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;
32 import jalview.util.MapList;
34 import java.util.ArrayList;
35 import java.util.Arrays;
36 import java.util.List;
37 import java.util.Vector;
39 import org.testng.Assert;
40 import org.testng.annotations.BeforeMethod;
41 import org.testng.annotations.Test;
43 public class SequenceTest
47 @BeforeMethod(alwaysRun = true)
50 seq = new Sequence("FER1", "AKPNGVL");
53 @Test(groups = { "Functional" })
54 public void testInsertGapsAndGapmaps()
56 SequenceI aseq = seq.deriveSequence();
57 aseq.insertCharAt(2, 3, '-');
58 aseq.insertCharAt(6, 3, '-');
59 assertEquals("Gap insertions not correct", "AK---P---NGVL",
60 aseq.getSequenceAsString());
61 List<int[]> gapInt = aseq.getInsertions();
62 assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
63 assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
64 assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
65 assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
68 @Test(groups = ("Functional"))
69 public void testIsProtein()
72 assertTrue(new Sequence("prot","ASDFASDFASDF").isProtein());
74 assertFalse(new Sequence("prot","ACGTACGTACGT").isProtein());
76 SequenceI sq = new Sequence("prot","ACGUACGUACGU");
77 assertFalse(sq.isProtein());
78 // change sequence, should trigger an update of cached result
79 sq.setSequence("ASDFASDFADSF");
80 assertTrue(sq.isProtein());
82 * in situ change of sequence doesn't change hashcode :-O
83 * (sequence should not expose internal implementation)
85 for (int i = 0; i < sq.getSequence().length; i++)
87 sq.getSequence()[i] = "acgtu".charAt(i % 5);
89 assertTrue(sq.isProtein()); // but it isn't
92 @Test(groups = { "Functional" })
93 public void testGetAnnotation()
95 // initial state returns null not an empty array
96 assertNull(seq.getAnnotation());
97 AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
99 AlignmentAnnotation[] anns = seq.getAnnotation();
100 assertEquals(1, anns.length);
101 assertSame(ann, anns[0]);
103 // removing all annotations reverts array to null
104 seq.removeAlignmentAnnotation(ann);
105 assertNull(seq.getAnnotation());
108 @Test(groups = { "Functional" })
109 public void testGetAnnotation_forLabel()
111 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
113 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
115 AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
117 AlignmentAnnotation[] anns = seq.getAnnotation("label1");
118 assertEquals(2, anns.length);
119 assertSame(ann1, anns[0]);
120 assertSame(ann3, anns[1]);
123 private AlignmentAnnotation addAnnotation(String label,
124 String description, String calcId, float value)
126 final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
128 annotation.setCalcId(calcId);
129 seq.addAlignmentAnnotation(annotation);
133 @Test(groups = { "Functional" })
134 public void testGetAlignmentAnnotations_forCalcIdAndLabel()
136 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
138 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
140 AlignmentAnnotation ann3 = addAnnotation("label2", "desc3", "calcId3",
142 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
144 AlignmentAnnotation ann5 = addAnnotation("label5", "desc3", null, 1f);
145 AlignmentAnnotation ann6 = addAnnotation(null, "desc3", "calcId3", 1f);
146 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
148 assertEquals(2, anns.size());
149 assertSame(ann2, anns.get(0));
150 assertSame(ann4, anns.get(1));
152 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
153 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
154 assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
155 assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
156 assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
160 * Tests for addAlignmentAnnotation. Note this method has the side-effect of
161 * setting the sequenceRef on the annotation. Adding the same annotation twice
164 @Test(groups = { "Functional" })
165 public void testAddAlignmentAnnotation()
167 assertNull(seq.getAnnotation());
168 final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
170 assertNull(annotation.sequenceRef);
171 seq.addAlignmentAnnotation(annotation);
172 assertSame(seq, annotation.sequenceRef);
173 AlignmentAnnotation[] anns = seq.getAnnotation();
174 assertEquals(1, anns.length);
175 assertSame(annotation, anns[0]);
177 // re-adding does nothing
178 seq.addAlignmentAnnotation(annotation);
179 anns = seq.getAnnotation();
180 assertEquals(1, anns.length);
181 assertSame(annotation, anns[0]);
183 // an identical but different annotation can be added
184 final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
186 seq.addAlignmentAnnotation(annotation2);
187 anns = seq.getAnnotation();
188 assertEquals(2, anns.length);
189 assertSame(annotation, anns[0]);
190 assertSame(annotation2, anns[1]);
193 @Test(groups = { "Functional" })
194 public void testGetStartGetEnd()
196 SequenceI sq = new Sequence("test", "ABCDEF");
197 assertEquals(1, sq.getStart());
198 assertEquals(6, sq.getEnd());
200 sq = new Sequence("test", "--AB-C-DEF--");
201 assertEquals(1, sq.getStart());
202 assertEquals(6, sq.getEnd());
204 sq = new Sequence("test", "----");
205 assertEquals(1, sq.getStart());
206 assertEquals(0, sq.getEnd()); // ??
