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;
33 import jalview.analysis.AlignmentGenerator;
34 import jalview.commands.EditCommand;
35 import jalview.commands.EditCommand.Action;
36 import jalview.datamodel.PDBEntry.Type;
37 import jalview.gui.JvOptionPane;
38 import jalview.util.MapList;
39 import jalview.ws.params.InvalidArgumentException;
42 import java.util.ArrayList;
43 import java.util.Arrays;
44 import java.util.BitSet;
45 import java.util.Iterator;
46 import java.util.List;
47 import java.util.Vector;
49 import org.testng.Assert;
50 import org.testng.annotations.BeforeClass;
51 import org.testng.annotations.BeforeMethod;
52 import org.testng.annotations.Test;
54 import junit.extensions.PA;
56 public class SequenceTest
58 @BeforeClass(alwaysRun = true)
59 public void setUpJvOptionPane()
61 JvOptionPane.setInteractiveMode(false);
62 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
67 @BeforeMethod(alwaysRun = true)
70 seq = new Sequence("FER1", "AKPNGVL");
73 @Test(groups = { "Functional" })
74 public void testInsertGapsAndGapmaps()
76 SequenceI aseq = seq.deriveSequence();
77 aseq.insertCharAt(2, 3, '-');
78 aseq.insertCharAt(6, 3, '-');
79 assertEquals("Gap insertions not correct", "AK---P---NGVL",
80 aseq.getSequenceAsString());
81 List<int[]> gapInt = aseq.getInsertions();
82 assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
83 assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
84 assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
85 assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
87 BitSet gapfield = aseq.getInsertionsAsBits();
88 BitSet expectedgaps = new BitSet();
89 expectedgaps.set(2, 5);
90 expectedgaps.set(6, 9);
92 assertEquals(6, expectedgaps.cardinality());
94 assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
95 6, gapfield.cardinality());
97 assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
100 @Test(groups = ("Functional"))
101 public void testIsProtein()
104 assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
106 assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
108 SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
109 assertFalse(sq.isProtein());
110 // change sequence, should trigger an update of cached result
111 sq.setSequence("ASDFASDFADSF");
112 assertTrue(sq.isProtein());
115 @Test(groups = ("Functional"))
116 public void testIsProteinWithXorNAmbiguityCodes()
118 // test Protein with N - poly asparagine
119 assertTrue(new Sequence("prot", "ASDFASDFASDFNNNNNNNNN").isProtein());
120 assertTrue(new Sequence("prot", "NNNNNNNNNNNNNNNNNNNNN").isProtein());
121 // test Protein with X
122 assertTrue(new Sequence("prot", "ASDFASDFASDFXXXXXXXXX").isProtein());
124 assertFalse(new Sequence("prot", "ACGTACGTACGTXXXXXXXX").isProtein());
126 assertFalse(new Sequence("prot", "ACGTACGTACGTNNNNNNNN").isProtein());
128 assertFalse(new Sequence("prot", "ACGUACGUACGUXXXXXXXXX").isProtein());
129 assertFalse(new Sequence("prot", "ACGUACGUACGUNNNNNNNNN").isProtein());
132 @Test(groups = { "Functional" })
133 public void testGetAnnotation()
135 // initial state returns null not an empty array
136 assertNull(seq.getAnnotation());
137 AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
139 AlignmentAnnotation[] anns = seq.getAnnotation();
140 assertEquals(1, anns.length);
141 assertSame(ann, anns[0]);
143 // removing all annotations reverts array to null
144 seq.removeAlignmentAnnotation(ann);
145 assertNull(seq.getAnnotation());
148 @Test(groups = { "Functional" })
149 public void testGetAnnotation_forLabel()
151 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
153 addAnnotation("label2", "desc2", "calcId2", 1f);
154 AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
156 AlignmentAnnotation[] anns = seq.getAnnotation("label1");
157 assertEquals(2, anns.length);
158 assertSame(ann1, anns[0]);
159 assertSame(ann3, anns[1]);
162 private AlignmentAnnotation addAnnotation(String label,
163 String description, String calcId, float value)
165 final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
167 annotation.setCalcId(calcId);
168 seq.addAlignmentAnnotation(annotation);
172 @Test(groups = { "Functional" })
173 public void testGetAlignmentAnnotations_forCalcIdAndLabel()
175 addAnnotation("label1", "desc1", "calcId1", 1f);
176 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
178 addAnnotation("label2", "desc3", "calcId3", 1f);
179 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
181 addAnnotation("label5", "desc3", null, 1f);
182 addAnnotation(null, "desc3", "calcId3", 1f);
184 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
186 assertEquals(2, anns.size());
187 assertSame(ann2, anns.get(0));
188 assertSame(ann4, anns.get(1));
190 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
191 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
192 assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
193 assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
194 assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
198 @Test(groups = { "Functional" })
199 public void testGetAlignmentAnnotations_forCalcIdLabelAndDescription()
201 addAnnotation("label1", "desc1", "calcId1", 1f);
202 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
204 addAnnotation("label2", "desc3", "calcId3", 1f);
205 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
207 addAnnotation("label5", "desc3", null, 1f);
208 addAnnotation(null, "desc3", "calcId3", 1f);
210 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
212 assertEquals(1, anns.size());
213 assertSame(ann4, anns.get(0));
215 * null matching should fail
