2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertNull;
27 import static org.testng.AssertJUnit.assertSame;
28 import static org.testng.AssertJUnit.assertTrue;
29 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
31 import jalview.datamodel.PDBEntry.Type;
33 import java.util.Arrays;
34 import java.util.List;
35 import java.util.Vector;
37 import org.testng.annotations.BeforeMethod;
38 import org.testng.annotations.Test;
40 public class SequenceTest
44 @BeforeMethod(alwaysRun = true)
47 seq = new Sequence("FER1", "AKPNGVL");
50 @Test(groups = { "Functional" })
51 public void testInsertGapsAndGapmaps()
53 SequenceI aseq = seq.deriveSequence();
54 aseq.insertCharAt(2, 3, '-');
55 aseq.insertCharAt(6, 3, '-');
56 assertEquals("Gap insertions not correct", "AK---P---NGVL",
57 aseq.getSequenceAsString());
58 List<int[]> gapInt = aseq.getInsertions();
59 assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
60 assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
61 assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
62 assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
65 @Test(groups = { "Functional" })
66 public void testGetAnnotation()
68 // initial state returns null not an empty array
69 assertNull(seq.getAnnotation());
70 AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
72 AlignmentAnnotation[] anns = seq.getAnnotation();
73 assertEquals(1, anns.length);
74 assertSame(ann, anns[0]);
76 // removing all annotations reverts array to null
77 seq.removeAlignmentAnnotation(ann);
78 assertNull(seq.getAnnotation());
81 @Test(groups = { "Functional" })
82 public void testGetAnnotation_forLabel()
84 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
86 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
88 AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
90 AlignmentAnnotation[] anns = seq.getAnnotation("label1");
91 assertEquals(2, anns.length);
92 assertSame(ann1, anns[0]);
93 assertSame(ann3, anns[1]);
96 private AlignmentAnnotation addAnnotation(String label,
97 String description, String calcId, float value)
99 final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
101 annotation.setCalcId(calcId);
102 seq.addAlignmentAnnotation(annotation);
106 @Test(groups = { "Functional" })
107 public void testGetAlignmentAnnotations_forCalcIdAndLabel()
109 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
111 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
113 AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
115 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
117 AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
118 AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3", 1f);
119 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
121 assertEquals(2, anns.size());
122 assertSame(ann2, anns.get(0));
123 assertSame(ann4, anns.get(1));
125 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
126 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
127 assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
128 assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
129 assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
133 * Tests for addAlignmentAnnotation. Note this method has the side-effect of
134 * setting the sequenceRef on the annotation. Adding the same annotation twice
137 @Test(groups = { "Functional" })
138 public void testAddAlignmentAnnotation()
140 assertNull(seq.getAnnotation());
141 final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
143 assertNull(annotation.sequenceRef);
144 seq.addAlignmentAnnotation(annotation);
145 assertSame(seq, annotation.sequenceRef);
146 AlignmentAnnotation[] anns = seq.getAnnotation();
147 assertEquals(1, anns.length);
148 assertSame(annotation, anns[0]);
150 // re-adding does nothing
151 seq.addAlignmentAnnotation(annotation);
152 anns = seq.getAnnotation();
153 assertEquals(1, anns.length);
154 assertSame(annotation, anns[0]);
156 // an identical but different annotation can be added
157 final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
159 seq.addAlignmentAnnotation(annotation2);
160 anns = seq.getAnnotation();
161 assertEquals(2, anns.length);
162 assertSame(annotation, anns[0]);
163 assertSame(annotation2, anns[1]);
166 @Test(groups = { "Functional" })
167 public void testGetStartGetEnd()
169 SequenceI sq = new Sequence("test", "ABCDEF");
170 assertEquals(1, sq.getStart());
171 assertEquals(6, sq.getEnd());
173 sq = new Sequence("test", "--AB-C-DEF--");
174 assertEquals(1, sq.getStart());
175 assertEquals(6, sq.getEnd());
177 sq = new Sequence("test", "----");
178 assertEquals(1, sq.getStart());
179 assertEquals(0, sq.getEnd()); // ??
