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 java.util.Locale;
25 import static org.testng.AssertJUnit.assertEquals;
26 import static org.testng.AssertJUnit.assertFalse;
27 import static org.testng.AssertJUnit.assertNotNull;
28 import static org.testng.AssertJUnit.assertNotSame;
29 import static org.testng.AssertJUnit.assertNull;
30 import static org.testng.AssertJUnit.assertSame;
31 import static org.testng.AssertJUnit.assertTrue;
34 import java.util.ArrayList;
35 import java.util.Arrays;
36 import java.util.BitSet;
37 import java.util.Iterator;
38 import java.util.List;
39 import java.util.Vector;
41 import org.testng.Assert;
42 import org.testng.annotations.BeforeClass;
43 import org.testng.annotations.BeforeMethod;
44 import org.testng.annotations.Test;
46 import jalview.analysis.AlignmentGenerator;
47 import jalview.commands.EditCommand;
48 import jalview.commands.EditCommand.Action;
49 import jalview.datamodel.PDBEntry.Type;
50 import jalview.gui.JvOptionPane;
51 import jalview.util.MapList;
53 import junit.extensions.PA;
55 public class SequenceTest
57 @BeforeClass(alwaysRun = true)
58 public void setUpJvOptionPane()
60 JvOptionPane.setInteractiveMode(false);
61 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
66 @BeforeMethod(alwaysRun = true)
69 seq = new Sequence("FER1", "AKPNGVL");
72 @Test(groups = { "Functional" })
73 public void testInsertGapsAndGapmaps()
75 SequenceI aseq = seq.deriveSequence();
76 aseq.insertCharAt(2, 3, '-');
77 aseq.insertCharAt(6, 3, '-');
78 assertEquals("Gap insertions not correct", "AK---P---NGVL",
79 aseq.getSequenceAsString());
80 List<int[]> gapInt = aseq.getInsertions();
81 assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
82 assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
83 assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
84 assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
86 BitSet gapfield = aseq.getInsertionsAsBits();
87 BitSet expectedgaps = new BitSet();
88 expectedgaps.set(2, 5);
89 expectedgaps.set(6, 9);
91 assertEquals(6, expectedgaps.cardinality());
93 assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
94 6, gapfield.cardinality());
96 assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
99 @Test(groups = ("Functional"))
100 public void testIsProtein()
103 assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
105 assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
107 SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
108 assertFalse(sq.isProtein());
109 // change sequence, should trigger an update of cached result
110 sq.setSequence("ASDFASDFADSF");
111 assertTrue(sq.isProtein());
114 @Test(groups = ("Functional"))
115 public void testIsProteinWithXorNAmbiguityCodes()
117 // test Protein with N - poly asparagine
118 assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
119 assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
120 // test Protein with X
121 assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
123 assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
125 assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
127 assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
128 assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
131 @Test(groups = { "Functional" })
132 public void testGetAnnotation()
134 // initial state returns null not an empty array
135 assertNull(seq.getAnnotation());
136 AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
138 AlignmentAnnotation[] anns = seq.getAnnotation();
139 assertEquals(1, anns.length);
140 assertSame(ann, anns[0]);
142 // removing all annotations reverts array to null
143 seq.removeAlignmentAnnotation(ann);
144 assertNull(seq.getAnnotation());
147 @Test(groups = { "Functional" })
148 public void testGetAnnotation_forLabel()
150 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
152 addAnnotation("label2", "desc2", "calcId2", 1f);
153 AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
155 AlignmentAnnotation[] anns = seq.getAnnotation("label1");
156 assertEquals(2, anns.length);
157 assertSame(ann1, anns[0]);
158 assertSame(ann3, anns[1]);
161 private AlignmentAnnotation addAnnotation(String label,
162 String description, String calcId, float value)
164 final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
166 annotation.setCalcId(calcId);
167 seq.addAlignmentAnnotation(annotation);
171 @Test(groups = { "Functional" })
172 public void testGetAlignmentAnnotations_forCalcIdAndLabel()
174 addAnnotation("label1", "desc1", "calcId1", 1f);
175 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
177 addAnnotation("label2", "desc3", "calcId3", 1f);
178 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
180 addAnnotation("label5", "desc3", null, 1f);
181 addAnnotation(null, "desc3", "calcId3", 1f);
183 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
185 assertEquals(2, anns.size());
186 assertSame(ann2, anns.get(0));
187 assertSame(ann4, anns.get(1));
189 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
190 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
191 assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
192 assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
193 assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
197 @Test(groups = { "Functional" })
198 public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
200 addAnnotation("label1", "desc1", "calcId1", 1f);
201 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
203 addAnnotation("label2", "desc3", "calcId3", 1f);
204 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
206 addAnnotation("label5", "desc3", null, 1f);
207 addAnnotation(null, "desc3", "calcId3", 1f);
209 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
211 assertEquals(1, anns.size());
212 assertSame(ann4, anns.get(0));
214 * null matching should fail
216 assertTrue(seq.getAlignmentAnnotations("calcId3", "label2",null).isEmpty());
218 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3",null).isEmpty());
219 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5",null).isEmpty());
220 assertTrue(seq.getAlignmentAnnotations("calcId2", null,null).isEmpty());
221 assertTrue(seq.getAlignmentAnnotations(null, "label3",null).isEmpty());
222 assertTrue(seq.getAlignmentAnnotations(null, null,null).isEmpty());
226 * Tests for addAlignmentAnnotation. Note this method has the side-effect of
227 * setting the sequenceRef on the annotation. Adding the same annotation twice
230 @Test(groups = { "Functional" })
231 public void testAddAlignmentAnnotation()
233 assertNull(seq.getAnnotation());
234 final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
236 assertNull(annotation.sequenceRef);
237 seq.addAlignmentAnnotation(annotation);
238 assertSame(seq, annotation.sequenceRef);
239 AlignmentAnnotation[] anns = seq.getAnnotation();
240 assertEquals(1, anns.length);
241 assertSame(annotation, anns[0]);
243 // re-adding does nothing
244 seq.addAlignmentAnnotation(annotation);
245 anns = seq.getAnnotation();
246 assertEquals(1, anns.length);
247 assertSame(annotation, anns[0]);
249 // an identical but different annotation can be added
250 final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
252 seq.addAlignmentAnnotation(annotation2);
253 anns = seq.getAnnotation();
254 assertEquals(2, anns.length);
255 assertSame(annotation, anns[0]);
256 assertSame(annotation2, anns[1]);
259 @Test(groups = { "Functional" })
260 public void testGetStartGetEnd()
262 SequenceI sq = new Sequence("test", "ABCDEF");
263 assertEquals(1, sq.getStart());
264 assertEquals(6, sq.getEnd());
266 sq = new Sequence("test", "--AB-C-DEF--");
267 assertEquals(1, sq.getStart());
268 assertEquals(6, sq.getEnd());
270 sq = new Sequence("test", "----");
271 assertEquals(1, sq.getStart());
272 assertEquals(0, sq.getEnd()); // ??
276 * Tests for the method that returns an alignment column position (base 1) for
277 * a given sequence position (base 1).
279 @Test(groups = { "Functional" })
280 public void testFindIndex()
283 * call sequenceChanged() after each test to invalidate any cursor,
284 * forcing the 1-arg findIndex to be executed
286 SequenceI sq = new Sequence("test", "ABCDEF");
287 assertEquals(0, sq.findIndex(0));
288 sq.sequenceChanged();
289 assertEquals(1, sq.findIndex(1));
290 sq.sequenceChanged();
291 assertEquals(5, sq.findIndex(5));
292 sq.sequenceChanged();
293 assertEquals(6, sq.findIndex(6));
294 sq.sequenceChanged();
295 assertEquals(6, sq.findIndex(9));
297 final String aligned = "-A--B-C-D-E-F--";
298 assertEquals(15, aligned.length());
299 sq = new Sequence("test/8-13", aligned);
300 assertEquals(2, sq.findIndex(8));
301 sq.sequenceChanged();
302 assertEquals(5, sq.findIndex(9));
303 sq.sequenceChanged();
304 assertEquals(7, sq.findIndex(10));
306 // before start returns 0
307 sq.sequenceChanged();
308 assertEquals(0, sq.findIndex(0));
309 sq.sequenceChanged();
310 assertEquals(0, sq.findIndex(-1));
312 // beyond end returns last residue column
313 sq.sequenceChanged();
314 assertEquals(13, sq.findIndex(99));
317 * residue before sequence 'end' but beyond end of sequence returns
318 * length of sequence (last column) (rightly or wrongly!)
320 sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case
321 assertEquals(6, sq.getLength());
322 sq.sequenceChanged();
323 assertEquals(sq.getLength(), sq.findIndex(14));
324 sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case
325 sq.sequenceChanged();
326 assertEquals(sq.getLength(), sq.findIndex(65));
329 * residue after sequence 'start' but before first residue returns
330 * zero (before first column) (rightly or wrongly!)