217 assertTrue(seq.getAlignmentAnnotations("calcId3", "label2",null).isEmpty());
219 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3",null).isEmpty());
220 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5",null).isEmpty());
221 assertTrue(seq.getAlignmentAnnotations("calcId2", null,null).isEmpty());
222 assertTrue(seq.getAlignmentAnnotations(null, "label3",null).isEmpty());
223 assertTrue(seq.getAlignmentAnnotations(null, null,null).isEmpty());
227 * Tests for addAlignmentAnnotation. Note this method has the side-effect of
228 * setting the sequenceRef on the annotation. Adding the same annotation twice
231 @Test(groups = { "Functional" })
232 public void testAddAlignmentAnnotation()
234 assertNull(seq.getAnnotation());
235 final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
237 assertNull(annotation.sequenceRef);
238 seq.addAlignmentAnnotation(annotation);
239 assertSame(seq, annotation.sequenceRef);
240 AlignmentAnnotation[] anns = seq.getAnnotation();
241 assertEquals(1, anns.length);
242 assertSame(annotation, anns[0]);
244 // re-adding does nothing
245 seq.addAlignmentAnnotation(annotation);
246 anns = seq.getAnnotation();
247 assertEquals(1, anns.length);
248 assertSame(annotation, anns[0]);
250 // an identical but different annotation can be added
251 final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
253 seq.addAlignmentAnnotation(annotation2);
254 anns = seq.getAnnotation();
255 assertEquals(2, anns.length);
256 assertSame(annotation, anns[0]);
257 assertSame(annotation2, anns[1]);
260 @Test(groups = { "Functional" })
261 public void testGetStartGetEnd()
263 SequenceI sq = new Sequence("test", "ABCDEF");
264 assertEquals(1, sq.getStart());
265 assertEquals(6, sq.getEnd());
267 sq = new Sequence("test", "--AB-C-DEF--");
268 assertEquals(1, sq.getStart());
269 assertEquals(6, sq.getEnd());
271 sq = new Sequence("test", "----");
272 assertEquals(1, sq.getStart());
273 assertEquals(0, sq.getEnd()); // ??
277 * Tests for the method that returns an alignment column position (base 1) for
278 * a given sequence position (base 1).
280 @Test(groups = { "Functional" })
281 public void testFindIndex()
284 * call sequenceChanged() after each test to invalidate any cursor,
285 * forcing the 1-arg findIndex to be executed
287 SequenceI sq = new Sequence("test", "ABCDEF");
288 assertEquals(0, sq.findIndex(0));
289 sq.sequenceChanged();
290 assertEquals(1, sq.findIndex(1));
291 sq.sequenceChanged();
292 assertEquals(5, sq.findIndex(5));
293 sq.sequenceChanged();
294 assertEquals(6, sq.findIndex(6));
295 sq.sequenceChanged();
296 assertEquals(6, sq.findIndex(9));
298 final String aligned = "-A--B-C-D-E-F--";
299 assertEquals(15, aligned.length());
300 sq = new Sequence("test/8-13", aligned);
301 assertEquals(2, sq.findIndex(8));
302 sq.sequenceChanged();
303 assertEquals(5, sq.findIndex(9));
304 sq.sequenceChanged();
305 assertEquals(7, sq.findIndex(10));
307 // before start returns 0
308 sq.sequenceChanged();
309 assertEquals(0, sq.findIndex(0));
310 sq.sequenceChanged();
311 assertEquals(0, sq.findIndex(-1));
313 // beyond end returns last residue column
314 sq.sequenceChanged();
315 assertEquals(13, sq.findIndex(99));
318 * residue before sequence 'end' but beyond end of sequence returns
319 * length of sequence (last column) (rightly or wrongly!)
321 sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case
322 assertEquals(6, sq.getLength());
323 sq.sequenceChanged();
324 assertEquals(sq.getLength(), sq.findIndex(14));
325 sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case
326 sq.sequenceChanged();
327 assertEquals(sq.getLength(), sq.findIndex(65));
330 * residue after sequence 'start' but before first residue returns
331 * zero (before first column) (rightly or wrongly!)
333 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
334 sq.sequenceChanged();
335 assertEquals(0, sq.findIndex(3));
336 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
337 sq.sequenceChanged();
338 assertEquals(0, sq.findIndex(2));
341 @Test(groups = { "Functional" })
342 public void testFindPositions()
344 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
349 assertNull(sq.findPositions(6, 5));
350 assertNull(sq.findPositions(0, 5));
351 assertNull(sq.findPositions(-1, 5));
356 assertNull(sq.findPositions(1, 1)); // 1-based columns
357 assertNull(sq.findPositions(5, 5));
358 assertNull(sq.findPositions(5, 6));
359 assertNull(sq.findPositions(5, 7));
362 * all ungapped ranges
364 assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
365 assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
366 assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
367 assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
370 * gap to ungapped range
372 assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
373 assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
376 * ungapped to gapped range
378 assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
379 assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
382 * ungapped to ungapped enclosing gaps
384 assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
385 assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
388 * gapped to gapped enclosing ungapped
390 assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
391 assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
392 assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
393 assertEquals(new Range(8, 13), sq.findPositions(1, 99));
397 * Tests for the method that returns a dataset sequence position (start..) for
398 * an aligned column position (base 0).