210 * Tests for the method that returns an alignment column position (base 1) for
211 * a given sequence position (base 1).
213 @Test(groups = { "Functional" })
214 public void testFindIndex()
216 SequenceI sq = new Sequence("test", "ABCDEF");
217 assertEquals(0, sq.findIndex(0));
218 assertEquals(1, sq.findIndex(1));
219 assertEquals(5, sq.findIndex(5));
220 assertEquals(6, sq.findIndex(6));
221 assertEquals(6, sq.findIndex(9));
223 sq = new Sequence("test", "-A--B-C-D-E-F--");
224 assertEquals(2, sq.findIndex(1));
225 assertEquals(5, sq.findIndex(2));
226 assertEquals(7, sq.findIndex(3));
228 // before start returns 0
229 assertEquals(0, sq.findIndex(0));
230 assertEquals(0, sq.findIndex(-1));
232 // beyond end returns last residue column
233 assertEquals(13, sq.findIndex(99));
238 * Tests for the method that returns a dataset sequence position (base 1) for
239 * an aligned column position (base 0).
241 @Test(groups = { "Functional" })
242 public void testFindPosition()
244 SequenceI sq = new Sequence("test", "ABCDEF");
245 assertEquals(1, sq.findPosition(0));
246 assertEquals(6, sq.findPosition(5));
247 // assertEquals(-1, seq.findPosition(6)); // fails
249 sq = new Sequence("test", "AB-C-D--");
250 assertEquals(1, sq.findPosition(0));
251 assertEquals(2, sq.findPosition(1));
252 // gap position 'finds' residue to the right (not the left as per javadoc)
253 assertEquals(3, sq.findPosition(2));
254 assertEquals(3, sq.findPosition(3));
255 assertEquals(4, sq.findPosition(4));
256 assertEquals(4, sq.findPosition(5));
257 // returns 1 more than sequence length if off the end ?!?
258 assertEquals(5, sq.findPosition(6));
259 assertEquals(5, sq.findPosition(7));
261 sq = new Sequence("test", "--AB-C-DEF--");
262 assertEquals(1, sq.findPosition(0));
263 assertEquals(1, sq.findPosition(1));
264 assertEquals(1, sq.findPosition(2));
265 assertEquals(2, sq.findPosition(3));
266 assertEquals(3, sq.findPosition(4));
267 assertEquals(3, sq.findPosition(5));
268 assertEquals(4, sq.findPosition(6));
269 assertEquals(4, sq.findPosition(7));
270 assertEquals(5, sq.findPosition(8));
271 assertEquals(6, sq.findPosition(9));
272 assertEquals(7, sq.findPosition(10));
273 assertEquals(7, sq.findPosition(11));
276 @Test(groups = { "Functional" })
277 public void testDeleteChars()
279 SequenceI sq = new Sequence("test", "ABCDEF");
280 assertEquals(1, sq.getStart());
281 assertEquals(6, sq.getEnd());
282 sq.deleteChars(2, 3);
283 assertEquals("ABDEF", sq.getSequenceAsString());
284 assertEquals(1, sq.getStart());
285 assertEquals(5, sq.getEnd());
287 sq = new Sequence("test", "ABCDEF");
288 sq.deleteChars(0, 2);
289 assertEquals("CDEF", sq.getSequenceAsString());
290 assertEquals(3, sq.getStart());
291 assertEquals(6, sq.getEnd());
294 @Test(groups = { "Functional" })
295 public void testInsertCharAt()
297 // non-static methods:
298 SequenceI sq = new Sequence("test", "ABCDEF");
299 sq.insertCharAt(0, 'z');
300 assertEquals("zABCDEF", sq.getSequenceAsString());
301 sq.insertCharAt(2, 2, 'x');
302 assertEquals("zAxxBCDEF", sq.getSequenceAsString());
304 // for static method see StringUtilsTest
308 * Test the method that returns an array of aligned sequence positions where
309 * the array index is the data sequence position (both base 0).