332 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
333 sq.sequenceChanged();
334 assertEquals(0, sq.findIndex(3));
335 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
336 sq.sequenceChanged();
337 assertEquals(0, sq.findIndex(2));
340 @Test(groups = { "Functional" })
341 public void testFindPositions()
343 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
348 assertNull(sq.findPositions(6, 5));
353 assertNull(sq.findPositions(1, 1)); // 1-based columns
354 assertNull(sq.findPositions(5, 5));
355 assertNull(sq.findPositions(5, 6));
356 assertNull(sq.findPositions(5, 7));
359 * all ungapped ranges
361 assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
362 assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
363 assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
364 assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
367 * gap to ungapped range
369 assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
370 assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
373 * ungapped to gapped range
375 assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
376 assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
379 * ungapped to ungapped enclosing gaps
381 assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
382 assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
385 * gapped to gapped enclosing ungapped
387 assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
388 assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
389 assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
390 assertEquals(new Range(8, 13), sq.findPositions(1, 99));
393 * now try on a sequence with no gaps
395 sq.createDatasetSequence();
396 assertEquals(new Range(8, 13),
397 sq.getDatasetSequence().findPositions(1, 99));
398 assertEquals(new Range(8, 13),
399 sq.getDatasetSequence().findPositions(0, 99));
404 * Tests for the method that returns a dataset sequence position (start..) for
405 * an aligned column position (base 0).
407 @Test(groups = { "Functional" })
408 public void testFindPosition()
411 * call sequenceChanged() after each test to invalidate any cursor,
412 * forcing the 1-arg findPosition to be executed
414 SequenceI sq = new Sequence("test/8-13", "ABCDEF");
415 assertEquals(8, sq.findPosition(0));
416 // Sequence should now hold a cursor at [8, 0]
417 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1",
418 PA.getValue(sq, "cursor").toString());
419 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
420 int token = (int) PA.getValue(sq, "changeCount");
421 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
423 sq.sequenceChanged();
426 * find F13 at column offset 5, cursor should update to [13, 6]
427 * endColumn is found and saved in cursor
429 assertEquals(13, sq.findPosition(5));
430 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
431 assertEquals(++token, (int) PA.getValue(sq, "changeCount"));
432 assertEquals(new SequenceCursor(sq, 13, 6, token), cursor);
433 assertEquals("test:Pos13:Col6:startCol1:endCol6:tok2",
434 PA.getValue(sq, "cursor").toString());
436 // assertEquals(-1, seq.findPosition(6)); // fails
438 sq = new Sequence("test/8-11", "AB-C-D--");
439 token = (int) PA.getValue(sq, "changeCount"); // 1 for setStart
440 assertEquals(8, sq.findPosition(0));
441 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
442 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
443 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1",
444 PA.getValue(sq, "cursor").toString());
446 sq.sequenceChanged();
447 assertEquals(9, sq.findPosition(1));
448 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
449 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
450 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2",
451 PA.getValue(sq, "cursor").toString());
453 sq.sequenceChanged();
454 // gap position 'finds' residue to the right (not the left as per javadoc)
455 // cursor is set to the last residue position found [B 2]
456 assertEquals(10, sq.findPosition(2));
457 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
458 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
459 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok3",
460 PA.getValue(sq, "cursor").toString());
462 sq.sequenceChanged();
463 assertEquals(10, sq.findPosition(3));
464 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
465 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
466 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4",
467 PA.getValue(sq, "cursor").toString());
469 sq.sequenceChanged();
470 // column[4] is the gap after C - returns D11
471 // cursor is set to [C 4]
472 assertEquals(11, sq.findPosition(4));
473 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
474 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
475 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok5",
476 PA.getValue(sq, "cursor").toString());
478 sq.sequenceChanged();
479 assertEquals(11, sq.findPosition(5)); // D
480 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
481 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
482 // lastCol has been found and saved in the cursor
483 assertEquals("test:Pos11:Col6:startCol1:endCol6:tok6",
484 PA.getValue(sq, "cursor").toString());
486 sq.sequenceChanged();
487 // returns 1 more than sequence length if off the end ?!?
488 assertEquals(12, sq.findPosition(6));
490 sq.sequenceChanged();
491 assertEquals(12, sq.findPosition(7));
494 * first findPosition should also set firstResCol in cursor
496 sq = new Sequence("test/8-13", "--AB-C-DEF--");
497 assertEquals(8, sq.findPosition(0));
498 assertNull(PA.getValue(sq, "cursor"));
499 assertEquals(1, PA.getValue(sq, "changeCount"));
501 sq.sequenceChanged();
502 assertEquals(8, sq.findPosition(1));
503 assertNull(PA.getValue(sq, "cursor"));
505 sq.sequenceChanged();
506 assertEquals(8, sq.findPosition(2));
507 assertEquals("test:Pos8:Col3:startCol3:endCol0:tok3",
508 PA.getValue(sq, "cursor").toString());
510 sq.sequenceChanged();
511 assertEquals(9, sq.findPosition(3));
512 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4",
513 PA.getValue(sq, "cursor").toString());
515 sq.sequenceChanged();
516 // column[4] is a gap, returns next residue pos (C10)
517 // cursor is set to last residue found [B]
518 assertEquals(10, sq.findPosition(4));
519 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok5",
520 PA.getValue(sq, "cursor").toString());
522 sq.sequenceChanged();
523 assertEquals(10, sq.findPosition(5));
524 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6",
525 PA.getValue(sq, "cursor").toString());
527 sq.sequenceChanged();
528 // column[6] is a gap, returns next residue pos (D11)
529 // cursor is set to last residue found [C]
530 assertEquals(11, sq.findPosition(6));
531 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok7",
532 PA.getValue(sq, "cursor").toString());
534 sq.sequenceChanged();
535 assertEquals(11, sq.findPosition(7));
536 assertEquals("test:Pos11:Col8:startCol3:endCol0:tok8",
537 PA.getValue(sq, "cursor").toString());
539 sq.sequenceChanged();
540 assertEquals(12, sq.findPosition(8));
541 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok9",
542 PA.getValue(sq, "cursor").toString());
545 * when the last residue column is found, it is set in the cursor
547 sq.sequenceChanged();
548 assertEquals(13, sq.findPosition(9));
549 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10",
550 PA.getValue(sq, "cursor").toString());
552 sq.sequenceChanged();
553 assertEquals(14, sq.findPosition(10));
554 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11",
555 PA.getValue(sq, "cursor").toString());
558 * findPosition for column beyond sequence length
559 * returns 1 more than last residue position
561 sq.sequenceChanged();
562 assertEquals(14, sq.findPosition(11));
563 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12",