400 @Test(groups = { "Functional" })
401 public void testFindPosition()
404 * call sequenceChanged() after each test to invalidate any cursor,
405 * forcing the 1-arg findPosition to be executed
407 SequenceI sq = new Sequence("test/8-13", "ABCDEF");
408 assertEquals(8, sq.findPosition(0));
409 // Sequence should now hold a cursor at [8, 0]
410 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1",
411 PA.getValue(sq, "cursor").toString());
412 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
413 int token = (int) PA.getValue(sq, "changeCount");
414 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
416 sq.sequenceChanged();
419 * find F13 at column offset 5, cursor should update to [13, 6]
420 * endColumn is found and saved in cursor
422 assertEquals(13, sq.findPosition(5));
423 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
424 assertEquals(++token, (int) PA.getValue(sq, "changeCount"));
425 assertEquals(new SequenceCursor(sq, 13, 6, token), cursor);
426 assertEquals("test:Pos13:Col6:startCol1:endCol6:tok2",
427 PA.getValue(sq, "cursor").toString());
429 // assertEquals(-1, seq.findPosition(6)); // fails
431 sq = new Sequence("test/8-11", "AB-C-D--");
432 token = (int) PA.getValue(sq, "changeCount"); // 1 for setStart
433 assertEquals(8, sq.findPosition(0));
434 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
435 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
436 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok1",
437 PA.getValue(sq, "cursor").toString());
439 sq.sequenceChanged();
440 assertEquals(9, sq.findPosition(1));
441 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
442 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
443 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2",
444 PA.getValue(sq, "cursor").toString());
446 sq.sequenceChanged();
447 // gap position 'finds' residue to the right (not the left as per javadoc)
448 // cursor is set to the last residue position found [B 2]
449 assertEquals(10, sq.findPosition(2));
450 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
451 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
452 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok3",
453 PA.getValue(sq, "cursor").toString());
455 sq.sequenceChanged();
456 assertEquals(10, sq.findPosition(3));
457 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
458 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
459 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4",
460 PA.getValue(sq, "cursor").toString());
462 sq.sequenceChanged();
463 // column[4] is the gap after C - returns D11
464 // cursor is set to [C 4]
465 assertEquals(11, sq.findPosition(4));
466 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
467 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
468 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok5",
469 PA.getValue(sq, "cursor").toString());
471 sq.sequenceChanged();
472 assertEquals(11, sq.findPosition(5)); // D
473 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
474 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
475 // lastCol has been found and saved in the cursor
476 assertEquals("test:Pos11:Col6:startCol1:endCol6:tok6",
477 PA.getValue(sq, "cursor").toString());
479 sq.sequenceChanged();
480 // returns 1 more than sequence length if off the end ?!?
481 assertEquals(12, sq.findPosition(6));
483 sq.sequenceChanged();
484 assertEquals(12, sq.findPosition(7));
487 * first findPosition should also set firstResCol in cursor
489 sq = new Sequence("test/8-13", "--AB-C-DEF--");
490 assertEquals(8, sq.findPosition(0));
491 assertNull(PA.getValue(sq, "cursor"));
492 assertEquals(1, PA.getValue(sq, "changeCount"));
494 sq.sequenceChanged();
495 assertEquals(8, sq.findPosition(1));
496 assertNull(PA.getValue(sq, "cursor"));
498 sq.sequenceChanged();
499 assertEquals(8, sq.findPosition(2));
500 assertEquals("test:Pos8:Col3:startCol3:endCol0:tok3",
501 PA.getValue(sq, "cursor").toString());
503 sq.sequenceChanged();
504 assertEquals(9, sq.findPosition(3));
505 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4",
506 PA.getValue(sq, "cursor").toString());
508 sq.sequenceChanged();
509 // column[4] is a gap, returns next residue pos (C10)
510 // cursor is set to last residue found [B]
511 assertEquals(10, sq.findPosition(4));
512 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok5",
513 PA.getValue(sq, "cursor").toString());
515 sq.sequenceChanged();
516 assertEquals(10, sq.findPosition(5));
517 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6",
518 PA.getValue(sq, "cursor").toString());
520 sq.sequenceChanged();
521 // column[6] is a gap, returns next residue pos (D11)
522 // cursor is set to last residue found [C]
523 assertEquals(11, sq.findPosition(6));
524 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok7",
525 PA.getValue(sq, "cursor").toString());
527 sq.sequenceChanged();
528 assertEquals(11, sq.findPosition(7));
529 assertEquals("test:Pos11:Col8:startCol3:endCol0:tok8",
530 PA.getValue(sq, "cursor").toString());
532 sq.sequenceChanged();
533 assertEquals(12, sq.findPosition(8));
534 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok9",
535 PA.getValue(sq, "cursor").toString());
538 * when the last residue column is found, it is set in the cursor
540 sq.sequenceChanged();
541 assertEquals(13, sq.findPosition(9));
542 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10",
543 PA.getValue(sq, "cursor").toString());
545 sq.sequenceChanged();
546 assertEquals(14, sq.findPosition(10));
547 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11",
548 PA.getValue(sq, "cursor").toString());
551 * findPosition for column beyond sequence length
552 * returns 1 more than last residue position
554 sq.sequenceChanged();
555 assertEquals(14, sq.findPosition(11));
556 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12",
557 PA.getValue(sq, "cursor").toString());
559 sq.sequenceChanged();
560 assertEquals(14, sq.findPosition(99));
