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.assertNotSame;
27 import static org.testng.AssertJUnit.assertNull;
28 import static org.testng.AssertJUnit.assertSame;
29 import static org.testng.AssertJUnit.assertTrue;
31 import jalview.analysis.AlignmentGenerator;
32 import jalview.commands.EditCommand;
33 import jalview.commands.EditCommand.Action;
34 import jalview.datamodel.PDBEntry.Type;
35 import jalview.gui.JvOptionPane;
36 import jalview.util.MapList;
37 import jalview.ws.params.InvalidArgumentException;
40 import java.util.ArrayList;
41 import java.util.Arrays;
42 import java.util.BitSet;
43 import java.util.Iterator;
44 import java.util.List;
45 import java.util.Vector;
47 import org.testng.Assert;
48 import org.testng.annotations.BeforeClass;
49 import org.testng.annotations.BeforeMethod;
50 import org.testng.annotations.Test;
52 import junit.extensions.PA;
54 public class SequenceTest
56 @BeforeClass(alwaysRun = true)
57 public void setUpJvOptionPane()
59 JvOptionPane.setInteractiveMode(false);
60 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
65 @BeforeMethod(alwaysRun = true)
68 seq = new Sequence("FER1", "AKPNGVL");
71 @Test(groups = { "Functional" })
72 public void testInsertGapsAndGapmaps()
74 SequenceI aseq = seq.deriveSequence();
75 aseq.insertCharAt(2, 3, '-');
76 aseq.insertCharAt(6, 3, '-');
77 assertEquals("Gap insertions not correct", "AK---P---NGVL",
78 aseq.getSequenceAsString());
79 List<int[]> gapInt = aseq.getInsertions();
80 assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
81 assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
82 assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
83 assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
85 BitSet gapfield = aseq.getInsertionsAsBits();
86 BitSet expectedgaps = new BitSet();
87 expectedgaps.set(2, 5);
88 expectedgaps.set(6, 9);
90 assertEquals(6, expectedgaps.cardinality());
92 assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
93 6, gapfield.cardinality());
95 assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
98 @Test(groups = ("Functional"))
99 public void testIsProtein()
102 assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
104 assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
106 SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
107 assertFalse(sq.isProtein());
108 // change sequence, should trigger an update of cached result
109 sq.setSequence("ASDFASDFADSF");
110 assertTrue(sq.isProtein());
113 @Test(groups = ("Functional"))
114 public void testIsProteinWithXorNAmbiguityCodes()
116 // test Protein with N - poly asparagine
117 assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
118 assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
119 // test Protein with X
120 assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
122 assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
124 assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
126 assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
127 assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
130 @Test(groups = { "Functional" })
131 public void testGetAnnotation()
133 // initial state returns null not an empty array
134 assertNull(seq.getAnnotation());
135 AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
137 AlignmentAnnotation[] anns = seq.getAnnotation();
138 assertEquals(1, anns.length);
139 assertSame(ann, anns[0]);
141 // removing all annotations reverts array to null
142 seq.removeAlignmentAnnotation(ann);
143 assertNull(seq.getAnnotation());
146 @Test(groups = { "Functional" })
147 public void testGetAnnotation_forLabel()
149 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
151 addAnnotation("label2", "desc2", "calcId2", 1f);
152 AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
154 AlignmentAnnotation[] anns = seq.getAnnotation("label1");
155 assertEquals(2, anns.length);
156 assertSame(ann1, anns[0]);
157 assertSame(ann3, anns[1]);
160 private AlignmentAnnotation addAnnotation(String label,
161 String description, String calcId, float value)
163 final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
165 annotation.setCalcId(calcId);
166 seq.addAlignmentAnnotation(annotation);
170 @Test(groups = { "Functional" })
171 public void testGetAlignmentAnnotations_forCalcIdAndLabel()
173 addAnnotation("label1", "desc1", "calcId1", 1f);
174 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
176 addAnnotation("label2", "desc3", "calcId3", 1f);
177 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
179 addAnnotation("label5", "desc3", null, 1f);
180 addAnnotation(null, "desc3", "calcId3", 1f);
182 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
184 assertEquals(2, anns.size());
185 assertSame(ann2, anns.get(0));
186 assertSame(ann4, anns.get(1));
188 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
189 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
190 assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
191 assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
192 assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
196 * Tests for addAlignmentAnnotation. Note this method has the side-effect of
197 * setting the sequenceRef on the annotation. Adding the same annotation twice
200 @Test(groups = { "Functional" })
201 public void testAddAlignmentAnnotation()
203 assertNull(seq.getAnnotation());
204 final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
206 assertNull(annotation.sequenceRef);
207 seq.addAlignmentAnnotation(annotation);
208 assertSame(seq, annotation.sequenceRef);
209 AlignmentAnnotation[] anns = seq.getAnnotation();
210 assertEquals(1, anns.length);
211 assertSame(annotation, anns[0]);
213 // re-adding does nothing
214 seq.addAlignmentAnnotation(annotation);
215 anns = seq.getAnnotation();
216 assertEquals(1, anns.length);
217 assertSame(annotation, anns[0]);
219 // an identical but different annotation can be added
220 final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
222 seq.addAlignmentAnnotation(annotation2);
223 anns = seq.getAnnotation();
224 assertEquals(2, anns.length);
225 assertSame(annotation, anns[0]);
226 assertSame(annotation2, anns[1]);
229 @Test(groups = { "Functional" })
230 public void testGetStartGetEnd()
232 SequenceI sq = new Sequence("test", "ABCDEF");
233 assertEquals(1, sq.getStart());
234 assertEquals(6, sq.getEnd());
236 sq = new Sequence("test", "--AB-C-DEF--");
237 assertEquals(1, sq.getStart());
238 assertEquals(6, sq.getEnd());
240 sq = new Sequence("test", "----");
241 assertEquals(1, sq.getStart());
242 assertEquals(0, sq.getEnd()); // ??
246 * Tests for the method that returns an alignment column position (base 1) for
247 * a given sequence position (base 1).
249 @Test(groups = { "Functional" })
250 public void testFindIndex()
253 * call sequenceChanged() after each test to invalidate any cursor,
254 * forcing the 1-arg findIndex to be executed
256 SequenceI sq = new Sequence("test", "ABCDEF");
257 assertEquals(0, sq.findIndex(0));
258 sq.sequenceChanged();
259 assertEquals(1, sq.findIndex(1));
260 sq.sequenceChanged();
261 assertEquals(5, sq.findIndex(5));
262 sq.sequenceChanged();
263 assertEquals(6, sq.findIndex(6));
264 sq.sequenceChanged();
265 assertEquals(6, sq.findIndex(9));
267 final String aligned = "-A--B-C-D-E-F--";
268 assertEquals(15, aligned.length());
269 sq = new Sequence("test/8-13", aligned);
270 assertEquals(2, sq.findIndex(8));
271 sq.sequenceChanged();
272 assertEquals(5, sq.findIndex(9));
273 sq.sequenceChanged();
274 assertEquals(7, sq.findIndex(10));
276 // before start returns 0
277 sq.sequenceChanged();
278 assertEquals(0, sq.findIndex(0));
279 sq.sequenceChanged();
280 assertEquals(0, sq.findIndex(-1));
282 // beyond end returns last residue column
283 sq.sequenceChanged();
284 assertEquals(13, sq.findIndex(99));
287 * residue before sequence 'end' but beyond end of sequence returns
288 * length of sequence (last column) (rightly or wrongly!)
290 sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case
291 assertEquals(6, sq.getLength());
292 sq.sequenceChanged();
293 assertEquals(sq.getLength(), sq.findIndex(14));
294 sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case
295 sq.sequenceChanged();
296 assertEquals(sq.getLength(), sq.findIndex(65));
299 * residue after sequence 'start' but before first residue returns
300 * zero (before first column) (rightly or wrongly!)
302 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
303 sq.sequenceChanged();
304 assertEquals(0, sq.findIndex(3));
305 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
306 sq.sequenceChanged();
307 assertEquals(0, sq.findIndex(2));
310 @Test(groups = { "Functional" })
311 public void testFindPositions()
313 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
318 assertNull(sq.findPositions(6, 5));
319 assertNull(sq.findPositions(0, 5));
320 assertNull(sq.findPositions(-1, 5));
325 assertNull(sq.findPositions(1, 1)); // 1-based columns
326 assertNull(sq.findPositions(5, 5));
327 assertNull(sq.findPositions(5, 6));
328 assertNull(sq.findPositions(5, 7));
331 * all ungapped ranges
333 assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
334 assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
335 assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
336 assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
339 * gap to ungapped range
341 assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
342 assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
345 * ungapped to gapped range
347 assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
348 assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
351 * ungapped to ungapped enclosing gaps
353 assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
354 assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
357 * gapped to gapped enclosing ungapped
359 assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
360 assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
361 assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
362 assertEquals(new Range(8, 13), sq.findPositions(1, 99));
366 * Tests for the method that returns a dataset sequence position (start..) for
367 * an aligned column position (base 0).