564 PA.getValue(sq, "cursor").toString());
566 sq.sequenceChanged();
567 assertEquals(14, sq.findPosition(99));
568 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok13",
569 PA.getValue(sq, "cursor").toString());
572 * gapped sequence ending in non-gap
574 sq = new Sequence("test/8-13", "--AB-C-DEF");
575 assertEquals(13, sq.findPosition(9));
576 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1",
577 PA.getValue(sq, "cursor").toString());
578 sq.sequenceChanged();
579 assertEquals(12, sq.findPosition(8)); // E12
580 // sequenceChanged() invalidates cursor.lastResidueColumn
581 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
582 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok2",
584 // findPosition with cursor accepts base 1 column values
585 assertEquals(13, ((Sequence) sq).findPosition(10, cursor));
586 assertEquals(13, sq.findPosition(9)); // F13
587 // lastResidueColumn has now been found and saved in cursor
588 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok2",
589 PA.getValue(sq, "cursor").toString());
592 @Test(groups = { "Functional" })
593 public void testDeleteChars()
598 SequenceI sq = new Sequence("test", "ABCDEF");
599 assertNull(PA.getValue(sq, "datasetSequence"));
600 assertEquals(1, sq.getStart());
601 assertEquals(6, sq.getEnd());
602 sq.deleteChars(2, 3);
603 assertEquals("ABDEF", sq.getSequenceAsString());
604 assertEquals(1, sq.getStart());
605 assertEquals(5, sq.getEnd());
606 assertNull(PA.getValue(sq, "datasetSequence"));
611 sq = new Sequence("test", "ABCDEF");
612 sq.deleteChars(0, 2);
613 assertEquals("CDEF", sq.getSequenceAsString());
614 assertEquals(3, sq.getStart());
615 assertEquals(6, sq.getEnd());
616 assertNull(PA.getValue(sq, "datasetSequence"));
618 sq = new Sequence("test", "ABCDE");
619 sq.deleteChars(0, 3);
620 assertEquals("DE", sq.getSequenceAsString());
621 assertEquals(4, sq.getStart());
622 assertEquals(5, sq.getEnd());
623 assertNull(PA.getValue(sq, "datasetSequence"));
628 sq = new Sequence("test", "ABCDEF");
629 sq.deleteChars(4, 6);
630 assertEquals("ABCD", sq.getSequenceAsString());
631 assertEquals(1, sq.getStart());
632 assertEquals(4, sq.getEnd());
633 assertNull(PA.getValue(sq, "datasetSequence"));
636 * delete more positions than there are
638 sq = new Sequence("test/8-11", "ABCD");
639 sq.deleteChars(0, 99);
640 assertEquals("", sq.getSequenceAsString());
641 assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
642 assertEquals(11, sq.getEnd());
644 sq = new Sequence("test/8-11", "----");
645 sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
646 assertEquals("", sq.getSequenceAsString());
647 assertEquals(8, sq.getStart());
648 assertEquals(11, sq.getEnd());
651 @Test(groups = { "Functional" })
652 public void testDeleteChars_withDbRefsAndFeatures()
655 * internal delete - new dataset sequence created
656 * gets a copy of any dbrefs
658 SequenceI sq = new Sequence("test", "ABCDEF");
659 sq.createDatasetSequence();
660 DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
662 Object ds = PA.getValue(sq, "datasetSequence");
664 assertEquals(1, sq.getStart());
665 assertEquals(6, sq.getEnd());
666 sq.deleteChars(2, 3);
667 assertEquals("ABDEF", sq.getSequenceAsString());
668 assertEquals(1, sq.getStart());
669 assertEquals(5, sq.getEnd());
670 Object newDs = PA.getValue(sq, "datasetSequence");
671 assertNotNull(newDs);
672 assertNotSame(ds, newDs);
673 assertNotNull(sq.getDBRefs());
674 assertEquals(1, sq.getDBRefs().size());
675 assertNotSame(dbr1, sq.getDBRefs().get(0));
676 assertEquals(dbr1, sq.getDBRefs().get(0));
679 * internal delete with sequence features
680 * (failure case for JAL-2541)
682 sq = new Sequence("test", "ABCDEF");
683 sq.createDatasetSequence();
684 SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
686 sq.addSequenceFeature(sf1);
687 ds = PA.getValue(sq, "datasetSequence");
689 assertEquals(1, sq.getStart());
690 assertEquals(6, sq.getEnd());
691 sq.deleteChars(2, 4);
692 assertEquals("ABEF", sq.getSequenceAsString());
693 assertEquals(1, sq.getStart());
694 assertEquals(4, sq.getEnd());
695 newDs = PA.getValue(sq, "datasetSequence");
696 assertNotNull(newDs);
697 assertNotSame(ds, newDs);
698 List<SequenceFeature> sfs = sq.getSequenceFeatures();
699 assertEquals(1, sfs.size());
700 assertNotSame(sf1, sfs.get(0));
701 assertEquals(sf1, sfs.get(0));
704 * delete at start - no new dataset sequence created
705 * any sequence features remain as before
707 sq = new Sequence("test", "ABCDEF");
708 sq.createDatasetSequence();
709 ds = PA.getValue(sq, "datasetSequence");
710 sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
711 sq.addSequenceFeature(sf1);
712 sq.deleteChars(0, 2);
713 assertEquals("CDEF", sq.getSequenceAsString());
714 assertEquals(3, sq.getStart());
715 assertEquals(6, sq.getEnd());
716 assertSame(ds, PA.getValue(sq, "datasetSequence"));
717 sfs = sq.getSequenceFeatures();
719 assertEquals(1, sfs.size());
720 assertSame(sf1, sfs.get(0));
723 * delete at end - no new dataset sequence created
724 * any dbrefs remain as before
726 sq = new Sequence("test", "ABCDEF");
727 sq.createDatasetSequence();
728 ds = PA.getValue(sq, "datasetSequence");
729 dbr1 = new DBRefEntry("Uniprot", "0", "a123");
731 sq.deleteChars(4, 6);
732 assertEquals("ABCD", sq.getSequenceAsString());
733 assertEquals(1, sq.getStart());
734 assertEquals(4, sq.getEnd());
735 assertSame(ds, PA.getValue(sq, "datasetSequence"));
736 assertNotNull(sq.getDBRefs());
737 assertEquals(1, sq.getDBRefs().size());
738 assertSame(dbr1, sq.getDBRefs().get(0));
741 @Test(groups = { "Functional" })
742 public void testInsertCharAt()
744 // non-static methods:
745 SequenceI sq = new Sequence("test", "ABCDEF");
746 sq.insertCharAt(0, 'z');
747 assertEquals("zABCDEF", sq.getSequenceAsString());
748 sq.insertCharAt(2, 2, 'x');
749 assertEquals("zAxxBCDEF", sq.getSequenceAsString());
751 // for static method see StringUtilsTest
755 * Test the method that returns an array of aligned sequence positions where
756 * the array index is the data sequence position (both base 0).
758 @Test(groups = { "Functional" })
759 public void testGapMap()
761 SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
762 sq.createDatasetSequence();
763 assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
767 * Test the method that gets sequence features, either from the sequence or
770 @Test(groups = { "Functional" })
771 public void testGetSequenceFeatures()
773 SequenceI sq = new Sequence("test", "GATCAT");
774 sq.createDatasetSequence();
776 assertTrue(sq.getSequenceFeatures().isEmpty());
779 * SequenceFeature on sequence
781 SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
782 sq.addSequenceFeature(sf);
783 List<SequenceFeature> sfs = sq.getSequenceFeatures();
784 assertEquals(1, sfs.size());
785 assertSame(sf, sfs.get(0));
788 * SequenceFeature on sequence and dataset sequence; returns that on
791 * Note JAL-2046: spurious: we have no use case for this at the moment.
792 * This test also buggy - as sf2.equals(sf), no new feature is added
794 SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
796 sq.getDatasetSequence().addSequenceFeature(sf2);
797 sfs = sq.getSequenceFeatures();
798 assertEquals(1, sfs.size());
799 assertSame(sf, sfs.get(0));
802 * SequenceFeature on dataset sequence only
803 * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
805 sq.setSequenceFeatures(null);
806 assertTrue(sq.getDatasetSequence().getSequenceFeatures().isEmpty());
809 * Corrupt case - no SequenceFeature, dataset's dataset is the original
810 * sequence. Test shows no infinite loop results.
812 sq.getDatasetSequence().setSequenceFeatures(null);
814 * is there a usecase for this ? setDatasetSequence should throw an error if
815 * this actually occurs.
819 sq.getDatasetSequence().setDatasetSequence(sq); // loop!