183 * Tests for the method that returns an alignment column position (base 1) for
184 * a given sequence position (base 1).
186 @Test(groups = { "Functional" })
187 public void testFindIndex()
189 SequenceI sq = new Sequence("test", "ABCDEF");
190 assertEquals(0, sq.findIndex(0));
191 assertEquals(1, sq.findIndex(1));
192 assertEquals(5, sq.findIndex(5));
193 assertEquals(6, sq.findIndex(6));
194 assertEquals(6, sq.findIndex(9));
196 sq = new Sequence("test", "-A--B-C-D-E-F--");
197 assertEquals(2, sq.findIndex(1));
198 assertEquals(5, sq.findIndex(2));
199 assertEquals(7, sq.findIndex(3));
201 // before start returns 0
202 assertEquals(0, sq.findIndex(0));
203 assertEquals(0, sq.findIndex(-1));
205 // beyond end returns last residue column
206 assertEquals(13, sq.findIndex(99));
211 * Tests for the method that returns a dataset sequence position (base 1) for
212 * an aligned column position (base 0).
214 @Test(groups = { "Functional" })
215 public void testFindPosition()
217 SequenceI sq = new Sequence("test", "ABCDEF");
218 assertEquals(1, sq.findPosition(0));
219 assertEquals(6, sq.findPosition(5));
220 // assertEquals(-1, seq.findPosition(6)); // fails
222 sq = new Sequence("test", "AB-C-D--");
223 assertEquals(1, sq.findPosition(0));
224 assertEquals(2, sq.findPosition(1));
225 // gap position 'finds' residue to the right (not the left as per javadoc)
226 assertEquals(3, sq.findPosition(2));
227 assertEquals(3, sq.findPosition(3));
228 assertEquals(4, sq.findPosition(4));
229 assertEquals(4, sq.findPosition(5));
230 // returns 1 more than sequence length if off the end ?!?
231 assertEquals(5, sq.findPosition(6));
232 assertEquals(5, sq.findPosition(7));
234 sq = new Sequence("test", "--AB-C-DEF--");
235 assertEquals(1, sq.findPosition(0));
236 assertEquals(1, sq.findPosition(1));
237 assertEquals(1, sq.findPosition(2));
238 assertEquals(2, sq.findPosition(3));
239 assertEquals(3, sq.findPosition(4));
240 assertEquals(3, sq.findPosition(5));
241 assertEquals(4, sq.findPosition(6));
242 assertEquals(4, sq.findPosition(7));
243 assertEquals(5, sq.findPosition(8));
244 assertEquals(6, sq.findPosition(9));
245 assertEquals(7, sq.findPosition(10));
246 assertEquals(7, sq.findPosition(11));
249 @Test(groups = { "Functional" })
250 public void testDeleteChars()
252 SequenceI sq = new Sequence("test", "ABCDEF");
253 assertEquals(1, sq.getStart());
254 assertEquals(6, sq.getEnd());
255 sq.deleteChars(2, 3);
256 assertEquals("ABDEF", sq.getSequenceAsString());
257 assertEquals(1, sq.getStart());
258 assertEquals(5, sq.getEnd());
260 sq = new Sequence("test", "ABCDEF");
261 sq.deleteChars(0, 2);
262 assertEquals("CDEF", sq.getSequenceAsString());
263 assertEquals(3, sq.getStart());
264 assertEquals(6, sq.getEnd());
267 @Test(groups = { "Functional" })
268 public void testInsertCharAt()
270 // non-static methods:
271 SequenceI sq = new Sequence("test", "ABCDEF");
272 sq.insertCharAt(0, 'z');
273 assertEquals("zABCDEF", sq.getSequenceAsString());
274 sq.insertCharAt(2, 2, 'x');
275 assertEquals("zAxxBCDEF", sq.getSequenceAsString());
277 // for static method see StringUtilsTest
281 * Test the method that returns an array of aligned sequence positions where
282 * the array index is the data sequence position (both base 0).