369 @Test(groups = { "Functional" })
370 public void testFindPosition()
373 * call sequenceChanged() after each test to invalidate any cursor,
374 * forcing the 1-arg findPosition to be executed
376 SequenceI sq = new Sequence("test/8-13", "ABCDEF");
377 assertEquals(8, sq.findPosition(0));
378 // Sequence should now hold a cursor at [8, 0]
379 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1",
380 PA.getValue(sq, "cursor").toString());
381 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
382 int token = (int) PA.getValue(sq, "changeCount");
383 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
385 sq.sequenceChanged();
388 * find F13 at column offset 5, cursor should update to [13, 6]
389 * endColumn is found and saved in cursor
391 assertEquals(13, sq.findPosition(5));
392 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
393 assertEquals(++token, (int) PA.getValue(sq, "changeCount"));
394 assertEquals(new SequenceCursor(sq, 13, 6, token), cursor);
395 assertEquals("test:Pos13:Col6:startCol1:endCol6:tok2",
396 PA.getValue(sq, "cursor").toString());
398 // assertEquals(-1, seq.findPosition(6)); // fails
400 sq = new Sequence("test/8-11", "AB-C-D--");
401 token = (int) PA.getValue(sq, "changeCount"); // 1 for setStart
402 assertEquals(8, sq.findPosition(0));
403 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
404 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
405 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1",
406 PA.getValue(sq, "cursor").toString());
408 sq.sequenceChanged();
409 assertEquals(9, sq.findPosition(1));
410 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
411 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
412 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2",
413 PA.getValue(sq, "cursor").toString());
415 sq.sequenceChanged();
416 // gap position 'finds' residue to the right (not the left as per javadoc)
417 // cursor is set to the last residue position found [B 2]
418 assertEquals(10, sq.findPosition(2));
419 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
420 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
421 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok3",
422 PA.getValue(sq, "cursor").toString());
424 sq.sequenceChanged();
425 assertEquals(10, sq.findPosition(3));
426 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
427 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
428 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4",
429 PA.getValue(sq, "cursor").toString());
431 sq.sequenceChanged();
432 // column[4] is the gap after C - returns D11
433 // cursor is set to [C 4]
434 assertEquals(11, sq.findPosition(4));
435 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
436 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
437 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok5",
438 PA.getValue(sq, "cursor").toString());
440 sq.sequenceChanged();
441 assertEquals(11, sq.findPosition(5)); // D
442 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
443 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
444 // lastCol has been found and saved in the cursor
445 assertEquals("test:Pos11:Col6:startCol1:endCol6:tok6",
446 PA.getValue(sq, "cursor").toString());
448 sq.sequenceChanged();
449 // returns 1 more than sequence length if off the end ?!?
450 assertEquals(12, sq.findPosition(6));
452 sq.sequenceChanged();
453 assertEquals(12, sq.findPosition(7));
456 * first findPosition should also set firstResCol in cursor
458 sq = new Sequence("test/8-13", "--AB-C-DEF--");
459 assertEquals(8, sq.findPosition(0));
460 assertNull(PA.getValue(sq, "cursor"));
461 assertEquals(1, PA.getValue(sq, "changeCount"));
463 sq.sequenceChanged();
464 assertEquals(8, sq.findPosition(1));
465 assertNull(PA.getValue(sq, "cursor"));
467 sq.sequenceChanged();
468 assertEquals(8, sq.findPosition(2));
469 assertEquals("test:Pos8:Col3:startCol3:endCol0:tok3",
470 PA.getValue(sq, "cursor").toString());
472 sq.sequenceChanged();
473 assertEquals(9, sq.findPosition(3));
474 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4",
475 PA.getValue(sq, "cursor").toString());
477 sq.sequenceChanged();
478 // column[4] is a gap, returns next residue pos (C10)
479 // cursor is set to last residue found [B]
480 assertEquals(10, sq.findPosition(4));
481 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok5",
482 PA.getValue(sq, "cursor").toString());
484 sq.sequenceChanged();
485 assertEquals(10, sq.findPosition(5));
486 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6",
487 PA.getValue(sq, "cursor").toString());
489 sq.sequenceChanged();
490 // column[6] is a gap, returns next residue pos (D11)
491 // cursor is set to last residue found [C]
492 assertEquals(11, sq.findPosition(6));
493 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok7",
494 PA.getValue(sq, "cursor").toString());
496 sq.sequenceChanged();
497 assertEquals(11, sq.findPosition(7));
498 assertEquals("test:Pos11:Col8:startCol3:endCol0:tok8",
499 PA.getValue(sq, "cursor").toString());
501 sq.sequenceChanged();
502 assertEquals(12, sq.findPosition(8));
503 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok9",
504 PA.getValue(sq, "cursor").toString());
507 * when the last residue column is found, it is set in the cursor
509 sq.sequenceChanged();
510 assertEquals(13, sq.findPosition(9));
511 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10",
512 PA.getValue(sq, "cursor").toString());
514 sq.sequenceChanged();
515 assertEquals(14, sq.findPosition(10));
516 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11",
517 PA.getValue(sq, "cursor").toString());
520 * findPosition for column beyond sequence length
521 * returns 1 more than last residue position
523 sq.sequenceChanged();
524 assertEquals(14, sq.findPosition(11));
525 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12",
526 PA.getValue(sq, "cursor").toString());
528 sq.sequenceChanged();
529 assertEquals(14, sq.findPosition(99));
530 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok13",
531 PA.getValue(sq, "cursor").toString());
534 * gapped sequence ending in non-gap
536 sq = new Sequence("test/8-13", "--AB-C-DEF");
537 assertEquals(13, sq.findPosition(9));
538 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1",
539 PA.getValue(sq, "cursor").toString());
540 sq.sequenceChanged();
541 assertEquals(12, sq.findPosition(8)); // E12
542 // sequenceChanged() invalidates cursor.lastResidueColumn
543 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
544 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok2",
546 // findPosition with cursor accepts base 1 column values
547 assertEquals(13, ((Sequence) sq).findPosition(10, cursor));
548 assertEquals(13, sq.findPosition(9)); // F13
549 // lastResidueColumn has now been found and saved in cursor
550 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok2",
551 PA.getValue(sq, "cursor").toString());
554 @Test(groups = { "Functional" })
555 public void testDeleteChars()
560 SequenceI sq = new Sequence("test", "ABCDEF");
561 assertNull(PA.getValue(sq, "datasetSequence"));
562 assertEquals(1, sq.getStart());
563 assertEquals(6, sq.getEnd());
564 sq.deleteChars(2, 3);
565 assertEquals("ABDEF", sq.getSequenceAsString());
566 assertEquals(1, sq.getStart());
567 assertEquals(5, sq.getEnd());
568 assertNull(PA.getValue(sq, "datasetSequence"));
573 sq = new Sequence("test", "ABCDEF");
574 sq.deleteChars(0, 2);
575 assertEquals("CDEF", sq.getSequenceAsString());
576 assertEquals(3, sq.getStart());
577 assertEquals(6, sq.getEnd());
578 assertNull(PA.getValue(sq, "datasetSequence"));
580 sq = new Sequence("test", "ABCDE");
581 sq.deleteChars(0, 3);
582 assertEquals("DE", sq.getSequenceAsString());
583 assertEquals(4, sq.getStart());
584 assertEquals(5, sq.getEnd());
585 assertNull(PA.getValue(sq, "datasetSequence"));
590 sq = new Sequence("test", "ABCDEF");
591 sq.deleteChars(4, 6);
592 assertEquals("ABCD", sq.getSequenceAsString());
593 assertEquals(1, sq.getStart());
594 assertEquals(4, sq.getEnd());
595 assertNull(PA.getValue(sq, "datasetSequence"));
598 * delete more positions than there are
600 sq = new Sequence("test/8-11", "ABCD");
601 sq.deleteChars(0, 99);
602 assertEquals("", sq.getSequenceAsString());
603 assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
604 assertEquals(11, sq.getEnd());
606 sq = new Sequence("test/8-11", "----");
607 sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
608 assertEquals("", sq.getSequenceAsString());
609 assertEquals(8, sq.getStart());
610 assertEquals(11, sq.getEnd());
613 @Test(groups = { "Functional" })
614 public void testDeleteChars_withDbRefsAndFeatures()
617 * internal delete - new dataset sequence created
618 * gets a copy of any dbrefs
620 SequenceI sq = new Sequence("test", "ABCDEF");
621 sq.createDatasetSequence();
622 DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
624 Object ds = PA.getValue(sq, "datasetSequence");