561 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok13",
562 PA.getValue(sq, "cursor").toString());
565 * gapped sequence ending in non-gap
567 sq = new Sequence("test/8-13", "--AB-C-DEF");
568 assertEquals(13, sq.findPosition(9));
569 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1",
570 PA.getValue(sq, "cursor").toString());
571 sq.sequenceChanged();
572 assertEquals(12, sq.findPosition(8)); // E12
573 // sequenceChanged() invalidates cursor.lastResidueColumn
574 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
575 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok2",
577 // findPosition with cursor accepts base 1 column values
578 assertEquals(13, ((Sequence) sq).findPosition(10, cursor));
579 assertEquals(13, sq.findPosition(9)); // F13
580 // lastResidueColumn has now been found and saved in cursor
581 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok2",
582 PA.getValue(sq, "cursor").toString());
585 @Test(groups = { "Functional" })
586 public void testDeleteChars()
591 SequenceI sq = new Sequence("test", "ABCDEF");
592 assertNull(PA.getValue(sq, "datasetSequence"));
593 assertEquals(1, sq.getStart());
594 assertEquals(6, sq.getEnd());
595 sq.deleteChars(2, 3);
596 assertEquals("ABDEF", sq.getSequenceAsString());
597 assertEquals(1, sq.getStart());
598 assertEquals(5, sq.getEnd());
599 assertNull(PA.getValue(sq, "datasetSequence"));
604 sq = new Sequence("test", "ABCDEF");
605 sq.deleteChars(0, 2);
606 assertEquals("CDEF", sq.getSequenceAsString());
607 assertEquals(3, sq.getStart());
608 assertEquals(6, sq.getEnd());
609 assertNull(PA.getValue(sq, "datasetSequence"));
611 sq = new Sequence("test", "ABCDE");
612 sq.deleteChars(0, 3);
613 assertEquals("DE", sq.getSequenceAsString());
614 assertEquals(4, sq.getStart());
615 assertEquals(5, sq.getEnd());
616 assertNull(PA.getValue(sq, "datasetSequence"));
621 sq = new Sequence("test", "ABCDEF");
622 sq.deleteChars(4, 6);
623 assertEquals("ABCD", sq.getSequenceAsString());
624 assertEquals(1, sq.getStart());
625 assertEquals(4, sq.getEnd());
626 assertNull(PA.getValue(sq, "datasetSequence"));
629 * delete more positions than there are
631 sq = new Sequence("test/8-11", "ABCD");
632 sq.deleteChars(0, 99);
633 assertEquals("", sq.getSequenceAsString());
634 assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
635 assertEquals(11, sq.getEnd());
637 sq = new Sequence("test/8-11", "----");
638 sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
639 assertEquals("", sq.getSequenceAsString());
640 assertEquals(8, sq.getStart());
641 assertEquals(11, sq.getEnd());
644 @Test(groups = { "Functional" })
645 public void testDeleteChars_withDbRefsAndFeatures()
648 * internal delete - new dataset sequence created
649 * gets a copy of any dbrefs
651 SequenceI sq = new Sequence("test", "ABCDEF");
652 sq.createDatasetSequence();
653 DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
655 Object ds = PA.getValue(sq, "datasetSequence");
657 assertEquals(1, sq.getStart());
658 assertEquals(6, sq.getEnd());
659 sq.deleteChars(2, 3);
660 assertEquals("ABDEF", sq.getSequenceAsString());
661 assertEquals(1, sq.getStart());
662 assertEquals(5, sq.getEnd());
663 Object newDs = PA.getValue(sq, "datasetSequence");
664 assertNotNull(newDs);
665 assertNotSame(ds, newDs);
666 assertNotNull(sq.getDBRefs());
667 assertEquals(1, sq.getDBRefs().size());
668 assertNotSame(dbr1, sq.getDBRefs().get(0));
669 assertEquals(dbr1, sq.getDBRefs().get(0));
672 * internal delete with sequence features
673 * (failure case for JAL-2541)
675 sq = new Sequence("test", "ABCDEF");
676 sq.createDatasetSequence();
677 SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
679 sq.addSequenceFeature(sf1);
680 ds = PA.getValue(sq, "datasetSequence");
682 assertEquals(1, sq.getStart());
683 assertEquals(6, sq.getEnd());
684 sq.deleteChars(2, 4);
685 assertEquals("ABEF", sq.getSequenceAsString());
686 assertEquals(1, sq.getStart());
687 assertEquals(4, sq.getEnd());
688 newDs = PA.getValue(sq, "datasetSequence");
689 assertNotNull(newDs);
690 assertNotSame(ds, newDs);
691 List<SequenceFeature> sfs = sq.getSequenceFeatures();
692 assertEquals(1, sfs.size());
693 assertNotSame(sf1, sfs.get(0));
694 assertEquals(sf1, sfs.get(0));
697 * delete at start - no new dataset sequence created
698 * any sequence features remain as before
700 sq = new Sequence("test", "ABCDEF");
701 sq.createDatasetSequence();
702 ds = PA.getValue(sq, "datasetSequence");
703 sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
704 sq.addSequenceFeature(sf1);
705 sq.deleteChars(0, 2);
706 assertEquals("CDEF", sq.getSequenceAsString());
707 assertEquals(3, sq.getStart());
708 assertEquals(6, sq.getEnd());
709 assertSame(ds, PA.getValue(sq, "datasetSequence"));
710 sfs = sq.getSequenceFeatures();
712 assertEquals(1, sfs.size());
713 assertSame(sf1, sfs.get(0));
716 * delete at end - no new dataset sequence created
717 * any dbrefs remain as before
719 sq = new Sequence("test", "ABCDEF");
720 sq.createDatasetSequence();
721 ds = PA.getValue(sq, "datasetSequence");
722 dbr1 = new DBRefEntry("Uniprot", "0", "a123");
724 sq.deleteChars(4, 6);
725 assertEquals("ABCD", sq.getSequenceAsString());
726 assertEquals(1, sq.getStart());
727 assertEquals(4, sq.getEnd());
728 assertSame(ds, PA.getValue(sq, "datasetSequence"));
729 assertNotNull(sq.getDBRefs());
730 assertEquals(1, sq.getDBRefs().size());
731 assertSame(dbr1, sq.getDBRefs().get(0));
734 @Test(groups = { "Functional" })
735 public void testInsertCharAt()
737 // non-static methods:
738 SequenceI sq = new Sequence("test", "ABCDEF");
739 sq.insertCharAt(0, 'z');
740 assertEquals("zABCDEF", sq.getSequenceAsString());
741 sq.insertCharAt(2, 2, 'x');
742 assertEquals("zAxxBCDEF", sq.getSequenceAsString());
744 // for static method see StringUtilsTest
748 * Test the method that returns an array of aligned sequence positions where
749 * the array index is the data sequence position (both base 0).