820 Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
821 } catch (IllegalArgumentException e)
823 // TODO Jalview error/exception class for raising implementation errors
824 assertTrue(e.getMessage().toLowerCase(Locale.ROOT)
825 .contains("implementation error"));
827 assertTrue(sq.getSequenceFeatures().isEmpty());
831 * Test the method that returns an array, indexed by sequence position, whose
832 * entries are the residue positions at the sequence position (or to the right
835 @Test(groups = { "Functional" })
836 public void testFindPositionMap()
839 * Note: Javadoc for findPosition says it returns the residue position to
840 * the left of a gapped position; in fact it returns the position to the
841 * right. Also it returns a non-existent residue position for a gap beyond
844 Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
845 int[] map = sq.findPositionMap();
846 assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
847 Arrays.toString(map));
851 * Test for getSubsequence
853 @Test(groups = { "Functional" })
854 public void testGetSubsequence()
856 SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
857 sq.createDatasetSequence();
859 // positions are base 0, end position is exclusive
860 SequenceI subseq = sq.getSubSequence(2, 4);
862 assertEquals("CD", subseq.getSequenceAsString());
863 // start/end are base 1 positions
864 assertEquals(3, subseq.getStart());
865 assertEquals(4, subseq.getEnd());
866 // subsequence shares the full dataset sequence
867 assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
871 * test createDatasetSequence behaves to doc
873 @Test(groups = { "Functional" })
874 public void testCreateDatasetSequence()
876 SequenceI sq = new Sequence("my", "ASDASD");
877 sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
879 sq.addDBRef(new DBRefEntry("source", "version", "accession"));
880 assertNull(sq.getDatasetSequence());
881 assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
882 assertNotNull(PA.getValue(sq, "dbrefs"));
884 SequenceI rds = sq.createDatasetSequence();
886 assertNull(rds.getDatasetSequence());
887 assertSame(sq.getDatasetSequence(), rds);
889 // sequence features and dbrefs transferred to dataset sequence
890 assertNull(PA.getValue(sq, "sequenceFeatureStore"));
891 assertNull(PA.getValue(sq, "dbrefs"));
892 assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
893 assertNotNull(PA.getValue(rds, "dbrefs"));
897 * Test for deriveSequence applied to a sequence with a dataset
899 @Test(groups = { "Functional" })
900 public void testDeriveSequence_existingDataset()
902 Sequence sq = new Sequence("Seq1", "CD");
903 sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
904 sq.getDatasetSequence().addSequenceFeature(
905 new SequenceFeature("", "", 1, 2, 0f, null));
909 sq.setDescription("Test sequence description..");
910 sq.setVamsasId("TestVamsasId");
911 sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
913 sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
914 sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
915 sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
916 sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
918 sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
919 sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
920 sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
921 sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
923 // these are the same as ones already added
924 DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
925 DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
927 List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
930 sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
931 sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
932 sq.getDatasetSequence().addDBRef(
933 new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
934 sq.getDatasetSequence().addDBRef(
935 new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
937 PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
938 PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
939 PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
941 PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
943 sq.getDatasetSequence().addPDBId(pdbe1a);
944 sq.getDatasetSequence().addPDBId(pdbe1b);
945 sq.getDatasetSequence().addPDBId(pdbe2a);
946 sq.getDatasetSequence().addPDBId(pdbe2b);
949 * test we added pdb entries to the dataset sequence
951 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
952 .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
953 "PDB Entries were not found on dataset sequence.");
956 * we should recover a pdb entry that is on the dataset sequence via PDBEntry
958 Assert.assertEquals(pdbe1a,
959 sq.getDatasetSequence().getPDBEntry("1PDB"),
960 "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
961 ArrayList<Annotation> annotsList = new ArrayList<>();
962 System.out.println(">>>>>> " + sq.getSequenceAsString().length());
963 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
964 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
965 Annotation[] annots = annotsList.toArray(new Annotation[0]);
966 sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
967 "Test annot description", annots));
968 sq.getDatasetSequence().addAlignmentAnnotation(
969 new AlignmentAnnotation("Test annot", "Test annot description",
971 Assert.assertEquals(sq.getDescription(), "Test sequence description..");
972 Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset
974 Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
975 Assert.assertNotNull(sq.getAnnotation());
976 Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
977 Assert.assertEquals(sq.getDatasetSequence().getDBRefs().size(), 5); // same
980 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
982 Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
984 Sequence derived = (Sequence) sq.deriveSequence();
986 Assert.assertEquals(derived.getDescription(),
987 "Test sequence description..");
988 Assert.assertEquals(derived.getDBRefs().size(), 5); // come from dataset
989 Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
990 Assert.assertNotNull(derived.getAnnotation());
991 Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
992 Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
993 Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
995 Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
997 assertEquals("CD", derived.getSequenceAsString());
998 assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
1000 // derived sequence should access dataset sequence features
1001 assertNotNull(sq.getSequenceFeatures());
1002 assertEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures());
1005 * verify we have primary db refs *just* for PDB IDs with associated
1009 assertEquals(primRefs, sq.getPrimaryDBRefs());
1010 assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
1012 assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
1017 * Test for deriveSequence applied to an ungapped sequence with no dataset
1019 @Test(groups = { "Functional" })
1020 public void testDeriveSequence_noDatasetUngapped()
1022 SequenceI sq = new Sequence("Seq1", "ABCDEF");
1023 assertEquals(1, sq.getStart());
1024 assertEquals(6, sq.getEnd());
1025 SequenceI derived = sq.deriveSequence();
1026 assertEquals("ABCDEF", derived.getSequenceAsString());
1027 assertEquals("ABCDEF", derived.getDatasetSequence()
1028 .getSequenceAsString());
1032 * Test for deriveSequence applied to a gapped sequence with no dataset
1034 @Test(groups = { "Functional" })
1035 public void testDeriveSequence_noDatasetGapped()
1037 SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
1038 assertEquals(1, sq.getStart());
1039 assertEquals(6, sq.getEnd());
1040 assertNull(sq.getDatasetSequence());
1041 SequenceI derived = sq.deriveSequence();
1042 assertEquals("AB-C.D EF", derived.getSequenceAsString());
1043 assertEquals("ABCDEF", derived.getDatasetSequence()
1044 .getSequenceAsString());
1047 @Test(groups = { "Functional" })
1048 public void testCopyConstructor_noDataset()
1050 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1051 seq1.setDescription("description");
1052 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1054 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1056 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1057 seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
1059 SequenceI copy = new Sequence(seq1);
1061 assertNull(copy.getDatasetSequence());
1063 verifyCopiedSequence(seq1, copy);
1065 // copy has a copy of the DBRefEntry
1066 // this is murky - DBrefs are only copied for dataset sequences
1067 // where the test for 'dataset sequence' is 'dataset is null'
1068 // but that doesn't distinguish it from an aligned sequence
1069 // which has not yet generated a dataset sequence
1070 // NB getDBRef looks inside dataset sequence if not null
1071 List<DBRefEntry> dbrefs = copy.getDBRefs();
1072 assertEquals(1, dbrefs.size());
1073 assertFalse(dbrefs.get(0) == seq1.getDBRefs().get(0));
1074 assertTrue(dbrefs.get(0).equals(seq1.getDBRefs().get(0)));
1077 @Test(groups = { "Functional" })
1078 public void testCopyConstructor_withDataset()
1080 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1081 seq1.createDatasetSequence();
1082 seq1.setDescription("description");
1083 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1085 // JAL-2046 - what is the contract for using a derived sequence's
1086 // addSequenceFeature ?
1087 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1089 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1090 // here we add DBRef to the dataset sequence:
1091 seq1.getDatasetSequence().addDBRef(
1092 new DBRefEntry("EMBL", "1.2", "AZ12345"));
1094 SequenceI copy = new Sequence(seq1);
1096 assertNotNull(copy.getDatasetSequence());
1097 assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
1099 verifyCopiedSequence(seq1, copy);