626 assertEquals(1, sq.getStart());
627 assertEquals(6, sq.getEnd());
628 sq.deleteChars(2, 3);
629 assertEquals("ABDEF", sq.getSequenceAsString());
630 assertEquals(1, sq.getStart());
631 assertEquals(5, sq.getEnd());
632 Object newDs = PA.getValue(sq, "datasetSequence");
633 assertNotNull(newDs);
634 assertNotSame(ds, newDs);
635 assertNotNull(sq.getDBRefs());
636 assertEquals(1, sq.getDBRefs().size());
637 assertNotSame(dbr1, sq.getDBRefs().get(0));
638 assertEquals(dbr1, sq.getDBRefs().get(0));
641 * internal delete with sequence features
642 * (failure case for JAL-2541)
644 sq = new Sequence("test", "ABCDEF");
645 sq.createDatasetSequence();
646 SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
648 sq.addSequenceFeature(sf1);
649 ds = PA.getValue(sq, "datasetSequence");
651 assertEquals(1, sq.getStart());
652 assertEquals(6, sq.getEnd());
653 sq.deleteChars(2, 4);
654 assertEquals("ABEF", sq.getSequenceAsString());
655 assertEquals(1, sq.getStart());
656 assertEquals(4, sq.getEnd());
657 newDs = PA.getValue(sq, "datasetSequence");
658 assertNotNull(newDs);
659 assertNotSame(ds, newDs);
660 List<SequenceFeature> sfs = sq.getSequenceFeatures();
661 assertEquals(1, sfs.size());
662 assertNotSame(sf1, sfs.get(0));
663 assertEquals(sf1, sfs.get(0));
666 * delete at start - no new dataset sequence created
667 * any sequence features remain as before
669 sq = new Sequence("test", "ABCDEF");
670 sq.createDatasetSequence();
671 ds = PA.getValue(sq, "datasetSequence");
672 sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
673 sq.addSequenceFeature(sf1);
674 sq.deleteChars(0, 2);
675 assertEquals("CDEF", sq.getSequenceAsString());
676 assertEquals(3, sq.getStart());
677 assertEquals(6, sq.getEnd());
678 assertSame(ds, PA.getValue(sq, "datasetSequence"));
679 sfs = sq.getSequenceFeatures();
681 assertEquals(1, sfs.size());
682 assertSame(sf1, sfs.get(0));
685 * delete at end - no new dataset sequence created
686 * any dbrefs remain as before
688 sq = new Sequence("test", "ABCDEF");
689 sq.createDatasetSequence();
690 ds = PA.getValue(sq, "datasetSequence");
691 dbr1 = new DBRefEntry("Uniprot", "0", "a123");
693 sq.deleteChars(4, 6);
694 assertEquals("ABCD", sq.getSequenceAsString());
695 assertEquals(1, sq.getStart());
696 assertEquals(4, sq.getEnd());
697 assertSame(ds, PA.getValue(sq, "datasetSequence"));
698 assertNotNull(sq.getDBRefs());
699 assertEquals(1, sq.getDBRefs().size());
700 assertSame(dbr1, sq.getDBRefs().get(0));
703 @Test(groups = { "Functional" })
704 public void testInsertCharAt()
706 // non-static methods:
707 SequenceI sq = new Sequence("test", "ABCDEF");
708 sq.insertCharAt(0, 'z');
709 assertEquals("zABCDEF", sq.getSequenceAsString());
710 sq.insertCharAt(2, 2, 'x');
711 assertEquals("zAxxBCDEF", sq.getSequenceAsString());
713 // for static method see StringUtilsTest
717 * Test the method that returns an array of aligned sequence positions where
718 * the array index is the data sequence position (both base 0).
720 @Test(groups = { "Functional" })
721 public void testGapMap()
723 SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
724 sq.createDatasetSequence();
725 assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
729 * Test the method that gets sequence features, either from the sequence or
732 @Test(groups = { "Functional" })
733 public void testGetSequenceFeatures()
735 SequenceI sq = new Sequence("test", "GATCAT");
736 sq.createDatasetSequence();
738 assertTrue(sq.getSequenceFeatures().isEmpty());
741 * SequenceFeature on sequence
743 SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
744 sq.addSequenceFeature(sf);
745 List<SequenceFeature> sfs = sq.getSequenceFeatures();
746 assertEquals(1, sfs.size());
747 assertSame(sf, sfs.get(0));
750 * SequenceFeature on sequence and dataset sequence; returns that on
753 * Note JAL-2046: spurious: we have no use case for this at the moment.
754 * This test also buggy - as sf2.equals(sf), no new feature is added
756 SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
758 sq.getDatasetSequence().addSequenceFeature(sf2);
759 sfs = sq.getSequenceFeatures();
760 assertEquals(1, sfs.size());
761 assertSame(sf, sfs.get(0));
764 * SequenceFeature on dataset sequence only
765 * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
767 sq.setSequenceFeatures(null);
768 assertTrue(sq.getDatasetSequence().getSequenceFeatures().isEmpty());
771 * Corrupt case - no SequenceFeature, dataset's dataset is the original
772 * sequence. Test shows no infinite loop results.
774 sq.getDatasetSequence().setSequenceFeatures(null);
776 * is there a usecase for this ? setDatasetSequence should throw an error if
777 * this actually occurs.
781 sq.getDatasetSequence().setDatasetSequence(sq); // loop!
782 Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
783 } catch (IllegalArgumentException e)
785 // TODO Jalview error/exception class for raising implementation errors
786 assertTrue(e.getMessage().toLowerCase()
787 .contains("implementation error"));
789 assertTrue(sq.getSequenceFeatures().isEmpty());
793 * Test the method that returns an array, indexed by sequence position, whose
794 * entries are the residue positions at the sequence position (or to the right
797 @Test(groups = { "Functional" })
798 public void testFindPositionMap()
801 * Note: Javadoc for findPosition says it returns the residue position to
802 * the left of a gapped position; in fact it returns the position to the
803 * right. Also it returns a non-existent residue position for a gap beyond
806 Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
807 int[] map = sq.findPositionMap();
808 assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
809 Arrays.toString(map));
813 * Test for getSubsequence
815 @Test(groups = { "Functional" })
816 public void testGetSubsequence()
818 SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
819 sq.createDatasetSequence();
821 // positions are base 0, end position is exclusive
822 SequenceI subseq = sq.getSubSequence(2, 4);
824 assertEquals("CD", subseq.getSequenceAsString());
825 // start/end are base 1 positions
826 assertEquals(3, subseq.getStart());
827 assertEquals(4, subseq.getEnd());
828 // subsequence shares the full dataset sequence
829 assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
833 * test createDatasetSequence behaves to doc
835 @Test(groups = { "Functional" })
836 public void testCreateDatasetSequence()
838 SequenceI sq = new Sequence("my", "ASDASD");
839 sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
841 sq.addDBRef(new DBRefEntry("source", "version", "accession"));
842 assertNull(sq.getDatasetSequence());
843 assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
844 assertNotNull(PA.getValue(sq, "dbrefs"));
846 SequenceI rds = sq.createDatasetSequence();
848 assertNull(rds.getDatasetSequence());
849 assertSame(sq.getDatasetSequence(), rds);
851 // sequence features and dbrefs transferred to dataset sequence
852 assertNull(PA.getValue(sq, "sequenceFeatureStore"));
853 assertNull(PA.getValue(sq, "dbrefs"));
854 assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
855 assertNotNull(PA.getValue(rds, "dbrefs"));
859 * Test for deriveSequence applied to a sequence with a dataset
861 @Test(groups = { "Functional" })
862 public void testDeriveSequence_existingDataset()
864 Sequence sq = new Sequence("Seq1", "CD");
865 sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
866 sq.getDatasetSequence().addSequenceFeature(
867 new SequenceFeature("", "", 1, 2, 0f, null));
871 sq.setDescription("Test sequence description..");
872 sq.setVamsasId("TestVamsasId");
873 sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
875 sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
876 sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
877 sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
878 sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
880 sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
881 sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
882 sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
883 sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
885 // these are the same as ones already added
886 DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
887 DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
889 List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
892 sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
893 sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
894 sq.getDatasetSequence().addDBRef(
895 new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
896 sq.getDatasetSequence().addDBRef(
897 new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
899 PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
900 PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
901 PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
903 PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
905 sq.getDatasetSequence().addPDBId(pdbe1a);