751 @Test(groups = { "Functional" })
752 public void testGapMap()
754 SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
755 sq.createDatasetSequence();
756 assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
760 * Test the method that gets sequence features, either from the sequence or
763 @Test(groups = { "Functional" })
764 public void testGetSequenceFeatures()
766 SequenceI sq = new Sequence("test", "GATCAT");
767 sq.createDatasetSequence();
769 assertTrue(sq.getSequenceFeatures().isEmpty());
772 * SequenceFeature on sequence
774 SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
775 sq.addSequenceFeature(sf);
776 List<SequenceFeature> sfs = sq.getSequenceFeatures();
777 assertEquals(1, sfs.size());
778 assertSame(sf, sfs.get(0));
781 * SequenceFeature on sequence and dataset sequence; returns that on
784 * Note JAL-2046: spurious: we have no use case for this at the moment.
785 * This test also buggy - as sf2.equals(sf), no new feature is added
787 SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
789 sq.getDatasetSequence().addSequenceFeature(sf2);
790 sfs = sq.getSequenceFeatures();
791 assertEquals(1, sfs.size());
792 assertSame(sf, sfs.get(0));
795 * SequenceFeature on dataset sequence only
796 * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
798 sq.setSequenceFeatures(null);
799 assertTrue(sq.getDatasetSequence().getSequenceFeatures().isEmpty());
802 * Corrupt case - no SequenceFeature, dataset's dataset is the original
803 * sequence. Test shows no infinite loop results.
805 sq.getDatasetSequence().setSequenceFeatures(null);
807 * is there a usecase for this ? setDatasetSequence should throw an error if
808 * this actually occurs.
812 sq.getDatasetSequence().setDatasetSequence(sq); // loop!
813 Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
814 } catch (IllegalArgumentException e)
816 // TODO Jalview error/exception class for raising implementation errors
817 assertTrue(e.getMessage().toLowerCase(Locale.ROOT)
818 .contains("implementation error"));
820 assertTrue(sq.getSequenceFeatures().isEmpty());
824 * Test the method that returns an array, indexed by sequence position, whose
825 * entries are the residue positions at the sequence position (or to the right
828 @Test(groups = { "Functional" })
829 public void testFindPositionMap()
832 * Note: Javadoc for findPosition says it returns the residue position to
833 * the left of a gapped position; in fact it returns the position to the
834 * right. Also it returns a non-existent residue position for a gap beyond
837 Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
838 int[] map = sq.findPositionMap();
839 assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
840 Arrays.toString(map));
844 * Test for getSubsequence
846 @Test(groups = { "Functional" })
847 public void testGetSubsequence()
849 SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
850 sq.createDatasetSequence();
852 // positions are base 0, end position is exclusive
853 SequenceI subseq = sq.getSubSequence(2, 4);
855 assertEquals("CD", subseq.getSequenceAsString());
856 // start/end are base 1 positions
857 assertEquals(3, subseq.getStart());
858 assertEquals(4, subseq.getEnd());
859 // subsequence shares the full dataset sequence
860 assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
864 * test createDatasetSequence behaves to doc
866 @Test(groups = { "Functional" })
867 public void testCreateDatasetSequence()
869 SequenceI sq = new Sequence("my", "ASDASD");
870 sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
872 sq.addDBRef(new DBRefEntry("source", "version", "accession"));
873 assertNull(sq.getDatasetSequence());
874 assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
875 assertNotNull(PA.getValue(sq, "dbrefs"));
877 SequenceI rds = sq.createDatasetSequence();
879 assertNull(rds.getDatasetSequence());
880 assertSame(sq.getDatasetSequence(), rds);
882 // sequence features and dbrefs transferred to dataset sequence
883 assertNull(PA.getValue(sq, "sequenceFeatureStore"));
884 assertNull(PA.getValue(sq, "dbrefs"));
885 assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
886 assertNotNull(PA.getValue(rds, "dbrefs"));
890 * Test for deriveSequence applied to a sequence with a dataset
892 @Test(groups = { "Functional" })
893 public void testDeriveSequence_existingDataset()
895 Sequence sq = new Sequence("Seq1", "CD");
896 sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
897 sq.getDatasetSequence().addSequenceFeature(
898 new SequenceFeature("", "", 1, 2, 0f, null));
902 sq.setDescription("Test sequence description..");
903 sq.setVamsasId("TestVamsasId");
904 sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
906 sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
907 sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
908 sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
909 sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
911 sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
912 sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
913 sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
914 sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
916 // these are the same as ones already added
917 DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
918 DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
920 List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
923 sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
924 sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
925 sq.getDatasetSequence().addDBRef(
926 new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