1101 // getDBRef looks inside dataset sequence and this is shared,
1102 // so holds the same dbref objects
1103 List<DBRefEntry> dbrefs = copy.getDBRefs();
1104 assertEquals(1, dbrefs.size());
1105 assertSame(dbrefs.get(0), seq1.getDBRefs().get(0));
1109 * Helper to make assertions about a copied sequence
1114 protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
1116 // verify basic properties:
1117 assertEquals(copy.getName(), seq1.getName());
1118 assertEquals(copy.getDescription(), seq1.getDescription());
1119 assertEquals(copy.getStart(), seq1.getStart());
1120 assertEquals(copy.getEnd(), seq1.getEnd());
1121 assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
1123 // copy has a copy of the annotation:
1124 AlignmentAnnotation[] anns = copy.getAnnotation();
1125 assertEquals(1, anns.length);
1126 assertFalse(anns[0] == seq1.getAnnotation()[0]);
1127 assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
1128 assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
1129 assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
1131 // copy has a copy of the sequence feature:
1132 List<SequenceFeature> sfs = copy.getSequenceFeatures();
1133 assertEquals(1, sfs.size());
1134 if (seq1.getDatasetSequence() != null
1135 && copy.getDatasetSequence() == seq1.getDatasetSequence())
1137 assertSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1141 assertNotSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1143 assertEquals(sfs.get(0), seq1.getSequenceFeatures().get(0));
1145 // copy has a copy of the PDB entry
1146 Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
1147 assertEquals(1, pdbs.size());
1148 assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
1149 assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
1152 @Test(groups = "Functional")
1153 public void testGetCharAt()
1155 SequenceI sq = new Sequence("", "abcde");
1156 assertEquals('a', sq.getCharAt(0));
1157 assertEquals('e', sq.getCharAt(4));
1158 assertEquals(' ', sq.getCharAt(5));
1159 assertEquals(' ', sq.getCharAt(-1));
1162 @Test(groups = { "Functional" })
1163 public void testAddSequenceFeatures()
1165 SequenceI sq = new Sequence("", "abcde");
1166 // type may not be null
1167 assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
1169 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1171 // can't add a duplicate feature
1172 assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
1174 // can add a different feature
1175 assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
1176 8, 0f, null))); // different type
1177 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
1178 "description", 4, 8, 0f, null)));// different description
1179 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
1180 8, 0f, null))); // different start position
1181 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1182 9, 0f, null))); // different end position
1183 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1184 8, 1f, null))); // different score
1185 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1186 8, Float.NaN, null))); // score NaN
1187 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1188 8, 0f, "Metal"))); // different group
1189 assertEquals(8, sq.getFeatures().getAllFeatures().size());
1193 * Tests for adding (or updating) dbrefs
1195 * @see DBRefEntry#updateFrom(DBRefEntry)
1197 @Test(groups = { "Functional" })
1198 public void testAddDBRef()
1200 SequenceI sq = new Sequence("", "abcde");
1201 assertNull(sq.getDBRefs());
1202 DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
1204 assertEquals(1, sq.getDBRefs().size());
1205 assertSame(dbref, sq.getDBRefs().get(0));
1208 * change of version - new entry
1210 DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
1211 sq.addDBRef(dbref2);
1212 assertEquals(2, sq.getDBRefs().size());
1213 assertSame(dbref, sq.getDBRefs().get(0));
1214 assertSame(dbref2, sq.getDBRefs().get(1));
1217 * matches existing entry - not added
1219 sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
1220 assertEquals(2, sq.getDBRefs().size());
1223 * different source = new entry
1225 DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
1226 sq.addDBRef(dbref3);
1227 assertEquals(3, sq.getDBRefs().size());
1228 assertSame(dbref3, sq.getDBRefs().get(2));
1231 * different ref = new entry
1233 DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
1234 sq.addDBRef(dbref4);
1235 assertEquals(4, sq.getDBRefs().size());
1236 assertSame(dbref4, sq.getDBRefs().get(3));
1239 * matching ref with a mapping - map updated
1241 DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
1242 Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
1245 sq.addDBRef(dbref5);
1246 assertEquals(4, sq.getDBRefs().size());
1247 assertSame(dbref4, sq.getDBRefs().get(3));
1248 assertSame(map, dbref4.getMap());
1251 * 'real' version replaces "0" version
1253 dbref2.setVersion("0");
1254 DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
1255 dbref2.getAccessionId());
1256 sq.addDBRef(dbref6);
1257 assertEquals(4, sq.getDBRefs().size());
1258 assertSame(dbref2, sq.getDBRefs().get(1));
1259 assertEquals("3", dbref2.getVersion());
1262 * 'real' version replaces "source:0" version
1264 dbref3.setVersion("Uniprot:0");
1265 DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
1266 dbref3.getAccessionId());
1267 sq.addDBRef(dbref7);
1268 assertEquals(4, sq.getDBRefs().size());
1269 assertSame(dbref3, sq.getDBRefs().get(2));
1270 assertEquals("3", dbref2.getVersion());
1273 @Test(groups = { "Functional" })
1274 public void testGetPrimaryDBRefs_peptide()
1276 SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22);
1279 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1280 assertTrue(primaryDBRefs.isEmpty());
1284 primaryDBRefs = sq.getPrimaryDBRefs();
1285 assertTrue(primaryDBRefs.isEmpty());
1287 // primary - uniprot
1288 DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760");
1289 sq.addDBRef(upentry1);
1291 // primary - uniprot with congruent map
1292 DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
1293 upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
1294 new int[] { 10, 22 }, 1, 1)));
1295 sq.addDBRef(upentry2);
1297 // primary - uniprot with map of enclosing sequence
1298 DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
1299 upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
1300 new int[] { 8, 24 }, 1, 1)));
1301 sq.addDBRef(upentry3);
1303 // not primary - uniprot with map of sub-sequence (5')
1304 DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
1305 upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
1306 new int[] { 10, 18 }, 1, 1)));
1307 sq.addDBRef(upentry4);
1309 // not primary - uniprot with map that overlaps 3'
1310 DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
1311 upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
1312 new int[] { 12, 22 }, 1, 1)));
1313 sq.addDBRef(upentry5);
1315 // not primary - uniprot with map to different coordinates frame
1316 DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
1317 upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
1318 new int[] { 112, 118 }, 1, 1)));
1319 sq.addDBRef(upentry6);
1321 // not primary - dbref to 'non-core' database
1322 DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903");
1323 sq.addDBRef(upentry7);
1325 // primary - type is PDB
1326 DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
1327 sq.addDBRef(pdbentry);
1329 // not primary - PDBEntry has no file
1330 sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
1332 // not primary - no PDBEntry
1333 sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
1335 // add corroborating PDB entry for primary DBref -
1336 // needs to have a file as well as matching ID
1337 // note PDB ID is not treated as case sensitive
1338 sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
1341 // not valid DBRef - no file..
1342 sq.addPDBId(new PDBEntry("1AAA", null, null, null));
1344 primaryDBRefs = sq.getPrimaryDBRefs();
1345 assertEquals(4, primaryDBRefs.size());
1346 assertTrue("Couldn't find simple primary reference (UNIPROT)",
1347 primaryDBRefs.contains(upentry1));
1348 assertTrue("Couldn't find mapped primary reference (UNIPROT)",
1349 primaryDBRefs.contains(upentry2));
1350 assertTrue("Couldn't find mapped context reference (UNIPROT)",
1351 primaryDBRefs.contains(upentry3));
1352 assertTrue("Couldn't find expected PDB primary reference",
1353 primaryDBRefs.contains(pdbentry));
1356 @Test(groups = { "Functional" })
1357 public void testGetPrimaryDBRefs_nucleotide()
1359 SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
1361 // primary - Ensembl
1362 DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
1365 // not primary - Ensembl 'transcript' mapping of sub-sequence
1366 DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
1367 dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
1368 new int[] { 1, 11 }, 1, 1)));
1371 // primary - EMBL with congruent map
1372 DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
1373 dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
1374 new int[] { 10, 34 }, 1, 1)));
1377 // not primary - to non-core database
1378 DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234");
1381 // not primary - to protein
1382 DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
1385 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1386 assertEquals(2, primaryDBRefs.size());
1387 assertTrue(primaryDBRefs.contains(dbr1));
1388 assertTrue(primaryDBRefs.contains(dbr3));
1392 * Test the method that updates the list of PDBEntry from any new DBRefEntry
1395 @Test(groups = { "Functional" })
1396 public void testUpdatePDBIds()
1398 PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
1399 seq.addPDBId(pdbe1);
1400 seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
1401 seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
1402 seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