906 sq.getDatasetSequence().addPDBId(pdbe1b);
907 sq.getDatasetSequence().addPDBId(pdbe2a);
908 sq.getDatasetSequence().addPDBId(pdbe2b);
911 * test we added pdb entries to the dataset sequence
913 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
914 .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
915 "PDB Entries were not found on dataset sequence.");
918 * we should recover a pdb entry that is on the dataset sequence via PDBEntry
920 Assert.assertEquals(pdbe1a,
921 sq.getDatasetSequence().getPDBEntry("1PDB"),
922 "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
923 ArrayList<Annotation> annotsList = new ArrayList<>();
924 System.out.println(">>>>>> " + sq.getSequenceAsString().length());
925 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
926 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
927 Annotation[] annots = annotsList.toArray(new Annotation[0]);
928 sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
929 "Test annot description", annots));
930 sq.getDatasetSequence().addAlignmentAnnotation(
931 new AlignmentAnnotation("Test annot", "Test annot description",
933 Assert.assertEquals(sq.getDescription(), "Test sequence description..");
934 Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset
936 Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
937 Assert.assertNotNull(sq.getAnnotation());
938 Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
939 Assert.assertEquals(sq.getDatasetSequence().getDBRefs().size(), 5); // same
942 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
944 Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
946 Sequence derived = (Sequence) sq.deriveSequence();
948 Assert.assertEquals(derived.getDescription(),
949 "Test sequence description..");
950 Assert.assertEquals(derived.getDBRefs().size(), 5); // come from dataset
951 Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
952 Assert.assertNotNull(derived.getAnnotation());
953 Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
954 Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
955 Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
957 Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
959 assertEquals("CD", derived.getSequenceAsString());
960 assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
962 // derived sequence should access dataset sequence features
963 assertNotNull(sq.getSequenceFeatures());
964 assertEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures());
967 * verify we have primary db refs *just* for PDB IDs with associated
971 assertEquals(primRefs, sq.getPrimaryDBRefs());
972 assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
974 assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
979 * Test for deriveSequence applied to an ungapped sequence with no dataset
981 @Test(groups = { "Functional" })
982 public void testDeriveSequence_noDatasetUngapped()
984 SequenceI sq = new Sequence("Seq1", "ABCDEF");
985 assertEquals(1, sq.getStart());
986 assertEquals(6, sq.getEnd());
987 SequenceI derived = sq.deriveSequence();
988 assertEquals("ABCDEF", derived.getSequenceAsString());
989 assertEquals("ABCDEF", derived.getDatasetSequence()
990 .getSequenceAsString());
994 * Test for deriveSequence applied to a gapped sequence with no dataset
996 @Test(groups = { "Functional" })
997 public void testDeriveSequence_noDatasetGapped()
999 SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
1000 assertEquals(1, sq.getStart());
1001 assertEquals(6, sq.getEnd());
1002 assertNull(sq.getDatasetSequence());
1003 SequenceI derived = sq.deriveSequence();
1004 assertEquals("AB-C.D EF", derived.getSequenceAsString());
1005 assertEquals("ABCDEF", derived.getDatasetSequence()
1006 .getSequenceAsString());
1009 @Test(groups = { "Functional" })
1010 public void testCopyConstructor_noDataset()
1012 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1013 seq1.setDescription("description");
1014 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1016 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1018 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1019 seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
1021 SequenceI copy = new Sequence(seq1);
1023 assertNull(copy.getDatasetSequence());
1025 verifyCopiedSequence(seq1, copy);
1027 // copy has a copy of the DBRefEntry
1028 // this is murky - DBrefs are only copied for dataset sequences
1029 // where the test for 'dataset sequence' is 'dataset is null'
1030 // but that doesn't distinguish it from an aligned sequence
1031 // which has not yet generated a dataset sequence
1032 // NB getDBRef looks inside dataset sequence if not null
1033 List<DBRefEntry> dbrefs = copy.getDBRefs();
1034 assertEquals(1, dbrefs.size());
1035 assertFalse(dbrefs.get(0) == seq1.getDBRefs().get(0));
1036 assertTrue(dbrefs.get(0).equals(seq1.getDBRefs().get(0)));
1039 @Test(groups = { "Functional" })
1040 public void testCopyConstructor_withDataset()
1042 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1043 seq1.createDatasetSequence();
1044 seq1.setDescription("description");
1045 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1047 // JAL-2046 - what is the contract for using a derived sequence's
1048 // addSequenceFeature ?
1049 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1051 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1052 // here we add DBRef to the dataset sequence:
1053 seq1.getDatasetSequence().addDBRef(
1054 new DBRefEntry("EMBL", "1.2", "AZ12345"));
1056 SequenceI copy = new Sequence(seq1);
1058 assertNotNull(copy.getDatasetSequence());
1059 assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
1061 verifyCopiedSequence(seq1, copy);
1063 // getDBRef looks inside dataset sequence and this is shared,
1064 // so holds the same dbref objects
1065 List<DBRefEntry> dbrefs = copy.getDBRefs();
1066 assertEquals(1, dbrefs.size());
1067 assertSame(dbrefs.get(0), seq1.getDBRefs().get(0));
1071 * Helper to make assertions about a copied sequence
1076 protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
1078 // verify basic properties:
1079 assertEquals(copy.getName(), seq1.getName());
1080 assertEquals(copy.getDescription(), seq1.getDescription());
1081 assertEquals(copy.getStart(), seq1.getStart());
1082 assertEquals(copy.getEnd(), seq1.getEnd());
1083 assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
1085 // copy has a copy of the annotation:
1086 AlignmentAnnotation[] anns = copy.getAnnotation();
1087 assertEquals(1, anns.length);
1088 assertFalse(anns[0] == seq1.getAnnotation()[0]);
1089 assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
1090 assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
1091 assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
1093 // copy has a copy of the sequence feature:
1094 List<SequenceFeature> sfs = copy.getSequenceFeatures();
1095 assertEquals(1, sfs.size());
1096 if (seq1.getDatasetSequence() != null
1097 && copy.getDatasetSequence() == seq1.getDatasetSequence())
1099 assertSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1103 assertNotSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1105 assertEquals(sfs.get(0), seq1.getSequenceFeatures().get(0));
1107 // copy has a copy of the PDB entry
1108 Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
1109 assertEquals(1, pdbs.size());
1110 assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
1111 assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
1114 @Test(groups = "Functional")
1115 public void testGetCharAt()
1117 SequenceI sq = new Sequence("", "abcde");
1118 assertEquals('a', sq.getCharAt(0));
1119 assertEquals('e', sq.getCharAt(4));
1120 assertEquals(' ', sq.getCharAt(5));
1121 assertEquals(' ', sq.getCharAt(-1));
1124 @Test(groups = { "Functional" })
1125 public void testAddSequenceFeatures()
1127 SequenceI sq = new Sequence("", "abcde");
1128 // type may not be null
1129 assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
1131 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1133 // can't add a duplicate feature
1134 assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
1136 // can add a different feature
1137 assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
1138 8, 0f, null))); // different type
1139 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
1140 "description", 4, 8, 0f, null)));// different description
1141 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
1142 8, 0f, null))); // different start position
1143 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1144 9, 0f, null))); // different end position
1145 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1146 8, 1f, null))); // different score
1147 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1148 8, Float.NaN, null))); // score NaN
1149 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1150 8, 0f, "Metal"))); // different group
1151 assertEquals(8, sq.getFeatures().getAllFeatures().size());
1155 * Tests for adding (or updating) dbrefs