311 @Test(groups = { "Functional" })
312 public void testGapMap()
314 SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
315 sq.createDatasetSequence();
316 assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
320 * Test the method that gets sequence features, either from the sequence or
323 @Test(groups = { "Functional" })
324 public void testGetSequenceFeatures()
326 SequenceI sq = new Sequence("test", "GATCAT");
327 sq.createDatasetSequence();
329 assertNull(sq.getSequenceFeatures());
332 * SequenceFeature on sequence
334 SequenceFeature sf = new SequenceFeature();
335 sq.addSequenceFeature(sf);
336 SequenceFeature[] sfs = sq.getSequenceFeatures();
337 assertEquals(1, sfs.length);
338 assertSame(sf, sfs[0]);
342 * SequenceFeature on sequence and dataset sequence; returns that on
345 * Note JAL-2046: spurious: we have no use case for this at the moment.
346 * This test also buggy - as sf2.equals(sf), no new feature is added
348 SequenceFeature sf2 = new SequenceFeature();
349 sq.getDatasetSequence().addSequenceFeature(sf2);
350 sfs = sq.getSequenceFeatures();
351 assertEquals(1, sfs.length);
352 assertSame(sf, sfs[0]);
355 * SequenceFeature on dataset sequence only
356 * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
358 sq.setSequenceFeatures(null);
359 assertNull(sq.getDatasetSequence().getSequenceFeatures());
362 * Corrupt case - no SequenceFeature, dataset's dataset is the original
363 * sequence. Test shows no infinite loop results.
365 sq.getDatasetSequence().setSequenceFeatures(null);
367 * is there a usecase for this ? setDatasetSequence should throw an error if
368 * this actually occurs.
370 sq.getDatasetSequence().setDatasetSequence(sq); // loop!
371 assertNull(sq.getSequenceFeatures());
375 * Test the method that returns an array, indexed by sequence position, whose
376 * entries are the residue positions at the sequence position (or to the right
379 @Test(groups = { "Functional" })
380 public void testFindPositionMap()
383 * Note: Javadoc for findPosition says it returns the residue position to
384 * the left of a gapped position; in fact it returns the position to the
385 * right. Also it returns a non-existent residue position for a gap beyond
388 Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
389 int[] map = sq.findPositionMap();
390 assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
391 Arrays.toString(map));
395 * Test for getSubsequence
397 @Test(groups = { "Functional" })
398 public void testGetSubsequence()
400 SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
401 sq.createDatasetSequence();
403 // positions are base 0, end position is exclusive
404 SequenceI subseq = sq.getSubSequence(2, 4);
406 assertEquals("CD", subseq.getSequenceAsString());
407 // start/end are base 1 positions
408 assertEquals(3, subseq.getStart());
409 assertEquals(4, subseq.getEnd());
410 // subsequence shares the full dataset sequence
411 assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
415 * test createDatasetSequence behaves to doc
417 @Test(groups = { "Functional" })
418 public void testCreateDatasetSequence()
420 SequenceI sq = new Sequence("my","ASDASD");
421 assertNull(sq.getDatasetSequence());
422 SequenceI rds = sq.createDatasetSequence();
424 assertNull(rds.getDatasetSequence());
425 assertEquals(sq.getDatasetSequence(), rds);
429 * Test for deriveSequence applied to a sequence with a dataset
431 @Test(groups = { "Functional" })
432 public void testDeriveSequence_existingDataset()
434 Sequence sq = new Sequence("Seq1", "CD");
435 sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
436 sq.getDatasetSequence().addSequenceFeature(
437 new SequenceFeature("", "", 1, 2, 0f, null));
441 sq.setDescription("Test sequence description..");
442 sq.setVamsasId("TestVamsasId");
443 sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
445 sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
446 sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
447 sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
448 sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
450 sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
451 sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
452 sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
453 sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
455 DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
456 DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version1", "2PDB");
457 List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
460 sq.getDatasetSequence().addDBRef(pdb1pdb);
461 sq.getDatasetSequence().addDBRef(pdb2pdb);
462 sq.getDatasetSequence().addDBRef(
463 new DBRefEntry("PDB", "version3", "3PDB"));
464 sq.getDatasetSequence().addDBRef(
465 new DBRefEntry("PDB", "version4", "4PDB"));
467 PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
468 PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
469 PDBEntry pdbe2a=new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2");
470 PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2");