927 sq.getDatasetSequence().addDBRef(
928 new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
930 PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
931 PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
932 PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
934 PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
936 sq.getDatasetSequence().addPDBId(pdbe1a);
937 sq.getDatasetSequence().addPDBId(pdbe1b);
938 sq.getDatasetSequence().addPDBId(pdbe2a);
939 sq.getDatasetSequence().addPDBId(pdbe2b);
942 * test we added pdb entries to the dataset sequence
944 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
945 .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
946 "PDB Entries were not found on dataset sequence.");
949 * we should recover a pdb entry that is on the dataset sequence via PDBEntry
951 Assert.assertEquals(pdbe1a,
952 sq.getDatasetSequence().getPDBEntry("1PDB"),
953 "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
954 ArrayList<Annotation> annotsList = new ArrayList<>();
955 System.out.println(">>>>>> " + sq.getSequenceAsString().length());
956 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
957 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
958 Annotation[] annots = annotsList.toArray(new Annotation[0]);
959 sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
960 "Test annot description", annots));
961 sq.getDatasetSequence().addAlignmentAnnotation(
962 new AlignmentAnnotation("Test annot", "Test annot description",
964 Assert.assertEquals(sq.getDescription(), "Test sequence description..");
965 Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset
967 Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
968 Assert.assertNotNull(sq.getAnnotation());
969 Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
970 Assert.assertEquals(sq.getDatasetSequence().getDBRefs().size(), 5); // same
973 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
975 Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
977 Sequence derived = (Sequence) sq.deriveSequence();
979 Assert.assertEquals(derived.getDescription(),
980 "Test sequence description..");
981 Assert.assertEquals(derived.getDBRefs().size(), 5); // come from dataset
982 Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
983 Assert.assertNotNull(derived.getAnnotation());
984 Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
985 Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
986 Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
988 Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
990 assertEquals("CD", derived.getSequenceAsString());
991 assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
993 // derived sequence should access dataset sequence features
994 assertNotNull(sq.getSequenceFeatures());
995 assertEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures());
998 * verify we have primary db refs *just* for PDB IDs with associated
1002 assertEquals(primRefs, sq.getPrimaryDBRefs());
1003 assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
1005 assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
1010 * Test for deriveSequence applied to an ungapped sequence with no dataset
1012 @Test(groups = { "Functional" })
1013 public void testDeriveSequence_noDatasetUngapped()
1015 SequenceI sq = new Sequence("Seq1", "ABCDEF");
1016 assertEquals(1, sq.getStart());
1017 assertEquals(6, sq.getEnd());
1018 SequenceI derived = sq.deriveSequence();
1019 assertEquals("ABCDEF", derived.getSequenceAsString());
1020 assertEquals("ABCDEF", derived.getDatasetSequence()
1021 .getSequenceAsString());
1025 * Test for deriveSequence applied to a gapped sequence with no dataset
1027 @Test(groups = { "Functional" })
1028 public void testDeriveSequence_noDatasetGapped()
1030 SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
1031 assertEquals(1, sq.getStart());
1032 assertEquals(6, sq.getEnd());
1033 assertNull(sq.getDatasetSequence());
1034 SequenceI derived = sq.deriveSequence();
1035 assertEquals("AB-C.D EF", derived.getSequenceAsString());
1036 assertEquals("ABCDEF", derived.getDatasetSequence()
1037 .getSequenceAsString());
1040 @Test(groups = { "Functional" })
1041 public void testCopyConstructor_noDataset()
1043 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1044 seq1.setDescription("description");
1045 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1047 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1049 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1050 seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
1052 SequenceI copy = new Sequence(seq1);
1054 assertNull(copy.getDatasetSequence());
1056 verifyCopiedSequence(seq1, copy);
1058 // copy has a copy of the DBRefEntry
1059 // this is murky - DBrefs are only copied for dataset sequences
1060 // where the test for 'dataset sequence' is 'dataset is null'
1061 // but that doesn't distinguish it from an aligned sequence
1062 // which has not yet generated a dataset sequence
1063 // NB getDBRef looks inside dataset sequence if not null
1064 List<DBRefEntry> dbrefs = copy.getDBRefs();
1065 assertEquals(1, dbrefs.size());
1066 assertFalse(dbrefs.get(0) == seq1.getDBRefs().get(0));
1067 assertTrue(dbrefs.get(0).equals(seq1.getDBRefs().get(0)));
1070 @Test(groups = { "Functional" })
1071 public void testCopyConstructor_withDataset()
1073 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1074 seq1.createDatasetSequence();
1075 seq1.setDescription("description");
1076 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1078 // JAL-2046 - what is the contract for using a derived sequence's
1079 // addSequenceFeature ?