1157 * @see DBRefEntry#updateFrom(DBRefEntry)
1159 @Test(groups = { "Functional" })
1160 public void testAddDBRef()
1162 SequenceI sq = new Sequence("", "abcde");
1163 assertNull(sq.getDBRefs());
1164 DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
1166 assertEquals(1, sq.getDBRefs().size());
1167 assertSame(dbref, sq.getDBRefs().get(0));
1170 * change of version - new entry
1172 DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
1173 sq.addDBRef(dbref2);
1174 assertEquals(2, sq.getDBRefs().size());
1175 assertSame(dbref, sq.getDBRefs().get(0));
1176 assertSame(dbref2, sq.getDBRefs().get(1));
1179 * matches existing entry - not added
1181 sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
1182 assertEquals(2, sq.getDBRefs().size());
1185 * different source = new entry
1187 DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
1188 sq.addDBRef(dbref3);
1189 assertEquals(3, sq.getDBRefs().size());
1190 assertSame(dbref3, sq.getDBRefs().get(2));
1193 * different ref = new entry
1195 DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
1196 sq.addDBRef(dbref4);
1197 assertEquals(4, sq.getDBRefs().size());
1198 assertSame(dbref4, sq.getDBRefs().get(3));
1201 * matching ref with a mapping - map updated
1203 DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
1204 Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
1207 sq.addDBRef(dbref5);
1208 assertEquals(4, sq.getDBRefs().size());
1209 assertSame(dbref4, sq.getDBRefs().get(3));
1210 assertSame(map, dbref4.getMap());
1213 * 'real' version replaces "0" version
1215 dbref2.setVersion("0");
1216 DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
1217 dbref2.getAccessionId());
1218 sq.addDBRef(dbref6);
1219 assertEquals(4, sq.getDBRefs().size());
1220 assertSame(dbref2, sq.getDBRefs().get(1));
1221 assertEquals("3", dbref2.getVersion());
1224 * 'real' version replaces "source:0" version
1226 dbref3.setVersion("Uniprot:0");
1227 DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
1228 dbref3.getAccessionId());
1229 sq.addDBRef(dbref7);
1230 assertEquals(4, sq.getDBRefs().size());
1231 assertSame(dbref3, sq.getDBRefs().get(2));
1232 assertEquals("3", dbref2.getVersion());
1235 @Test(groups = { "Functional" })
1236 public void testGetPrimaryDBRefs_peptide()
1238 SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22);
1241 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1242 assertTrue(primaryDBRefs.isEmpty());
1246 primaryDBRefs = sq.getPrimaryDBRefs();
1247 assertTrue(primaryDBRefs.isEmpty());
1249 // primary - uniprot
1250 DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760");
1251 sq.addDBRef(upentry1);
1253 // primary - uniprot with congruent map
1254 DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
1255 upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
1256 new int[] { 10, 22 }, 1, 1)));
1257 sq.addDBRef(upentry2);
1259 // primary - uniprot with map of enclosing sequence
1260 DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
1261 upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
1262 new int[] { 8, 24 }, 1, 1)));
1263 sq.addDBRef(upentry3);
1265 // not primary - uniprot with map of sub-sequence (5')
1266 DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
1267 upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
1268 new int[] { 10, 18 }, 1, 1)));
1269 sq.addDBRef(upentry4);
1271 // not primary - uniprot with map that overlaps 3'
1272 DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
1273 upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
1274 new int[] { 12, 22 }, 1, 1)));
1275 sq.addDBRef(upentry5);
1277 // not primary - uniprot with map to different coordinates frame
1278 DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
1279 upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
1280 new int[] { 112, 118 }, 1, 1)));
1281 sq.addDBRef(upentry6);
1283 // not primary - dbref to 'non-core' database
1284 DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903");
1285 sq.addDBRef(upentry7);
1287 // primary - type is PDB
1288 DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
1289 sq.addDBRef(pdbentry);
1291 // not primary - PDBEntry has no file
1292 sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
1294 // not primary - no PDBEntry
1295 sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
1297 // add corroborating PDB entry for primary DBref -
1298 // needs to have a file as well as matching ID
1299 // note PDB ID is not treated as case sensitive
1300 sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
1303 // not valid DBRef - no file..
1304 sq.addPDBId(new PDBEntry("1AAA", null, null, null));
1306 primaryDBRefs = sq.getPrimaryDBRefs();
1307 assertEquals(4, primaryDBRefs.size());
1308 assertTrue("Couldn't find simple primary reference (UNIPROT)",
1309 primaryDBRefs.contains(upentry1));
1310 assertTrue("Couldn't find mapped primary reference (UNIPROT)",
1311 primaryDBRefs.contains(upentry2));
1312 assertTrue("Couldn't find mapped context reference (UNIPROT)",
1313 primaryDBRefs.contains(upentry3));
1314 assertTrue("Couldn't find expected PDB primary reference",
1315 primaryDBRefs.contains(pdbentry));
1318 @Test(groups = { "Functional" })
1319 public void testGetPrimaryDBRefs_nucleotide()
1321 SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
1323 // primary - Ensembl
1324 DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
1327 // not primary - Ensembl 'transcript' mapping of sub-sequence
1328 DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
1329 dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
1330 new int[] { 1, 11 }, 1, 1)));
1333 // primary - EMBL with congruent map
1334 DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
1335 dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
1336 new int[] { 10, 34 }, 1, 1)));
1339 // not primary - to non-core database
1340 DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234");
1343 // not primary - to protein
1344 DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
1347 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1348 assertEquals(2, primaryDBRefs.size());
1349 assertTrue(primaryDBRefs.contains(dbr1));
1350 assertTrue(primaryDBRefs.contains(dbr3));
1354 * Test the method that updates the list of PDBEntry from any new DBRefEntry
1357 @Test(groups = { "Functional" })
1358 public void testUpdatePDBIds()
1360 PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
1361 seq.addPDBId(pdbe1);
1362 seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
1363 seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
1364 seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
1365 seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
1366 // 7 is not a valid chain code:
1367 seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
1370 List<PDBEntry> pdbIds = seq.getAllPDBEntries();
1371 assertEquals(4, pdbIds.size());
1372 assertSame(pdbe1, pdbIds.get(0));
1373 // chain code got added to 3A6S:
1374 assertEquals("B", pdbe1.getChainCode());
1375 assertEquals("1A70", pdbIds.get(1).getId());
1376 // 4BQGA is parsed into id + chain
1377 assertEquals("4BQG", pdbIds.get(2).getId());
1378 assertEquals("a", pdbIds.get(2).getChainCode());
1379 assertEquals("2GIS7", pdbIds.get(3).getId());
1380 assertNull(pdbIds.get(3).getChainCode());
1384 * Test the method that either adds a pdbid or updates an existing one
1386 @Test(groups = { "Functional" })
1387 public void testAddPDBId()
1389 PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
1391 assertEquals(1, seq.getAllPDBEntries().size());
1392 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1393 assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
1395 // add the same entry
1397 assertEquals(1, seq.getAllPDBEntries().size());
1398 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1400 // add an identical entry
1401 seq.addPDBId(new PDBEntry("3A6S", null, null, null));
1402 assertEquals(1, seq.getAllPDBEntries().size());
1403 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1405 // add a different entry
1406 PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
1407 seq.addPDBId(pdbe2);
1408 assertEquals(2, seq.getAllPDBEntries().size());
1409 assertSame(pdbe, seq.getAllPDBEntries().get(0));
1410 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1412 // update pdbe with chain code, file, type
1413 PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
1414 seq.addPDBId(pdbe3);
1415 assertEquals(2, seq.getAllPDBEntries().size());
1416 assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
1417 assertEquals("3A6S", pdbe.getId()); // unchanged
1418 assertEquals("A", pdbe.getChainCode()); // updated
1419 assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
1420 assertEquals("filepath", pdbe.getFile()); // updated
1421 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1423 // add with a different file path
1424 PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
1425 seq.addPDBId(pdbe4);