1403 seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
1404 // 7 is not a valid chain code:
1405 seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
1408 List<PDBEntry> pdbIds = seq.getAllPDBEntries();
1409 assertEquals(4, pdbIds.size());
1410 assertSame(pdbe1, pdbIds.get(0));
1411 // chain code got added to 3A6S:
1412 assertEquals("B", pdbe1.getChainCode());
1413 assertEquals("1A70", pdbIds.get(1).getId());
1414 // 4BQGA is parsed into id + chain
1415 assertEquals("4BQG", pdbIds.get(2).getId());
1416 assertEquals("a", pdbIds.get(2).getChainCode());
1417 assertEquals("2GIS7", pdbIds.get(3).getId());
1418 assertNull(pdbIds.get(3).getChainCode());
1422 * Test the method that either adds a pdbid or updates an existing one
1424 @Test(groups = { "Functional" })
1425 public void testAddPDBId()
1427 PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
1429 assertEquals(1, seq.getAllPDBEntries().size());
1430 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1431 assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
1433 // add the same entry
1435 assertEquals(1, seq.getAllPDBEntries().size());
1436 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1438 // add an identical entry
1439 seq.addPDBId(new PDBEntry("3A6S", null, null, null));
1440 assertEquals(1, seq.getAllPDBEntries().size());
1441 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1443 // add a different entry
1444 PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
1445 seq.addPDBId(pdbe2);
1446 assertEquals(2, seq.getAllPDBEntries().size());
1447 assertSame(pdbe, seq.getAllPDBEntries().get(0));
1448 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1450 // update pdbe with chain code, file, type
1451 PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
1452 seq.addPDBId(pdbe3);
1453 assertEquals(2, seq.getAllPDBEntries().size());
1454 assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
1455 assertEquals("3A6S", pdbe.getId()); // unchanged
1456 assertEquals("A", pdbe.getChainCode()); // updated
1457 assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
1458 assertEquals("filepath", pdbe.getFile()); // updated
1459 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1461 // add with a different file path
1462 PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
1463 seq.addPDBId(pdbe4);
1464 assertEquals(3, seq.getAllPDBEntries().size());
1465 assertSame(pdbe4, seq.getAllPDBEntries().get(2));
1467 // add with a different chain code
1468 PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
1469 seq.addPDBId(pdbe5);
1470 assertEquals(4, seq.getAllPDBEntries().size());
1471 assertSame(pdbe5, seq.getAllPDBEntries().get(3));
1473 // add with a fake pdbid
1474 // (models don't have an embedded ID)
1475 String realId = "RealIDQ";
1476 PDBEntry pdbe6 = new PDBEntry(realId,null,Type.PDB,"real/localpath");
1477 PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath","C",Type.MMCIF,"real/localpath");
1478 pdbe7.setFakedPDBId(true);
1479 seq.addPDBId(pdbe6);
1480 assertEquals(5,seq.getAllPDBEntries().size());
1481 seq.addPDBId(pdbe7);
1482 assertEquals(5,seq.getAllPDBEntries().size());
1483 assertFalse(pdbe6.fakedPDBId());
1484 assertSame(pdbe6,seq.getAllPDBEntries().get(4));
1485 assertEquals("C",pdbe6.getChainCode());
1486 assertEquals(realId, pdbe6.getId());
1490 groups = { "Functional" },
1491 expectedExceptions = { IllegalArgumentException.class })
1492 public void testSetDatasetSequence_toSelf()
1494 seq.setDatasetSequence(seq);
1498 groups = { "Functional" },
1499 expectedExceptions = { IllegalArgumentException.class })
1500 public void testSetDatasetSequence_cascading()
1502 SequenceI seq2 = new Sequence("Seq2", "xyz");
1503 seq2.createDatasetSequence();
1504 seq.setDatasetSequence(seq2);
1507 @Test(groups = { "Functional" })
1508 public void testFindFeatures()
1510 SequenceI sq = new Sequence("test/8-16", "-ABC--DEF--GHI--");
1511 sq.createDatasetSequence();
1513 assertTrue(sq.findFeatures(1, 99).isEmpty());
1515 // add non-positional feature
1516 SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f,
1518 sq.addSequenceFeature(sf0);
1519 // add feature on BCD
1520 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
1522 sq.addSequenceFeature(sfBCD);
1523 // add feature on DE
1524 SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
1526 sq.addSequenceFeature(sfDE);
1527 // add contact feature at [B, H]
1528 SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
1529 "desc", 9, 15, 2f, null);
1530 sq.addSequenceFeature(sfContactBH);
1531 // add contact feature at [F, G]
1532 SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
1533 "desc", 13, 14, 2f, null);
1534 sq.addSequenceFeature(sfContactFG);
1535 // add single position feature at [I]
1536 SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
1537 "desc", 16, 16, null);
1538 sq.addSequenceFeature(sfI);
1540 // no features in columns 1-2 (-A)
1541 List<SequenceFeature> found = sq.findFeatures(1, 2);
1542 assertTrue(found.isEmpty());
1544 // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
1545 found = sq.findFeatures(1, 6);
1546 assertEquals(2, found.size());
1547 assertTrue(found.contains(sfBCD));
1548 assertTrue(found.contains(sfContactBH));
1550 // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
1551 found = sq.findFeatures(5, 6);
1552 assertEquals(1, found.size());
1553 assertTrue(found.contains(sfBCD));
1555 // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
1556 found = sq.findFeatures(7, 10);
1557 assertEquals(3, found.size());
1558 assertTrue(found.contains(sfBCD));
1559 assertTrue(found.contains(sfDE));
1560 assertTrue(found.contains(sfContactFG));
1562 // columns 10-11 (--) should find nothing
1563 found = sq.findFeatures(10, 11);
1564 assertEquals(0, found.size());
1566 // columns 14-14 (I) should find variant feature
1567 found = sq.findFeatures(14, 14);
1568 assertEquals(1, found.size());
1569 assertTrue(found.contains(sfI));
1572 @Test(groups = { "Functional" })
1573 public void testFindIndex_withCursor()
1575 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1576 final int tok = (int) PA.getValue(sq, "changeCount");
1577 assertEquals(1, tok);
1579 // find F given A, check cursor is now at the found position
1580 assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, tok)));
1581 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1582 assertEquals(13, cursor.residuePosition);
1583 assertEquals(10, cursor.columnPosition);
1586 assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, tok)));
1587 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1588 assertEquals(8, cursor.residuePosition);
1589 assertEquals(2, cursor.columnPosition);
1591 // find C given C (no cursor update is done for this case)
1592 assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, tok)));
1593 SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1594 assertSame(cursor2, cursor);
1597 * sequence 'end' beyond end of sequence returns length of sequence
1598 * (for compatibility with pre-cursor code)
1599 * - also verify the cursor is left in a valid state
1601 sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
1602 assertEquals(7, sq.findIndex(10)); // establishes a cursor
1603 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1604 assertEquals(10, cursor.residuePosition);
1605 assertEquals(7, cursor.columnPosition);
1606 assertEquals(sq.getLength(), sq.findIndex(65));
1607 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1608 assertSame(cursor, cursor2); // not updated for this case!
1610 sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
1611 sq.findIndex(10); // establishes a cursor
1612 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1613 assertEquals(sq.getLength(), sq.findIndex(65));
1614 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1615 assertSame(cursor, cursor2); // not updated for this case!
1618 * residue after sequence 'start' but before first residue should return
1619 * zero (for compatibility with pre-cursor code)
1621 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
1622 sq.findIndex(10); // establishes a cursor
1623 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1624 assertEquals(0, sq.findIndex(3));
1625 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1626 assertSame(cursor, cursor2); // not updated for this case!
1628 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
1629 sq.findIndex(10); // establishes a cursor
1630 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1631 assertEquals(0, sq.findIndex(2));
1632 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1633 assertSame(cursor, cursor2); // not updated for this case!
1636 @Test(groups = { "Functional" })
1637 public void testFindPosition_withCursor()
1639 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1640 final int tok = (int) PA.getValue(sq, "changeCount");
1641 assertEquals(1, tok);
1643 // find F pos given A - lastCol gets set in cursor
1645 sq.findPosition(10, new SequenceCursor(sq, 8, 2, tok)));
1646 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1647 PA.getValue(sq, "cursor").toString());
1649 // find A pos given F - first residue column is saved in cursor
1651 sq.findPosition(2, new SequenceCursor(sq, 13, 10, tok)));
1652 assertEquals("test:Pos8:Col2:startCol2:endCol10:tok1",
1653 PA.getValue(sq, "cursor").toString());
1655 // find C pos given C (neither startCol nor endCol is set)
1657 sq.findPosition(6, new SequenceCursor(sq, 10, 6, tok)));
1658 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1",
1659 PA.getValue(sq, "cursor").toString());
1661 // now the grey area - what residue position for a gapped column? JAL-2562
1663 // find 'residue' for column 3 given cursor for D (so working left)
1664 // returns B9; cursor is updated to [B 5]
1665 assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, tok)));
1666 assertEquals("test:Pos9:Col5:startCol0:endCol0:tok1",
1667 PA.getValue(sq, "cursor").toString());