1080 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1082 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1083 // here we add DBRef to the dataset sequence:
1084 seq1.getDatasetSequence().addDBRef(
1085 new DBRefEntry("EMBL", "1.2", "AZ12345"));
1087 SequenceI copy = new Sequence(seq1);
1089 assertNotNull(copy.getDatasetSequence());
1090 assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
1092 verifyCopiedSequence(seq1, copy);
1094 // getDBRef looks inside dataset sequence and this is shared,
1095 // so holds the same dbref objects
1096 List<DBRefEntry> dbrefs = copy.getDBRefs();
1097 assertEquals(1, dbrefs.size());
1098 assertSame(dbrefs.get(0), seq1.getDBRefs().get(0));
1102 * Helper to make assertions about a copied sequence
1107 protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
1109 // verify basic properties:
1110 assertEquals(copy.getName(), seq1.getName());
1111 assertEquals(copy.getDescription(), seq1.getDescription());
1112 assertEquals(copy.getStart(), seq1.getStart());
1113 assertEquals(copy.getEnd(), seq1.getEnd());
1114 assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
1116 // copy has a copy of the annotation:
1117 AlignmentAnnotation[] anns = copy.getAnnotation();
1118 assertEquals(1, anns.length);
1119 assertFalse(anns[0] == seq1.getAnnotation()[0]);
1120 assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
1121 assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
1122 assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
1124 // copy has a copy of the sequence feature:
1125 List<SequenceFeature> sfs = copy.getSequenceFeatures();
1126 assertEquals(1, sfs.size());
1127 if (seq1.getDatasetSequence() != null
1128 && copy.getDatasetSequence() == seq1.getDatasetSequence())
1130 assertSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1134 assertNotSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1136 assertEquals(sfs.get(0), seq1.getSequenceFeatures().get(0));
1138 // copy has a copy of the PDB entry
1139 Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
1140 assertEquals(1, pdbs.size());
1141 assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
1142 assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
1145 @Test(groups = "Functional")
1146 public void testGetCharAt()
1148 SequenceI sq = new Sequence("", "abcde");
1149 assertEquals('a', sq.getCharAt(0));
1150 assertEquals('e', sq.getCharAt(4));
1151 assertEquals(' ', sq.getCharAt(5));
1152 assertEquals(' ', sq.getCharAt(-1));
1155 @Test(groups = { "Functional" })
1156 public void testAddSequenceFeatures()
1158 SequenceI sq = new Sequence("", "abcde");
1159 // type may not be null
1160 assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
1162 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1164 // can't add a duplicate feature
1165 assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
1167 // can add a different feature
1168 assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
1169 8, 0f, null))); // different type
1170 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
1171 "description", 4, 8, 0f, null)));// different description
1172 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
1173 8, 0f, null))); // different start position
1174 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1175 9, 0f, null))); // different end position
1176 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1177 8, 1f, null))); // different score
1178 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1179 8, Float.NaN, null))); // score NaN
1180 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1181 8, 0f, "Metal"))); // different group
1182 assertEquals(8, sq.getFeatures().getAllFeatures().size());
1186 * Tests for adding (or updating) dbrefs
1188 * @see DBRefEntry#updateFrom(DBRefEntry)
1190 @Test(groups = { "Functional" })
1191 public void testAddDBRef()
1193 SequenceI sq = new Sequence("", "abcde");
1194 assertNull(sq.getDBRefs());
1195 DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
1197 assertEquals(1, sq.getDBRefs().size());
1198 assertSame(dbref, sq.getDBRefs().get(0));
1201 * change of version - new entry
1203 DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
1204 sq.addDBRef(dbref2);
1205 assertEquals(2, sq.getDBRefs().size());
1206 assertSame(dbref, sq.getDBRefs().get(0));
1207 assertSame(dbref2, sq.getDBRefs().get(1));
1210 * matches existing entry - not added
1212 sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
1213 assertEquals(2, sq.getDBRefs().size());
1216 * different source = new entry
1218 DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
1219 sq.addDBRef(dbref3);
1220 assertEquals(3, sq.getDBRefs().size());
1221 assertSame(dbref3, sq.getDBRefs().get(2));
1224 * different ref = new entry
1226 DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
1227 sq.addDBRef(dbref4);
1228 assertEquals(4, sq.getDBRefs().size());
1229 assertSame(dbref4, sq.getDBRefs().get(3));
1232 * matching ref with a mapping - map updated
1234 DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
1235 Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
1238 sq.addDBRef(dbref5);
1239 assertEquals(4, sq.getDBRefs().size());
1240 assertSame(dbref4, sq.getDBRefs().get(3));
1241 assertSame(map, dbref4.getMap());
1244 * 'real' version replaces "0" version
1246 dbref2.setVersion("0");
1247 DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
1248 dbref2.getAccessionId());
1249 sq.addDBRef(dbref6);
1250 assertEquals(4, sq.getDBRefs().size());
1251 assertSame(dbref2, sq.getDBRefs().get(1));
1252 assertEquals("3", dbref2.getVersion());
1255 * 'real' version replaces "source:0" version
1257 dbref3.setVersion("Uniprot:0");
1258 DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
1259 dbref3.getAccessionId());
1260 sq.addDBRef(dbref7);
1261 assertEquals(4, sq.getDBRefs().size());
1262 assertSame(dbref3, sq.getDBRefs().get(2));
1263 assertEquals("3", dbref2.getVersion());
1266 @Test(groups = { "Functional" })
1267 public void testGetPrimaryDBRefs_peptide()
1269 SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22);
1272 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1273 assertTrue(primaryDBRefs.isEmpty());
1277 primaryDBRefs = sq.getPrimaryDBRefs();
1278 assertTrue(primaryDBRefs.isEmpty());
1280 // primary - uniprot
1281 DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760");
1282 sq.addDBRef(upentry1);
1284 // primary - uniprot with congruent map
1285 DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
1286 upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
1287 new int[] { 10, 22 }, 1, 1)));
1288 sq.addDBRef(upentry2);
1290 // primary - uniprot with map of enclosing sequence
1291 DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
1292 upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
1293 new int[] { 8, 24 }, 1, 1)));
1294 sq.addDBRef(upentry3);
1296 // not primary - uniprot with map of sub-sequence (5')
1297 DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
1298 upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
1299 new int[] { 10, 18 }, 1, 1)));
1300 sq.addDBRef(upentry4);
1302 // not primary - uniprot with map that overlaps 3'
1303 DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
1304 upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
1305 new int[] { 12, 22 }, 1, 1)));
1306 sq.addDBRef(upentry5);
1308 // not primary - uniprot with map to different coordinates frame
1309 DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
1310 upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
1311 new int[] { 112, 118 }, 1, 1)));
1312 sq.addDBRef(upentry6);
1314 // not primary - dbref to 'non-core' database
1315 DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903");
1316 sq.addDBRef(upentry7);
1318 // primary - type is PDB
1319 DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
1320 sq.addDBRef(pdbentry);
1322 // not primary - PDBEntry has no file
1323 sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
1325 // not primary - no PDBEntry
1326 sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
1328 // add corroborating PDB entry for primary DBref -
1329 // needs to have a file as well as matching ID
1330 // note PDB ID is not treated as case sensitive
1331 sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
1334 // not valid DBRef - no file..