1426 assertEquals(3, seq.getAllPDBEntries().size());
1427 assertSame(pdbe4, seq.getAllPDBEntries().get(2));
1429 // add with a different chain code
1430 PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
1431 seq.addPDBId(pdbe5);
1432 assertEquals(4, seq.getAllPDBEntries().size());
1433 assertSame(pdbe5, seq.getAllPDBEntries().get(3));
1437 groups = { "Functional" },
1438 expectedExceptions = { IllegalArgumentException.class })
1439 public void testSetDatasetSequence_toSelf()
1441 seq.setDatasetSequence(seq);
1445 groups = { "Functional" },
1446 expectedExceptions = { IllegalArgumentException.class })
1447 public void testSetDatasetSequence_cascading()
1449 SequenceI seq2 = new Sequence("Seq2", "xyz");
1450 seq2.createDatasetSequence();
1451 seq.setDatasetSequence(seq2);
1454 @Test(groups = { "Functional" })
1455 public void testFindFeatures()
1457 SequenceI sq = new Sequence("test/8-16", "-ABC--DEF--GHI--");
1458 sq.createDatasetSequence();
1460 assertTrue(sq.findFeatures(1, 99).isEmpty());
1462 // add non-positional feature
1463 SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f,
1465 sq.addSequenceFeature(sf0);
1466 // add feature on BCD
1467 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
1469 sq.addSequenceFeature(sfBCD);
1470 // add feature on DE
1471 SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
1473 sq.addSequenceFeature(sfDE);
1474 // add contact feature at [B, H]
1475 SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
1476 "desc", 9, 15, 2f, null);
1477 sq.addSequenceFeature(sfContactBH);
1478 // add contact feature at [F, G]
1479 SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
1480 "desc", 13, 14, 2f, null);
1481 sq.addSequenceFeature(sfContactFG);
1482 // add single position feature at [I]
1483 SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
1484 "desc", 16, 16, null);
1485 sq.addSequenceFeature(sfI);
1487 // no features in columns 1-2 (-A)
1488 List<SequenceFeature> found = sq.findFeatures(1, 2);
1489 assertTrue(found.isEmpty());
1491 // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
1492 found = sq.findFeatures(1, 6);
1493 assertEquals(2, found.size());
1494 assertTrue(found.contains(sfBCD));
1495 assertTrue(found.contains(sfContactBH));
1497 // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
1498 found = sq.findFeatures(5, 6);
1499 assertEquals(1, found.size());
1500 assertTrue(found.contains(sfBCD));
1502 // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
1503 found = sq.findFeatures(7, 10);
1504 assertEquals(3, found.size());
1505 assertTrue(found.contains(sfBCD));
1506 assertTrue(found.contains(sfDE));
1507 assertTrue(found.contains(sfContactFG));
1509 // columns 10-11 (--) should find nothing
1510 found = sq.findFeatures(10, 11);
1511 assertEquals(0, found.size());
1513 // columns 14-14 (I) should find variant feature
1514 found = sq.findFeatures(14, 14);
1515 assertEquals(1, found.size());
1516 assertTrue(found.contains(sfI));
1519 @Test(groups = { "Functional" })
1520 public void testFindIndex_withCursor()
1522 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1523 final int tok = (int) PA.getValue(sq, "changeCount");
1524 assertEquals(1, tok);
1526 // find F given A, check cursor is now at the found position
1527 assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, tok)));
1528 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1529 assertEquals(13, cursor.residuePosition);
1530 assertEquals(10, cursor.columnPosition);
1533 assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, tok)));
1534 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1535 assertEquals(8, cursor.residuePosition);
1536 assertEquals(2, cursor.columnPosition);
1538 // find C given C (no cursor update is done for this case)
1539 assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, tok)));
1540 SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1541 assertSame(cursor2, cursor);
1544 * sequence 'end' beyond end of sequence returns length of sequence
1545 * (for compatibility with pre-cursor code)
1546 * - also verify the cursor is left in a valid state
1548 sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
1549 assertEquals(7, sq.findIndex(10)); // establishes a cursor
1550 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1551 assertEquals(10, cursor.residuePosition);
1552 assertEquals(7, cursor.columnPosition);
1553 assertEquals(sq.getLength(), sq.findIndex(65));
1554 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1555 assertSame(cursor, cursor2); // not updated for this case!
1557 sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
1558 sq.findIndex(10); // establishes a cursor
1559 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1560 assertEquals(sq.getLength(), sq.findIndex(65));
1561 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1562 assertSame(cursor, cursor2); // not updated for this case!
1565 * residue after sequence 'start' but before first residue should return
1566 * zero (for compatibility with pre-cursor code)
1568 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
1569 sq.findIndex(10); // establishes a cursor
1570 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1571 assertEquals(0, sq.findIndex(3));
1572 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1573 assertSame(cursor, cursor2); // not updated for this case!
1575 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
1576 sq.findIndex(10); // establishes a cursor
1577 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1578 assertEquals(0, sq.findIndex(2));
1579 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1580 assertSame(cursor, cursor2); // not updated for this case!
1583 @Test(groups = { "Functional" })
1584 public void testFindPosition_withCursor()
1586 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1587 final int tok = (int) PA.getValue(sq, "changeCount");
1588 assertEquals(1, tok);
1590 // find F pos given A - lastCol gets set in cursor
1592 sq.findPosition(10, new SequenceCursor(sq, 8, 2, tok)));
1593 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1594 PA.getValue(sq, "cursor").toString());
1596 // find A pos given F - first residue column is saved in cursor
1598 sq.findPosition(2, new SequenceCursor(sq, 13, 10, tok)));
1599 assertEquals("test:Pos8:Col2:startCol2:endCol10:tok1",
1600 PA.getValue(sq, "cursor").toString());
1602 // find C pos given C (neither startCol nor endCol is set)
1604 sq.findPosition(6, new SequenceCursor(sq, 10, 6, tok)));
1605 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1",
1606 PA.getValue(sq, "cursor").toString());
1608 // now the grey area - what residue position for a gapped column? JAL-2562
1610 // find 'residue' for column 3 given cursor for D (so working left)
1611 // returns B9; cursor is updated to [B 5]
1612 assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, tok)));
1613 assertEquals("test:Pos9:Col5:startCol0:endCol0:tok1",
1614 PA.getValue(sq, "cursor").toString());
1616 // find 'residue' for column 8 given cursor for D (so working right)
1617 // returns E12; cursor is updated to [D 7]
1619 sq.findPosition(8, new SequenceCursor(sq, 11, 7, tok)));
1620 assertEquals("test:Pos11:Col7:startCol0:endCol0:tok1",
1621 PA.getValue(sq, "cursor").toString());
1623 // find 'residue' for column 12 given cursor for B
1624 // returns 1 more than last residue position; cursor is updated to [F 10]
1625 // lastCol position is saved in cursor
1627 sq.findPosition(12, new SequenceCursor(sq, 9, 5, tok)));
1628 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1629 PA.getValue(sq, "cursor").toString());
1632 * findPosition for column beyond length of sequence
1633 * returns 1 more than the last residue position
1634 * cursor is set to last real residue position [F 10]
1637 sq.findPosition(99, new SequenceCursor(sq, 8, 2, tok)));
1638 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1639 PA.getValue(sq, "cursor").toString());
1642 * and the case without a trailing gap
1644 sq = new Sequence("test/8-13", "-A--BCD-EF");
1645 // first find C from A
1646 assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, tok)));
1647 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1648 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1",
1650 // now 'find' 99 from C
1651 // cursor is set to [F 10] and saved lastCol
1652 assertEquals(14, sq.findPosition(99, cursor));
1653 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1654 PA.getValue(sq, "cursor").toString());
1658 public void testIsValidCursor()
1660 Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
1661 assertFalse(sq.isValidCursor(null));
1664 * cursor is valid if it has valid sequence ref and changeCount token
1665 * and positions within the range of the sequence
1667 int changeCount = (int) PA.getValue(sq, "changeCount");
1668 SequenceCursor cursor = new SequenceCursor(sq, 13, 1, changeCount);
1669 assertTrue(sq.isValidCursor(cursor));
1672 * column position outside [0 - length] is rejected
