X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FSequenceTest.java;h=a084a8e61cfbb19500fd6f7f8a6c7b16a06cabe5;hb=406881e2d77e85afa29c580abcc94e5b20fd9bb0;hp=e40d1a59316000511d312f66659a6eb565d2a32a;hpb=e6798fd04b1d7a35836a2e84deae5a94a35b88b9;p=jalview.git

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index e40d1a5..a084a8e 100644
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -1343,23 +1343,25 @@ public class SequenceTest
             null);
     sq.addSequenceFeature(sf0);
     // add feature on BCD
-    SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 9, 11, 2f,
+    SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
             null);
-    sq.addSequenceFeature(sf1);
+    sq.addSequenceFeature(sfBCD);
     // add feature on DE
-    SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 11, 12, 2f,
+    SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
             null);
-    sq.addSequenceFeature(sf2);
+    sq.addSequenceFeature(sfDE);
     // add contact feature at [B, H]
-    SequenceFeature sf3 = new SequenceFeature("Disulphide bond", "desc", 9,
-            15, 2f,
-            null);
-    sq.addSequenceFeature(sf3);
+    SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
+            "desc", 9, 15, 2f, null);
+    sq.addSequenceFeature(sfContactBH);
     // add contact feature at [F, G]
-    SequenceFeature sf4 = new SequenceFeature("Disulfide Bond", "desc", 13,
-            14, 2f,
-            null);
-    sq.addSequenceFeature(sf4);
+    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);
@@ -1368,20 +1370,29 @@ public class SequenceTest
     // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
     found = sq.findFeatures(1, 6);
     assertEquals(2, found.size());
-    assertTrue(found.contains(sf1));
-    assertTrue(found.contains(sf3));
+    assertTrue(found.contains(sfBCD));
+    assertTrue(found.contains(sfContactBH));
 
     // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
     found = sq.findFeatures(5, 6);
     assertEquals(1, found.size());
-    assertTrue(found.contains(sf1));
+    assertTrue(found.contains(sfBCD));
 
     // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
     found = sq.findFeatures(7, 10);
     assertEquals(3, found.size());
-    assertTrue(found.contains(sf1));
-    assertTrue(found.contains(sf2));
-    assertTrue(found.contains(sf4));
+    assertTrue(found.contains(sfBCD));
+    assertTrue(found.contains(sfDE));
+    assertTrue(found.contains(sfContactFG));
+
+    // 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" })
@@ -1606,4 +1617,268 @@ public class SequenceTest
     assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
     assertEquals(2, PA.getValue(sq, "changeCount"));
   }
+
+  @Test(groups = { "Functional" })
+  public void testFindPositions()
+  {
+    SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
+
+    /*
+     * invalid inputs
+     */
+    assertNull(sq.findPositions(6, 5));
+    assertNull(sq.findPositions(0, 5));
+    assertNull(sq.findPositions(-1, 5));
+
+    /*
+     * all gapped ranges
+     */
+    assertNull(sq.findPositions(1, 1)); // 1-based columns
+    assertNull(sq.findPositions(5, 5));
+    assertNull(sq.findPositions(5, 6));
+    assertNull(sq.findPositions(5, 7));
+
+    /*
+     * all ungapped ranges
+     */
+    assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
+    assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
+    assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
+    assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
+
+    /*
+     * gap to ungapped range
+     */
+    assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
+    assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
+
+    /*
+     * ungapped to gapped range
+     */
+    assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
+    assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
+
+    /*
+     * ungapped to ungapped enclosing gaps
+     */
+    assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
+    assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
+
+    /*
+     * gapped to gapped enclosing ungapped
+     */
+    assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
+    assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
+    assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
+    assertEquals(new Range(8, 13), sq.findPositions(1, 99));
+  }
+
+  @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--");
+    assertEquals("test", sq.getName());
+    assertEquals(1, sq.getStart());
+    assertEquals(6, sq.getEnd());
+
+    sq.setName("testing");
+    assertEquals("testing", sq.getName());
+
+    sq.setName("test/8-10");
+    assertEquals("test", sq.getName());
+    assertEquals(8, sq.getStart());
+    assertEquals(13, sq.getEnd()); // note end is recomputed
+
+    sq.setName("testing/7-99");
+    assertEquals("testing", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd()); // end may be beyond physical end
+
+    sq.setName("/2-3");
+    assertEquals("", sq.getName());
+    assertEquals(2, sq.getStart());
+    assertEquals(7, sq.getEnd());
+
+    sq.setName("test/"); // invalid
+    assertEquals("test/", sq.getName());
+    assertEquals(2, sq.getStart());
+    assertEquals(7, sq.getEnd());
+
+    sq.setName("test/6-13/7-99");
+    assertEquals("test/6-13", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/0-5"); // 0 is invalid - ignored
+    assertEquals("test/0-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/a-5"); // a is invalid - ignored
+    assertEquals("test/a-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/6-5"); // start > end is invalid - ignored
+    assertEquals("test/6-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/5"); // invalid - ignored
+    assertEquals("test/5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/-5"); // invalid - ignored
+    assertEquals("test/-5", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/5-"); // invalid - ignored
+    assertEquals("test/5-", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName("test/5-6-7"); // invalid - ignored
+    assertEquals("test/5-6-7", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+
+    sq.setName(null); // invalid, gets converted to space
+    assertEquals("", sq.getName());
+    assertEquals(7, sq.getStart());
+    assertEquals(99, sq.getEnd());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCheckValidRange()
+  {
+    Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
+    assertEquals(7, sq.getStart());
+    assertEquals(12, sq.getEnd());
+
+    /*
+     * checkValidRange ensures end is at least the last residue position
+     */
+    PA.setValue(sq, "end", 2);
+    sq.checkValidRange();
+    assertEquals(12, sq.getEnd());
+
+    /*
+     * end may be beyond the last residue position
+     */
+    PA.setValue(sq, "end", 22);
+    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());
+  }
 }