471 sq.getDatasetSequence().addPDBId(
473 sq.getDatasetSequence().addPDBId(
475 sq.getDatasetSequence().addPDBId(pdbe2a);
476 sq.getDatasetSequence().addPDBId(pdbe2b);
479 * test we added pdb entries to the dataset sequence
481 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
482 .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
483 "PDB Entries were not found on dataset sequence.");
486 * we should recover a pdb entry that is on the dataset sequence via PDBEntry
488 Assert.assertEquals(pdbe1a,
489 sq.getDatasetSequence().getPDBEntry("1PDB"),
490 "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
491 ArrayList<Annotation> annotsList = new ArrayList<Annotation>();
492 System.out.println(">>>>>> " + sq.getSequenceAsString().length());
493 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
494 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
495 Annotation[] annots = annotsList.toArray(new Annotation[0]);
496 sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
497 "Test annot description", annots));
498 sq.getDatasetSequence().addAlignmentAnnotation(
499 new AlignmentAnnotation("Test annot", "Test annot description",
501 Assert.assertEquals(sq.getDescription(), "Test sequence description..");
502 Assert.assertEquals(sq.getDBRefs().length, 4);
503 Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
504 Assert.assertNotNull(sq.getAnnotation());
505 Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
506 Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 4);
507 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
509 Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
511 Sequence derived = (Sequence) sq.deriveSequence();
513 Assert.assertEquals(derived.getDescription(),
514 "Test sequence description..");
515 Assert.assertEquals(derived.getDBRefs().length, 4);
516 Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
517 Assert.assertNotNull(derived.getAnnotation());
518 Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
519 Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 4);
520 Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
522 Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
524 assertEquals("CD", derived.getSequenceAsString());
525 assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
527 assertNull(sq.sequenceFeatures);
528 assertNull(derived.sequenceFeatures);
529 // derived sequence should access dataset sequence features
530 assertNotNull(sq.getSequenceFeatures());
531 assertArrayEquals(sq.getSequenceFeatures(),
532 derived.getSequenceFeatures());
536 * Test for deriveSequence applied to an ungapped sequence with no dataset
538 @Test(groups = { "Functional" })
539 public void testDeriveSequence_noDatasetUngapped()
541 SequenceI sq = new Sequence("Seq1", "ABCDEF");
542 assertEquals(1, sq.getStart());
543 assertEquals(6, sq.getEnd());
544 SequenceI derived = sq.deriveSequence();
545 assertEquals("ABCDEF", derived.getSequenceAsString());
546 assertEquals("ABCDEF", derived.getDatasetSequence()
547 .getSequenceAsString());
551 * Test for deriveSequence applied to a gapped sequence with no dataset
553 @Test(groups = { "Functional" })
554 public void testDeriveSequence_noDatasetGapped()
556 SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
557 assertEquals(1, sq.getStart());
558 assertEquals(6, sq.getEnd());
559 assertNull(sq.getDatasetSequence());
560 SequenceI derived = sq.deriveSequence();
561 assertEquals("AB-C.D EF", derived.getSequenceAsString());
562 assertEquals("ABCDEF", derived.getDatasetSequence()
563 .getSequenceAsString());
566 @Test(groups = { "Functional" })
567 public void testCopyConstructor_noDataset()
569 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
570 seq1.setDescription("description");
571 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
573 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
575 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
576 seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
578 SequenceI copy = new Sequence(seq1);
580 assertNull(copy.getDatasetSequence());
582 verifyCopiedSequence(seq1, copy);
584 // copy has a copy of the DBRefEntry
585 // this is murky - DBrefs are only copied for dataset sequences
586 // where the test for 'dataset sequence' is 'dataset is null'
587 // but that doesn't distinguish it from an aligned sequence
588 // which has not yet generated a dataset sequence
589 // NB getDBRef looks inside dataset sequence if not null
590 DBRefEntry[] dbrefs = copy.getDBRefs();
591 assertEquals(1, dbrefs.length);
592 assertFalse(dbrefs[0] == seq1.getDBRefs()[0]);
593 assertTrue(dbrefs[0].equals(seq1.getDBRefs()[0]));
596 @Test(groups = { "Functional" })
597 public void testCopyConstructor_withDataset()
599 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
600 seq1.createDatasetSequence();
601 seq1.setDescription("description");
602 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
604 // JAL-2046 - what is the contract for using a derived sequence's
605 // addSequenceFeature ?