1674 cursor = new SequenceCursor(sq, 13, -1, changeCount);
1675 assertFalse(sq.isValidCursor(cursor));
1676 cursor = new SequenceCursor(sq, 13, 10, changeCount);
1677 assertFalse(sq.isValidCursor(cursor));
1678 cursor = new SequenceCursor(sq, 7, 8, changeCount);
1679 assertFalse(sq.isValidCursor(cursor));
1680 cursor = new SequenceCursor(sq, 14, 2, changeCount);
1681 assertFalse(sq.isValidCursor(cursor));
1684 * wrong sequence is rejected
1686 cursor = new SequenceCursor(null, 13, 1, changeCount);
1687 assertFalse(sq.isValidCursor(cursor));
1688 cursor = new SequenceCursor(new Sequence("Seq", "abc"), 13, 1,
1690 assertFalse(sq.isValidCursor(cursor));
1693 * wrong token value is rejected
1695 cursor = new SequenceCursor(sq, 13, 1, changeCount + 1);
1696 assertFalse(sq.isValidCursor(cursor));
1697 cursor = new SequenceCursor(sq, 13, 1, changeCount - 1);
1698 assertFalse(sq.isValidCursor(cursor));
1701 @Test(groups = { "Functional" })
1702 public void testFindPosition_withCursorAndEdits()
1704 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1706 // find F pos given A
1707 assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
1708 int token = (int) PA.getValue(sq, "changeCount"); // 0
1709 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1710 assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
1713 * setSequence should invalidate the cursor cached by the sequence
1715 sq.setSequence("-A-BCD-EF---"); // one gap removed
1716 assertEquals(8, sq.getStart()); // sanity check
1717 assertEquals(11, sq.findPosition(5)); // D11
1718 // cursor should now be at [D 6]
1719 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1720 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
1721 assertEquals(0, cursor.lastColumnPosition); // not yet found
1722 assertEquals(13, sq.findPosition(8)); // E13
1723 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1724 assertEquals(9, cursor.lastColumnPosition); // found
1727 * deleteChars should invalidate the cached cursor
1729 sq.deleteChars(2, 5); // delete -BC
1730 assertEquals("-AD-EF---", sq.getSequenceAsString());
1731 assertEquals(8, sq.getStart()); // sanity check
1732 assertEquals(10, sq.findPosition(4)); // E10
1733 // cursor should now be at [E 5]
1734 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1735 assertEquals(new SequenceCursor(sq, 10, 5, ++token), cursor);
1738 * Edit to insert gaps should invalidate the cached cursor
1739 * insert 2 gaps at column[3] to make -AD---EF---
1741 SequenceI[] seqs = new SequenceI[] { sq };
1742 AlignmentI al = new Alignment(seqs);
1743 new EditCommand().appendEdit(Action.INSERT_GAP, seqs, 3, 2, al, true);
1744 assertEquals("-AD---EF---", sq.getSequenceAsString());
1745 assertEquals(10, sq.findPosition(4)); // E10
1746 // cursor should now be at [D 3]
1747 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1748 assertEquals(new SequenceCursor(sq, 9, 3, ++token), cursor);
1751 * insertCharAt should invalidate the cached cursor
1752 * insert CC at column[4] to make -AD-CC--EF---
1754 sq.insertCharAt(4, 2, 'C');
1755 assertEquals("-AD-CC--EF---", sq.getSequenceAsString());
1756 assertEquals(13, sq.findPosition(9)); // F13
1757 // cursor should now be at [F 10]
1758 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1759 assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
1762 * changing sequence start should invalidate cursor
1764 sq = new Sequence("test/8-13", "-A--BCD-EF--");
1765 assertEquals(8, sq.getStart());
1766 assertEquals(9, sq.findPosition(4)); // B(9)
1768 assertEquals(8, sq.findPosition(4)); // is now B(8)
1770 assertEquals(11, sq.findPosition(4)); // is now B(11)
1773 @Test(groups = { "Functional" })
1774 public void testGetSequence()
1776 String seqstring = "-A--BCD-EF--";
1777 Sequence sq = new Sequence("test/8-13", seqstring);
1778 sq.createDatasetSequence();
1779 assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray()));
1780 assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(),
1781 "ABCDEF".toCharArray()));
1783 // verify a copy of the sequence array is returned
1784 char[] theSeq = (char[]) PA.getValue(sq, "sequence");
1785 assertNotSame(theSeq, sq.getSequence());
1786 theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence");
1787 assertNotSame(theSeq, sq.getDatasetSequence().getSequence());
1790 @Test(groups = { "Functional" })
1791 public void testReplace()
1793 String seqstring = "-A--BCD-EF--";
1794 SequenceI sq = new Sequence("test/8-13", seqstring);
1795 // changeCount is incremented for setStart
1796 assertEquals(1, PA.getValue(sq, "changeCount"));
1798 assertEquals(0, sq.replace('A', 'A')); // same char
1799 assertEquals(seqstring, sq.getSequenceAsString());
1800 assertEquals(1, PA.getValue(sq, "changeCount"));
1802 assertEquals(0, sq.replace('X', 'Y')); // not there
1803 assertEquals(seqstring, sq.getSequenceAsString());
1804 assertEquals(1, PA.getValue(sq, "changeCount"));
1806 assertEquals(1, sq.replace('A', 'K'));
1807 assertEquals("-K--BCD-EF--", sq.getSequenceAsString());
1808 assertEquals(2, PA.getValue(sq, "changeCount"));
1810 assertEquals(6, sq.replace('-', '.'));
1811 assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
1812 assertEquals(3, PA.getValue(sq, "changeCount"));
1815 @Test(groups = { "Functional" })
1816 public void testGapBitset()
1818 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
1819 BitSet bs = sq.gapBitset();
1820 BitSet expected = new BitSet();
1824 expected.set(11, 13);
1826 assertTrue(bs.equals(expected));
1830 public void testFindFeatures_largeEndPos()
1833 * imitate a PDB sequence where end is larger than end position
1835 SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
1836 sq.createDatasetSequence();
1838 assertTrue(sq.findFeatures(1, 9).isEmpty());
1839 // should be no array bounds exception - JAL-2772
1840 assertTrue(sq.findFeatures(1, 15).isEmpty());
1842 // add feature on BCD
1843 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
1845 sq.addSequenceFeature(sfBCD);
1847 // no features in columns 1-2 (-A)
1848 List<SequenceFeature> found = sq.findFeatures(1, 2);
1849 assertTrue(found.isEmpty());
1851 // columns 1-6 (-ABC--) includes BCD
1852 found = sq.findFeatures(1, 6);
1853 assertEquals(1, found.size());
1854 assertTrue(found.contains(sfBCD));
1856 // columns 10-11 (--) should find nothing
1857 found = sq.findFeatures(10, 11);
1858 assertEquals(0, found.size());
1861 @Test(groups = { "Functional" })
1862 public void testSetName()
1864 SequenceI sq = new Sequence("test", "-ABC---DE-F--");
1865 assertEquals("test", sq.getName());
1866 assertEquals(1, sq.getStart());
1867 assertEquals(6, sq.getEnd());
1869 sq.setName("testing");
1870 assertEquals("testing", sq.getName());
1872 sq.setName("test/8-10");
1873 assertEquals("test", sq.getName());
1874 assertEquals(8, sq.getStart());
1875 assertEquals(13, sq.getEnd()); // note end is recomputed
1877 sq.setName("testing/7-99");
1878 assertEquals("testing", sq.getName());
1879 assertEquals(7, sq.getStart());
1880 assertEquals(99, sq.getEnd()); // end may be beyond physical end
1883 assertEquals("", sq.getName());
1884 assertEquals(2, sq.getStart());
1885 assertEquals(7, sq.getEnd());
1887 sq.setName("test/"); // invalid
1888 assertEquals("test/", sq.getName());
1889 assertEquals(2, sq.getStart());
1890 assertEquals(7, sq.getEnd());
1892 sq.setName("test/6-13/7-99");
1893 assertEquals("test/6-13", sq.getName());
1894 assertEquals(7, sq.getStart());
1895 assertEquals(99, sq.getEnd());
1897 sq.setName("test/0-5"); // 0 is invalid - ignored
1898 assertEquals("test/0-5", sq.getName());
1899 assertEquals(7, sq.getStart());
1900 assertEquals(99, sq.getEnd());
1902 sq.setName("test/a-5"); // a is invalid - ignored
1903 assertEquals("test/a-5", sq.getName());
1904 assertEquals(7, sq.getStart());
1905 assertEquals(99, sq.getEnd());
1907 sq.setName("test/6-5"); // start > end is invalid - ignored
1908 assertEquals("test/6-5", sq.getName());
1909 assertEquals(7, sq.getStart());
1910 assertEquals(99, sq.getEnd());
1912 sq.setName("test/5"); // invalid - ignored
1913 assertEquals("test/5", sq.getName());
1914 assertEquals(7, sq.getStart());
1915 assertEquals(99, sq.getEnd());
1917 sq.setName("test/-5"); // invalid - ignored
1918 assertEquals("test/-5", sq.getName());
1919 assertEquals(7, sq.getStart());
1920 assertEquals(99, sq.getEnd());
1922 sq.setName("test/5-"); // invalid - ignored
1923 assertEquals("test/5-", sq.getName());
1924 assertEquals(7, sq.getStart());
1925 assertEquals(99, sq.getEnd());
1927 sq.setName("test/5-6-7"); // invalid - ignored
1928 assertEquals("test/5-6-7", sq.getName());
1929 assertEquals(7, sq.getStart());
1930 assertEquals(99, sq.getEnd());
1932 sq.setName(null); // invalid, gets converted to space
1933 assertEquals("", sq.getName());
1934 assertEquals(7, sq.getStart());
1935 assertEquals(99, sq.getEnd());
1938 @Test(groups = { "Functional" })
1939 public void testCheckValidRange()
