(1, 3); // delete -B
+    assertEquals("A-C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+
+    /*
+     * internal delete from gap to gap
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(1, 4); // delete -B-
+    assertEquals("AC", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+
+    /*
+     * internal delete from residue to residue
+     */
+    sq = new Sequence("test/8-10", "A-B-C");
+    sq.createDatasetSequence();
+    sq.deleteChars(2, 3); // delete B
+    assertEquals("A--C", sq.getSequenceAsString());
+    assertEquals(8, sq.getStart());
+    assertEquals(9, sq.getEnd());
+    assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
+    assertEquals(8, sq.getDatasetSequence().getStart());
+    assertEquals(9, sq.getDatasetSequence().getEnd());
+  }
 }