1669 // find 'residue' for column 8 given cursor for D (so working right)
1670 // returns E12; cursor is updated to [D 7]
1672 sq.findPosition(8, new SequenceCursor(sq, 11, 7, tok)));
1673 assertEquals("test:Pos11:Col7:startCol0:endCol0:tok1",
1674 PA.getValue(sq, "cursor").toString());
1676 // find 'residue' for column 12 given cursor for B
1677 // returns 1 more than last residue position; cursor is updated to [F 10]
1678 // lastCol position is saved in cursor
1680 sq.findPosition(12, new SequenceCursor(sq, 9, 5, tok)));
1681 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1682 PA.getValue(sq, "cursor").toString());
1685 * findPosition for column beyond length of sequence
1686 * returns 1 more than the last residue position
1687 * cursor is set to last real residue position [F 10]
1690 sq.findPosition(99, new SequenceCursor(sq, 8, 2, tok)));
1691 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1692 PA.getValue(sq, "cursor").toString());
1695 * and the case without a trailing gap
1697 sq = new Sequence("test/8-13", "-A--BCD-EF");
1698 // first find C from A
1699 assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, tok)));
1700 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1701 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1",
1703 // now 'find' 99 from C
1704 // cursor is set to [F 10] and saved lastCol
1705 assertEquals(14, sq.findPosition(99, cursor));
1706 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1707 PA.getValue(sq, "cursor").toString());
1711 public void testIsValidCursor()
1713 Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
1714 assertFalse(sq.isValidCursor(null));
1717 * cursor is valid if it has valid sequence ref and changeCount token
1718 * and positions within the range of the sequence
1720 int changeCount = (int) PA.getValue(sq, "changeCount");
1721 SequenceCursor cursor = new SequenceCursor(sq, 13, 1, changeCount);
1722 assertTrue(sq.isValidCursor(cursor));
1725 * column position outside [0 - length] is rejected
1727 cursor = new SequenceCursor(sq, 13, -1, changeCount);
1728 assertFalse(sq.isValidCursor(cursor));
1729 cursor = new SequenceCursor(sq, 13, 10, changeCount);
1730 assertFalse(sq.isValidCursor(cursor));
1731 cursor = new SequenceCursor(sq, 7, 8, changeCount);
1732 assertFalse(sq.isValidCursor(cursor));
1733 cursor = new SequenceCursor(sq, 14, 2, changeCount);
1734 assertFalse(sq.isValidCursor(cursor));
1737 * wrong sequence is rejected
1739 cursor = new SequenceCursor(null, 13, 1, changeCount);
1740 assertFalse(sq.isValidCursor(cursor));
1741 cursor = new SequenceCursor(new Sequence("Seq", "abc"), 13, 1,
1743 assertFalse(sq.isValidCursor(cursor));
1746 * wrong token value is rejected
1748 cursor = new SequenceCursor(sq, 13, 1, changeCount + 1);
1749 assertFalse(sq.isValidCursor(cursor));
1750 cursor = new SequenceCursor(sq, 13, 1, changeCount - 1);
1751 assertFalse(sq.isValidCursor(cursor));
1754 @Test(groups = { "Functional" })
1755 public void testFindPosition_withCursorAndEdits()
1757 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1759 // find F pos given A
1760 assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
1761 int token = (int) PA.getValue(sq, "changeCount"); // 0
1762 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1763 assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
1766 * setSequence should invalidate the cursor cached by the sequence
1768 sq.setSequence("-A-BCD-EF---"); // one gap removed
1769 assertEquals(8, sq.getStart()); // sanity check
1770 assertEquals(11, sq.findPosition(5)); // D11
1771 // cursor should now be at [D 6]
1772 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1773 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
1774 assertEquals(0, cursor.lastColumnPosition); // not yet found
1775 assertEquals(13, sq.findPosition(8)); // E13
1776 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1777 assertEquals(9, cursor.lastColumnPosition); // found
1780 * deleteChars should invalidate the cached cursor
1782 sq.deleteChars(2, 5); // delete -BC
1783 assertEquals("-AD-EF---", sq.getSequenceAsString());
1784 assertEquals(8, sq.getStart()); // sanity check
1785 assertEquals(10, sq.findPosition(4)); // E10
1786 // cursor should now be at [E 5]
1787 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1788 assertEquals(new SequenceCursor(sq, 10, 5, ++token), cursor);
1791 * Edit to insert gaps should invalidate the cached cursor
1792 * insert 2 gaps at column[3] to make -AD---EF---
1794 SequenceI[] seqs = new SequenceI[] { sq };
1795 AlignmentI al = new Alignment(seqs);
1796 new EditCommand().appendEdit(Action.INSERT_GAP, seqs, 3, 2, al, true);
1797 assertEquals("-AD---EF---", sq.getSequenceAsString());
1798 assertEquals(10, sq.findPosition(4)); // E10
1799 // cursor should now be at [D 3]
1800 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1801 assertEquals(new SequenceCursor(sq, 9, 3, ++token), cursor);
1804 * insertCharAt should invalidate the cached cursor
1805 * insert CC at column[4] to make -AD-CC--EF---
1807 sq.insertCharAt(4, 2, 'C');
1808 assertEquals("-AD-CC--EF---", sq.getSequenceAsString());
1809 assertEquals(13, sq.findPosition(9)); // F13
1810 // cursor should now be at [F 10]
1811 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1812 assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
1815 * changing sequence start should invalidate cursor
1817 sq = new Sequence("test/8-13", "-A--BCD-EF--");
1818 assertEquals(8, sq.getStart());
1819 assertEquals(9, sq.findPosition(4)); // B(9)
1821 assertEquals(8, sq.findPosition(4)); // is now B(8)
1823 assertEquals(11, sq.findPosition(4)); // is now B(11)
1826 @Test(groups = { "Functional" })
1827 public void testGetSequence()
1829 String seqstring = "-A--BCD-EF--";
1830 Sequence sq = new Sequence("test/8-13", seqstring);
1831 sq.createDatasetSequence();
1832 assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray()));
1833 assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(),
1834 "ABCDEF".toCharArray()));
1836 // verify a copy of the sequence array is returned
1837 char[] theSeq = (char[]) PA.getValue(sq, "sequence");
1838 assertNotSame(theSeq, sq.getSequence());
1839 theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence");
1840 assertNotSame(theSeq, sq.getDatasetSequence().getSequence());
1843 @Test(groups = { "Functional" })
1844 public void testReplace()
1846 String seqstring = "-A--BCD-EF--";
1847 SequenceI sq = new Sequence("test/8-13", seqstring);
1848 // changeCount is incremented for setStart
1849 assertEquals(1, PA.getValue(sq, "changeCount"));
1851 assertEquals(0, sq.replace('A', 'A')); // same char
1852 assertEquals(seqstring, sq.getSequenceAsString());
1853 assertEquals(1, PA.getValue(sq, "changeCount"));
1855 assertEquals(0, sq.replace('X', 'Y')); // not there
1856 assertEquals(seqstring, sq.getSequenceAsString());
1857 assertEquals(1, PA.getValue(sq, "changeCount"));
1859 assertEquals(1, sq.replace('A', 'K'));
1860 assertEquals("-K--BCD-EF--", sq.getSequenceAsString());
1861 assertEquals(2, PA.getValue(sq, "changeCount"));
1863 assertEquals(6, sq.replace('-', '.'));
1864 assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
1865 assertEquals(3, PA.getValue(sq, "changeCount"));
1868 @Test(groups = { "Functional" })
1869 public void testGapBitset()
1871 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
1872 BitSet bs = sq.gapBitset();
1873 BitSet expected = new BitSet();
1877 expected.set(11, 13);
1879 assertTrue(bs.equals(expected));
1883 public void testFindFeatures_largeEndPos()
1886 * imitate a PDB sequence where end is larger than end position
1888 SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
1889 sq.createDatasetSequence();
1891 assertTrue(sq.findFeatures(1, 9).isEmpty());
1892 // should be no array bounds exception - JAL-2772
1893 assertTrue(sq.findFeatures(1, 15).isEmpty());
1895 // add feature on BCD
1896 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
1898 sq.addSequenceFeature(sfBCD);
1900 // no features in columns 1-2 (-A)
1901 List<SequenceFeature> found = sq.findFeatures(1, 2);
1902 assertTrue(found.isEmpty());
1904 // columns 1-6 (-ABC--) includes BCD
1905 found = sq.findFeatures(1, 6);
1906 assertEquals(1, found.size());
1907 assertTrue(found.contains(sfBCD));
1909 // columns 10-11 (--) should find nothing
1910 found = sq.findFeatures(10, 11);
1911 assertEquals(0, found.size());
1914 @Test(groups = { "Functional" })
1915 public void testSetName()
1917 SequenceI sq = new Sequence("test", "-ABC---DE-F--");
1918 assertEquals("test", sq.getName());
1919 assertEquals(1, sq.getStart());
1920 assertEquals(6, sq.getEnd());
1922 sq.setName("testing");
1923 assertEquals("testing", sq.getName());
1925 sq.setName("test/8-10");
1926 assertEquals("test", sq.getName());
1927 assertEquals(8, sq.getStart());
1928 assertEquals(13, sq.getEnd()); // note end is recomputed
1930 sq.setName("testing/7-99");
1931 assertEquals("testing", sq.getName());
1932 assertEquals(7, sq.getStart());
1933 assertEquals(99, sq.getEnd()); // end may be beyond physical end
1936 assertEquals("", sq.getName());
1937 assertEquals(2, sq.getStart());
1938 assertEquals(7, sq.getEnd());
1940 sq.setName("test/"); // invalid
1941 assertEquals("test/", sq.getName());
1942 assertEquals(2, sq.getStart());
1943 assertEquals(7, sq.getEnd());
1945 sq.setName("test/6-13/7-99");
1946 assertEquals("test/6-13", sq.getName());
1947 assertEquals(7, sq.getStart());
1948 assertEquals(99, sq.getEnd());
1950 sq.setName("test/0-5"); // 0 is invalid - ignored
1951 assertEquals("test/0-5", sq.getName());
1952 assertEquals(7, sq.getStart());
1953 assertEquals(99, sq.getEnd());
1955 sq.setName("test/a-5"); // a is invalid - ignored
1956 assertEquals("test/a-5", sq.getName());
1957 assertEquals(7, sq.getStart());
1958 assertEquals(99, sq.getEnd());
1960 sq.setName("test/6-5"); // start > end is invalid - ignored
1961 assertEquals("test/6-5", sq.getName());
1962 assertEquals(7, sq.getStart());