284 @Test(groups = { "Functional" })
285 public void testGapMap()
287 SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
288 sq.createDatasetSequence();
289 assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
293 * Test the method that gets sequence features, either from the sequence or
296 @Test(groups = { "Functional" })
297 public void testGetSequenceFeatures()
299 SequenceI sq = new Sequence("test", "GATCAT");
300 sq.createDatasetSequence();
302 assertNull(sq.getSequenceFeatures());
305 * SequenceFeature on sequence
307 SequenceFeature sf = new SequenceFeature();
308 sq.addSequenceFeature(sf);
309 SequenceFeature[] sfs = sq.getSequenceFeatures();
310 assertEquals(1, sfs.length);
311 assertSame(sf, sfs[0]);
315 * SequenceFeature on sequence and dataset sequence; returns that on
318 * Note JAL-2046: spurious: we have no use case for this at the moment.
319 * This test also buggy - as sf2.equals(sf), no new feature is added
321 SequenceFeature sf2 = new SequenceFeature();
322 sq.getDatasetSequence().addSequenceFeature(sf2);
323 sfs = sq.getSequenceFeatures();
324 assertEquals(1, sfs.length);
325 assertSame(sf, sfs[0]);
328 * SequenceFeature on dataset sequence only
329 * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
331 sq.setSequenceFeatures(null);
332 assertNull(sq.getDatasetSequence().getSequenceFeatures());
335 * Corrupt case - no SequenceFeature, dataset's dataset is the original
336 * sequence. Test shows no infinite loop results.
338 sq.getDatasetSequence().setSequenceFeatures(null);
339 sq.getDatasetSequence().setDatasetSequence(sq); // loop!
340 assertNull(sq.getSequenceFeatures());
344 * Test the method that returns an array, indexed by sequence position, whose
345 * entries are the residue positions at the sequence position (or to the right
348 @Test(groups = { "Functional" })
349 public void testFindPositionMap()
352 * Note: Javadoc for findPosition says it returns the residue position to
353 * the left of a gapped position; in fact it returns the position to the
354 * right. Also it returns a non-existent residue position for a gap beyond
357 Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
358 int[] map = sq.findPositionMap();
359 assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
360 Arrays.toString(map));
364 * Test for getSubsequence
366 @Test(groups = { "Functional" })
367 public void testGetSubsequence()
369 SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
370 sq.createDatasetSequence();
372 // positions are base 0, end position is exclusive
373 SequenceI subseq = sq.getSubSequence(2, 4);
375 assertEquals("CD", subseq.getSequenceAsString());
376 // start/end are base 1 positions
377 assertEquals(3, subseq.getStart());
378 assertEquals(4, subseq.getEnd());
379 // subsequence shares the full dataset sequence
380 assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
384 * Test for deriveSequence applied to a sequence with a dataset
386 @Test(groups = { "Functional" })
387 public void testDeriveSequence_existingDataset()
389 Sequence sq = new Sequence("Seq1", "CD");
390 sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
391 sq.getDatasetSequence().addSequenceFeature(
392 new SequenceFeature("", "", 1, 2, 0f, null));
396 Sequence derived = (Sequence) sq.deriveSequence();
397 assertEquals("CD", derived.getSequenceAsString());
398 assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
400 assertNull(sq.sequenceFeatures);
401 assertNull(derived.sequenceFeatures);
402 // derived sequence should access dataset sequence features
403 assertNotNull(sq.getSequenceFeatures());
404 assertArrayEquals(sq.getSequenceFeatures(),
405 derived.getSequenceFeatures());
409 * Test for deriveSequence applied to an ungapped sequence with no dataset
411 @Test(groups = { "Functional" })
412 public void testDeriveSequence_noDatasetUngapped()
414 SequenceI sq = new Sequence("Seq1", "ABCDEF");
415 assertEquals(1, sq.getStart());
416 assertEquals(6, sq.getEnd());
417 SequenceI derived = sq.deriveSequence();
418 assertEquals("ABCDEF", derived.getSequenceAsString());
419 assertEquals("ABCDEF", derived.getDatasetSequence()
420 .getSequenceAsString());
424 * Test for deriveSequence applied to a gapped sequence with no dataset
426 @Test(groups = { "Functional" })