606 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
608 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
609 // here we add DBRef to the dataset sequence:
610 seq1.getDatasetSequence().addDBRef(
611 new DBRefEntry("EMBL", "1.2", "AZ12345"));
613 SequenceI copy = new Sequence(seq1);
615 assertNotNull(copy.getDatasetSequence());
616 assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
618 verifyCopiedSequence(seq1, copy);
620 // getDBRef looks inside dataset sequence and this is shared,
621 // so holds the same dbref objects
622 DBRefEntry[] dbrefs = copy.getDBRefs();
623 assertEquals(1, dbrefs.length);
624 assertSame(dbrefs[0], seq1.getDBRefs()[0]);
628 * Helper to make assertions about a copied sequence
633 protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
635 // verify basic properties:
636 assertEquals(copy.getName(), seq1.getName());
637 assertEquals(copy.getDescription(), seq1.getDescription());
638 assertEquals(copy.getStart(), seq1.getStart());
639 assertEquals(copy.getEnd(), seq1.getEnd());
640 assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
642 // copy has a copy of the annotation:
643 AlignmentAnnotation[] anns = copy.getAnnotation();
644 assertEquals(1, anns.length);
645 assertFalse(anns[0] == seq1.getAnnotation()[0]);
646 assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
647 assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
648 assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
650 // copy has a copy of the sequence feature:
651 SequenceFeature[] sfs = copy.getSequenceFeatures();
652 assertEquals(1, sfs.length);
653 if (seq1.getDatasetSequence()!=null && copy.getDatasetSequence()==seq1.getDatasetSequence()) {
654 assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
656 assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
658 assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
660 // copy has a copy of the PDB entry
661 Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
662 assertEquals(1, pdbs.size());
663 assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
664 assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
667 @Test(groups = "Functional")
668 public void testGetCharAt()
670 SequenceI sq = new Sequence("", "abcde");
671 assertEquals('a', sq.getCharAt(0));
672 assertEquals('e', sq.getCharAt(4));
673 assertEquals(' ', sq.getCharAt(5));
674 assertEquals(' ', sq.getCharAt(-1));
678 * Tests for adding (or updating) dbrefs
680 * @see DBRefEntry#updateFrom(DBRefEntry)
682 @Test(groups = { "Functional" })
683 public void testAddDBRef()
685 SequenceI sq = new Sequence("", "abcde");
686 assertNull(sq.getDBRefs());
687 DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
689 assertEquals(1, sq.getDBRefs().length);
690 assertSame(dbref, sq.getDBRefs()[0]);
693 * change of version - new entry
695 DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
697 assertEquals(2, sq.getDBRefs().length);
698 assertSame(dbref, sq.getDBRefs()[0]);
699 assertSame(dbref2, sq.getDBRefs()[1]);
702 * matches existing entry - not added
704 sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
705 assertEquals(2, sq.getDBRefs().length);
708 * different source = new entry
710 DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
712 assertEquals(3, sq.getDBRefs().length);
713 assertSame(dbref3, sq.getDBRefs()[2]);
716 * different ref = new entry
718 DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
720 assertEquals(4, sq.getDBRefs().length);
721 assertSame(dbref4, sq.getDBRefs()[3]);
724 * matching ref with a mapping - map updated
726 DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
727 Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
731 assertEquals(4, sq.getDBRefs().length);
732 assertSame(dbref4, sq.getDBRefs()[3]);
733 assertSame(map, dbref4.getMap());
736 * 'real' version replaces "0" version
738 dbref2.setVersion("0");
739 DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
740 dbref2.getAccessionId());
742 assertEquals(4, sq.getDBRefs().length);
743 assertSame(dbref2, sq.getDBRefs()[1]);
744 assertEquals("3", dbref2.getVersion());
747 * 'real' version replaces "source:0" version
749 dbref3.setVersion("Uniprot:0");
750 DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
751 dbref3.getAccessionId());
753 assertEquals(4, sq.getDBRefs().length);
754 assertSame(dbref3, sq.getDBRefs()[2]);
755 assertEquals("3", dbref2.getVersion());