1963 assertEquals(99, sq.getEnd());
1965 sq.setName("test/5"); // invalid - ignored
1966 assertEquals("test/5", sq.getName());
1967 assertEquals(7, sq.getStart());
1968 assertEquals(99, sq.getEnd());
1970 sq.setName("test/-5"); // invalid - ignored
1971 assertEquals("test/-5", sq.getName());
1972 assertEquals(7, sq.getStart());
1973 assertEquals(99, sq.getEnd());
1975 sq.setName("test/5-"); // invalid - ignored
1976 assertEquals("test/5-", sq.getName());
1977 assertEquals(7, sq.getStart());
1978 assertEquals(99, sq.getEnd());
1980 sq.setName("test/5-6-7"); // invalid - ignored
1981 assertEquals("test/5-6-7", sq.getName());
1982 assertEquals(7, sq.getStart());
1983 assertEquals(99, sq.getEnd());
1985 sq.setName(null); // invalid, gets converted to space
1986 assertEquals("", sq.getName());
1987 assertEquals(7, sq.getStart());
1988 assertEquals(99, sq.getEnd());
1991 @Test(groups = { "Functional" })
1992 public void testCheckValidRange()
1994 Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
1995 assertEquals(7, sq.getStart());
1996 assertEquals(12, sq.getEnd());
1999 * checkValidRange ensures end is at least the last residue position
2001 PA.setValue(sq, "end", 2);
2002 sq.checkValidRange();
2003 assertEquals(12, sq.getEnd());
2006 * end may be beyond the last residue position
2008 PA.setValue(sq, "end", 22);
2009 sq.checkValidRange();
2010 assertEquals(22, sq.getEnd());
2013 @Test(groups = { "Functional" })
2014 public void testDeleteChars_withGaps()
2019 SequenceI sq = new Sequence("test/8-10", "A-B-C");
2020 sq.createDatasetSequence();
2021 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2022 sq.deleteChars(1, 2); // delete first gap
2023 assertEquals("AB-C", sq.getSequenceAsString());
2024 assertEquals(8, sq.getStart());
2025 assertEquals(10, sq.getEnd());
2026 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2029 * delete gaps and residues at start (no new dataset sequence)
2031 sq = new Sequence("test/8-10", "A-B-C");
2032 sq.createDatasetSequence();
2033 sq.deleteChars(0, 3); // delete A-B
2034 assertEquals("-C", sq.getSequenceAsString());
2035 assertEquals(10, sq.getStart());
2036 assertEquals(10, sq.getEnd());
2037 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2040 * delete gaps and residues at end (no new dataset sequence)
2042 sq = new Sequence("test/8-10", "A-B-C");
2043 sq.createDatasetSequence();
2044 sq.deleteChars(2, 5); // delete B-C
2045 assertEquals("A-", sq.getSequenceAsString());
2046 assertEquals(8, sq.getStart());
2047 assertEquals(8, sq.getEnd());
2048 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2051 * delete gaps and residues internally (new dataset sequence)
2052 * first delete from gap to residue
2054 sq = new Sequence("test/8-10", "A-B-C");
2055 sq.createDatasetSequence();
2056 sq.deleteChars(1, 3); // delete -B
2057 assertEquals("A-C", sq.getSequenceAsString());
2058 assertEquals(8, sq.getStart());
2059 assertEquals(9, sq.getEnd());
2060 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2061 assertEquals(8, sq.getDatasetSequence().getStart());
2062 assertEquals(9, sq.getDatasetSequence().getEnd());
2065 * internal delete from gap to gap
2067 sq = new Sequence("test/8-10", "A-B-C");
2068 sq.createDatasetSequence();
2069 sq.deleteChars(1, 4); // delete -B-
2070 assertEquals("AC", sq.getSequenceAsString());
2071 assertEquals(8, sq.getStart());
2072 assertEquals(9, sq.getEnd());
2073 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2074 assertEquals(8, sq.getDatasetSequence().getStart());
2075 assertEquals(9, sq.getDatasetSequence().getEnd());
2078 * internal delete from residue to residue
2080 sq = new Sequence("test/8-10", "A-B-C");
2081 sq.createDatasetSequence();
2082 sq.deleteChars(2, 3); // delete B
2083 assertEquals("A--C", sq.getSequenceAsString());
2084 assertEquals(8, sq.getStart());
2085 assertEquals(9, sq.getEnd());
2086 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2087 assertEquals(8, sq.getDatasetSequence().getStart());
2088 assertEquals(9, sq.getDatasetSequence().getEnd());
2092 * Test the code used to locate the reference sequence ruler origin
2094 @Test(groups = { "Functional" })
2095 public void testLocateVisibleStartofSequence()
2097 // create random alignment
2098 AlignmentGenerator gen = new AlignmentGenerator(false);
2099 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
2101 HiddenColumns cs = al.getHiddenColumns();
2102 ColumnSelection colsel = new ColumnSelection();
2104 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
2105 assertEquals(2, seq.findIndex(seq.getStart()));
2107 // no hidden columns
2108 assertEquals(seq.findIndex(seq.getStart()) - 1,
2109 seq.firstResidueOutsideIterator(cs.iterator()));
2111 // hidden column on gap after end of sequence - should not affect bounds
2112 colsel.hideSelectedColumns(13, al.getHiddenColumns());
2113 assertEquals(seq.findIndex(seq.getStart()) - 1,
2114 seq.firstResidueOutsideIterator(cs.iterator()));
2116 cs.revealAllHiddenColumns(colsel);
2117 // hidden column on gap before beginning of sequence - should vis bounds by
2119 colsel.hideSelectedColumns(0, al.getHiddenColumns());
2120 assertEquals(seq.findIndex(seq.getStart()) - 2,
2121 cs.absoluteToVisibleColumn(
2122 seq.firstResidueOutsideIterator(cs.iterator())));
2124 cs.revealAllHiddenColumns(colsel);
2125 // hide columns around most of sequence - leave one residue remaining
2126 cs.hideColumns(1, 3);
2127 cs.hideColumns(6, 11);
2129 Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
2131 assertEquals("-D", seq.getSequenceStringFromIterator(it));
2132 // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
2135 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2136 cs.revealAllHiddenColumns(colsel);
2138 // hide whole sequence - should just get location of hidden region
2139 // containing sequence
2140 cs.hideColumns(1, 11);
2141 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2143 cs.revealAllHiddenColumns(colsel);
2144 cs.hideColumns(0, 15);
2145 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2147 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
2149 cs.revealAllHiddenColumns(colsel);
2150 cs.hideColumns(7, 17);
2151 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2153 cs.revealAllHiddenColumns(colsel);
2154 cs.hideColumns(3, 17);
2155 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2157 cs.revealAllHiddenColumns(colsel);
2158 cs.hideColumns(3, 19);
2159 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2161 cs.revealAllHiddenColumns(colsel);
2162 cs.hideColumns(0, 0);
2163 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2165 cs.revealAllHiddenColumns(colsel);
2166 cs.hideColumns(0, 1);
2167 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2169 cs.revealAllHiddenColumns(colsel);
2170 cs.hideColumns(0, 2);
2171 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2173 cs.revealAllHiddenColumns(colsel);
2174 cs.hideColumns(1, 1);
2175 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2177 cs.revealAllHiddenColumns(colsel);
2178 cs.hideColumns(1, 2);
2179 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2181 cs.revealAllHiddenColumns(colsel);
2182 cs.hideColumns(1, 3);
2183 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2185 cs.revealAllHiddenColumns(colsel);
2186 cs.hideColumns(0, 2);
2187 cs.hideColumns(5, 6);
2188 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2190 cs.revealAllHiddenColumns(colsel);
2191 cs.hideColumns(0, 2);
2192 cs.hideColumns(5, 6);
2193 cs.hideColumns(9, 10);
2194 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2196 cs.revealAllHiddenColumns(colsel);
2197 cs.hideColumns(0, 2);
2198 cs.hideColumns(7, 11);
2199 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2201 cs.revealAllHiddenColumns(colsel);
2202 cs.hideColumns(2, 4);
2203 cs.hideColumns(7, 11);
2204 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2206 cs.revealAllHiddenColumns(colsel);
2207 cs.hideColumns(2, 4);
2208 cs.hideColumns(7, 12);
2209 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2211 cs.revealAllHiddenColumns(colsel);
2212 cs.hideColumns(1, 11);
2213 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2215 cs.revealAllHiddenColumns(colsel);
2216 cs.hideColumns(0, 12);
2217 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2219 cs.revealAllHiddenColumns(colsel);
2220 cs.hideColumns(0, 4);
2221 cs.hideColumns(6, 12);
2222 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2224 cs.revealAllHiddenColumns(colsel);
2225 cs.hideColumns(0, 1);
2226 cs.hideColumns(3, 12);
2227 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2229 cs.revealAllHiddenColumns(colsel);
2230 cs.hideColumns(3, 14);
2231 cs.hideColumns(17, 19);
2232 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2234 cs.revealAllHiddenColumns(colsel);
2235 cs.hideColumns(3, 7);
2236 cs.hideColumns(9, 14);
2237 cs.hideColumns(17, 19);
2238 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2240 cs.revealAllHiddenColumns(colsel);
2241 cs.hideColumns(0, 1);
2242 cs.hideColumns(3, 4);
2243 cs.hideColumns(6, 8);
2244 cs.hideColumns(10, 12);
2245 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2248 @Test(groups= {"Functional"})
2249 public void testTransferAnnotation() {
2250 Sequence origSeq = new Sequence("MYSEQ","THISISASEQ");
2251 Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
2252 origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
2253 toSeq.transferAnnotation(origSeq, null);
2254 assertTrue(toSeq.getDBRefs().size()==1);
2256 assertTrue(toSeq.getDBRefs().get(0).isCanonical());
2258 // check for promotion of non-canonical
2259 // to canonical (e.g. fetch-db-refs on a jalview project pre 2.11.2)
2260 toSeq.setDBRefs(null);
2261 toSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, false));
2262 toSeq.transferAnnotation(origSeq, null);
2263 assertTrue(toSeq.getDBRefs().size()==1);
2265 assertTrue("Promotion of non-canonical DBRefEntry failed",toSeq.getDBRefs().get(0).isCanonical());