427 public void testDeriveSequence_noDatasetGapped()
429 SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
430 assertEquals(1, sq.getStart());
431 assertEquals(6, sq.getEnd());
432 assertNull(sq.getDatasetSequence());
433 SequenceI derived = sq.deriveSequence();
434 assertEquals("AB-C.D EF", derived.getSequenceAsString());
435 assertEquals("ABCDEF", derived.getDatasetSequence()
436 .getSequenceAsString());
439 @Test(groups = { "Functional" })
440 public void testCopyConstructor_noDataset()
442 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
443 seq1.setDescription("description");
444 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
446 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
448 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
449 seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
451 SequenceI copy = new Sequence(seq1);
453 assertNull(copy.getDatasetSequence());
455 verifyCopiedSequence(seq1, copy);
457 // copy has a copy of the DBRefEntry
458 // this is murky - DBrefs are only copied for dataset sequences
459 // where the test for 'dataset sequence' is 'dataset is null'
460 // but that doesn't distinguish it from an aligned sequence
461 // which has not yet generated a dataset sequence
462 // NB getDBRef looks inside dataset sequence if not null
463 DBRefEntry[] dbrefs = copy.getDBRefs();
464 assertEquals(1, dbrefs.length);
465 assertFalse(dbrefs[0] == seq1.getDBRefs()[0]);
466 assertTrue(dbrefs[0].equals(seq1.getDBRefs()[0]));
469 @Test(groups = { "Functional" })
470 public void testCopyConstructor_withDataset()
472 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
473 seq1.createDatasetSequence();
474 seq1.setDescription("description");
475 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
477 // JAL-2046 - what is the contract for using a derived sequence's
478 // addSequenceFeature ?
479 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
481 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
482 // here we add DBRef to the dataset sequence:
483 seq1.getDatasetSequence().addDBRef(
484 new DBRefEntry("EMBL", "1.2", "AZ12345"));
486 SequenceI copy = new Sequence(seq1);
488 assertNotNull(copy.getDatasetSequence());
489 assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
491 verifyCopiedSequence(seq1, copy);
493 // getDBRef looks inside dataset sequence and this is shared,
494 // so holds the same dbref objects
495 DBRefEntry[] dbrefs = copy.getDBRefs();
496 assertEquals(1, dbrefs.length);
497 assertSame(dbrefs[0], seq1.getDBRefs()[0]);
501 * Helper to make assertions about a copied sequence
506 protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
508 // verify basic properties:
509 assertEquals(copy.getName(), seq1.getName());
510 assertEquals(copy.getDescription(), seq1.getDescription());
511 assertEquals(copy.getStart(), seq1.getStart());
512 assertEquals(copy.getEnd(), seq1.getEnd());
513 assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
515 // copy has a copy of the annotation:
516 AlignmentAnnotation[] anns = copy.getAnnotation();
517 assertEquals(1, anns.length);
518 assertFalse(anns[0] == seq1.getAnnotation()[0]);
519 assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
520 assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
521 assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
523 // copy has a copy of the sequence feature:
524 SequenceFeature[] sfs = copy.getSequenceFeatures();
525 assertEquals(1, sfs.length);
526 if (seq1.getDatasetSequence()!=null && copy.getDatasetSequence()==seq1.getDatasetSequence()) {
527 assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
529 assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
531 assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
533 // copy has a copy of the PDB entry
534 Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
535 assertEquals(1, pdbs.size());
536 assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
537 assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
540 @Test(groups = "Functional")
541 public void testGetCharAt()
543 SequenceI sq = new Sequence("", "abcde");
544 assertEquals('a', sq.getCharAt(0));
545 assertEquals('e', sq.getCharAt(4));
546 assertEquals(' ', sq.getCharAt(5));
547 assertEquals(' ', sq.getCharAt(-1));