1941 Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
1942 assertEquals(7, sq.getStart());
1943 assertEquals(12, sq.getEnd());
1946 * checkValidRange ensures end is at least the last residue position
1948 PA.setValue(sq, "end", 2);
1949 sq.checkValidRange();
1950 assertEquals(12, sq.getEnd());
1953 * end may be beyond the last residue position
1955 PA.setValue(sq, "end", 22);
1956 sq.checkValidRange();
1957 assertEquals(22, sq.getEnd());
1960 @Test(groups = { "Functional" })
1961 public void testDeleteChars_withGaps()
1966 SequenceI sq = new Sequence("test/8-10", "A-B-C");
1967 sq.createDatasetSequence();
1968 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1969 sq.deleteChars(1, 2); // delete first gap
1970 assertEquals("AB-C", sq.getSequenceAsString());
1971 assertEquals(8, sq.getStart());
1972 assertEquals(10, sq.getEnd());
1973 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1976 * delete gaps and residues at start (no new dataset sequence)
1978 sq = new Sequence("test/8-10", "A-B-C");
1979 sq.createDatasetSequence();
1980 sq.deleteChars(0, 3); // delete A-B
1981 assertEquals("-C", sq.getSequenceAsString());
1982 assertEquals(10, sq.getStart());
1983 assertEquals(10, sq.getEnd());
1984 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1987 * delete gaps and residues at end (no new dataset sequence)
1989 sq = new Sequence("test/8-10", "A-B-C");
1990 sq.createDatasetSequence();
1991 sq.deleteChars(2, 5); // delete B-C
1992 assertEquals("A-", sq.getSequenceAsString());
1993 assertEquals(8, sq.getStart());
1994 assertEquals(8, sq.getEnd());
1995 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1998 * delete gaps and residues internally (new dataset sequence)
1999 * first delete from gap to residue
2001 sq = new Sequence("test/8-10", "A-B-C");
2002 sq.createDatasetSequence();
2003 sq.deleteChars(1, 3); // delete -B
2004 assertEquals("A-C", sq.getSequenceAsString());
2005 assertEquals(8, sq.getStart());
2006 assertEquals(9, sq.getEnd());
2007 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2008 assertEquals(8, sq.getDatasetSequence().getStart());
2009 assertEquals(9, sq.getDatasetSequence().getEnd());
2012 * internal delete from gap to gap
2014 sq = new Sequence("test/8-10", "A-B-C");
2015 sq.createDatasetSequence();
2016 sq.deleteChars(1, 4); // delete -B-
2017 assertEquals("AC", sq.getSequenceAsString());
2018 assertEquals(8, sq.getStart());
2019 assertEquals(9, sq.getEnd());
2020 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2021 assertEquals(8, sq.getDatasetSequence().getStart());
2022 assertEquals(9, sq.getDatasetSequence().getEnd());
2025 * internal delete from residue to residue
2027 sq = new Sequence("test/8-10", "A-B-C");
2028 sq.createDatasetSequence();
2029 sq.deleteChars(2, 3); // delete B
2030 assertEquals("A--C", sq.getSequenceAsString());
2031 assertEquals(8, sq.getStart());
2032 assertEquals(9, sq.getEnd());
2033 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2034 assertEquals(8, sq.getDatasetSequence().getStart());
2035 assertEquals(9, sq.getDatasetSequence().getEnd());
2039 * Test the code used to locate the reference sequence ruler origin
2041 @Test(groups = { "Functional" })
2042 public void testLocateVisibleStartofSequence()
2044 // create random alignment
2045 AlignmentGenerator gen = new AlignmentGenerator(false);
2046 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
2048 HiddenColumns cs = al.getHiddenColumns();
2049 ColumnSelection colsel = new ColumnSelection();
2051 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
2052 assertEquals(2, seq.findIndex(seq.getStart()));
2054 // no hidden columns
2055 assertEquals(seq.findIndex(seq.getStart()) - 1,
2056 seq.firstResidueOutsideIterator(cs.iterator()));
2058 // hidden column on gap after end of sequence - should not affect bounds
2059 colsel.hideSelectedColumns(13, al.getHiddenColumns());
2060 assertEquals(seq.findIndex(seq.getStart()) - 1,
2061 seq.firstResidueOutsideIterator(cs.iterator()));
2063 cs.revealAllHiddenColumns(colsel);
2064 // hidden column on gap before beginning of sequence - should vis bounds by
2066 colsel.hideSelectedColumns(0, al.getHiddenColumns());
2067 assertEquals(seq.findIndex(seq.getStart()) - 2,
2068 cs.absoluteToVisibleColumn(
2069 seq.firstResidueOutsideIterator(cs.iterator())));
2071 cs.revealAllHiddenColumns(colsel);
2072 // hide columns around most of sequence - leave one residue remaining
2073 cs.hideColumns(1, 3);
2074 cs.hideColumns(6, 11);
2076 Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
2078 assertEquals("-D", seq.getSequenceStringFromIterator(it));
2079 // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
2082 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2083 cs.revealAllHiddenColumns(colsel);
2085 // hide whole sequence - should just get location of hidden region
2086 // containing sequence
2087 cs.hideColumns(1, 11);
2088 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2090 cs.revealAllHiddenColumns(colsel);
2091 cs.hideColumns(0, 15);
2092 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2094 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
2096 cs.revealAllHiddenColumns(colsel);
2097 cs.hideColumns(7, 17);
2098 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2100 cs.revealAllHiddenColumns(colsel);
2101 cs.hideColumns(3, 17);
2102 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2104 cs.revealAllHiddenColumns(colsel);
2105 cs.hideColumns(3, 19);
2106 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2108 cs.revealAllHiddenColumns(colsel);
2109 cs.hideColumns(0, 0);
2110 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2112 cs.revealAllHiddenColumns(colsel);
2113 cs.hideColumns(0, 1);
2114 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2116 cs.revealAllHiddenColumns(colsel);
2117 cs.hideColumns(0, 2);
2118 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2120 cs.revealAllHiddenColumns(colsel);
2121 cs.hideColumns(1, 1);
2122 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2124 cs.revealAllHiddenColumns(colsel);
2125 cs.hideColumns(1, 2);
2126 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2128 cs.revealAllHiddenColumns(colsel);
2129 cs.hideColumns(1, 3);
2130 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2132 cs.revealAllHiddenColumns(colsel);
2133 cs.hideColumns(0, 2);
2134 cs.hideColumns(5, 6);
2135 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2137 cs.revealAllHiddenColumns(colsel);
2138 cs.hideColumns(0, 2);
2139 cs.hideColumns(5, 6);
2140 cs.hideColumns(9, 10);
2141 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2143 cs.revealAllHiddenColumns(colsel);
2144 cs.hideColumns(0, 2);
2145 cs.hideColumns(7, 11);
2146 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2148 cs.revealAllHiddenColumns(colsel);
2149 cs.hideColumns(2, 4);
2150 cs.hideColumns(7, 11);
2151 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2153 cs.revealAllHiddenColumns(colsel);
2154 cs.hideColumns(2, 4);
2155 cs.hideColumns(7, 12);
2156 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2158 cs.revealAllHiddenColumns(colsel);
2159 cs.hideColumns(1, 11);
2160 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2162 cs.revealAllHiddenColumns(colsel);
2163 cs.hideColumns(0, 12);
2164 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2166 cs.revealAllHiddenColumns(colsel);
2167 cs.hideColumns(0, 4);
2168 cs.hideColumns(6, 12);
2169 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2171 cs.revealAllHiddenColumns(colsel);
2172 cs.hideColumns(0, 1);
2173 cs.hideColumns(3, 12);
2174 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2176 cs.revealAllHiddenColumns(colsel);
2177 cs.hideColumns(3, 14);
2178 cs.hideColumns(17, 19);
2179 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2181 cs.revealAllHiddenColumns(colsel);
2182 cs.hideColumns(3, 7);
2183 cs.hideColumns(9, 14);
2184 cs.hideColumns(17, 19);
2185 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2187 cs.revealAllHiddenColumns(colsel);
2188 cs.hideColumns(0, 1);
2189 cs.hideColumns(3, 4);
2190 cs.hideColumns(6, 8);
2191 cs.hideColumns(10, 12);
2192 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2195 @Test(groups= {"Functional"})
2196 public void testTransferAnnotation() {
2197 Sequence origSeq = new Sequence("MYSEQ","THISISASEQ");
2198 Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
2199 origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
2200 toSeq.transferAnnotation(origSeq, null);
2201 assertTrue(toSeq.getDBRefs().size()==1);
2203 assertTrue(toSeq.getDBRefs().get(0).isCanonical());
2205 // check for promotion of non-canonical
2206 // to canonical (e.g. fetch-db-refs on a jalview project pre 2.11.2)
2207 toSeq.setDBRefs(null);
2208 toSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, false));
2209 toSeq.transferAnnotation(origSeq, null);
2210 assertTrue(toSeq.getDBRefs().size()==1);
2212 assertTrue("Promotion of non-canonical DBRefEntry failed",toSeq.getDBRefs().get(0).isCanonical());