1335 sq.addPDBId(new PDBEntry("1AAA", null, null, null));
1337 primaryDBRefs = sq.getPrimaryDBRefs();
1338 assertEquals(4, primaryDBRefs.size());
1339 assertTrue("Couldn't find simple primary reference (UNIPROT)",
1340 primaryDBRefs.contains(upentry1));
1341 assertTrue("Couldn't find mapped primary reference (UNIPROT)",
1342 primaryDBRefs.contains(upentry2));
1343 assertTrue("Couldn't find mapped context reference (UNIPROT)",
1344 primaryDBRefs.contains(upentry3));
1345 assertTrue("Couldn't find expected PDB primary reference",
1346 primaryDBRefs.contains(pdbentry));
1349 @Test(groups = { "Functional" })
1350 public void testGetPrimaryDBRefs_nucleotide()
1352 SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
1354 // primary - Ensembl
1355 DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
1358 // not primary - Ensembl 'transcript' mapping of sub-sequence
1359 DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
1360 dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
1361 new int[] { 1, 11 }, 1, 1)));
1364 // primary - EMBL with congruent map
1365 DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
1366 dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
1367 new int[] { 10, 34 }, 1, 1)));
1370 // not primary - to non-core database
1371 DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234");
1374 // not primary - to protein
1375 DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
1378 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1379 assertEquals(2, primaryDBRefs.size());
1380 assertTrue(primaryDBRefs.contains(dbr1));
1381 assertTrue(primaryDBRefs.contains(dbr3));
1385 * Test the method that updates the list of PDBEntry from any new DBRefEntry
1388 @Test(groups = { "Functional" })
1389 public void testUpdatePDBIds()
1391 PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
1392 seq.addPDBId(pdbe1);
1393 seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
1394 seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
1395 seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
1396 seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
1397 // 7 is not a valid chain code:
1398 seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
1401 List<PDBEntry> pdbIds = seq.getAllPDBEntries();
1402 assertEquals(4, pdbIds.size());
1403 assertSame(pdbe1, pdbIds.get(0));
1404 // chain code got added to 3A6S:
1405 assertEquals("B", pdbe1.getChainCode());
1406 assertEquals("1A70", pdbIds.get(1).getId());
1407 // 4BQGA is parsed into id + chain
1408 assertEquals("4BQG", pdbIds.get(2).getId());
1409 assertEquals("a", pdbIds.get(2).getChainCode());
1410 assertEquals("2GIS7", pdbIds.get(3).getId());
1411 assertNull(pdbIds.get(3).getChainCode());
1415 * Test the method that either adds a pdbid or updates an existing one
1417 @Test(groups = { "Functional" })
1418 public void testAddPDBId()
1420 PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
1422 assertEquals(1, seq.getAllPDBEntries().size());
1423 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1424 assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
1426 // add the same entry
1428 assertEquals(1, seq.getAllPDBEntries().size());
1429 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1431 // add an identical entry
1432 seq.addPDBId(new PDBEntry("3A6S", null, null, null));
1433 assertEquals(1, seq.getAllPDBEntries().size());
1434 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1436 // add a different entry
1437 PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
1438 seq.addPDBId(pdbe2);
1439 assertEquals(2, seq.getAllPDBEntries().size());
1440 assertSame(pdbe, seq.getAllPDBEntries().get(0));
1441 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1443 // update pdbe with chain code, file, type
1444 PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
1445 seq.addPDBId(pdbe3);
1446 assertEquals(2, seq.getAllPDBEntries().size());
1447 assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
1448 assertEquals("3A6S", pdbe.getId()); // unchanged
1449 assertEquals("A", pdbe.getChainCode()); // updated
1450 assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
1451 assertEquals("filepath", pdbe.getFile()); // updated
1452 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1454 // add with a different file path
1455 PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
1456 seq.addPDBId(pdbe4);
1457 assertEquals(3, seq.getAllPDBEntries().size());
1458 assertSame(pdbe4, seq.getAllPDBEntries().get(2));
1460 // add with a different chain code
1461 PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
1462 seq.addPDBId(pdbe5);
1463 assertEquals(4, seq.getAllPDBEntries().size());
1464 assertSame(pdbe5, seq.getAllPDBEntries().get(3));
1466 // add with a fake pdbid
1467 // (models don't have an embedded ID)
1468 String realId = "RealIDQ";
1469 PDBEntry pdbe6 = new PDBEntry(realId,null,Type.PDB,"real/localpath");
1470 PDBEntry pdbe7 = new PDBEntry("RealID/real/localpath","C",Type.MMCIF,"real/localpath");
1471 pdbe7.setFakedPDBId(true);
1472 seq.addPDBId(pdbe6);
1473 assertEquals(5,seq.getAllPDBEntries().size());
1474 seq.addPDBId(pdbe7);
1475 assertEquals(5,seq.getAllPDBEntries().size());
1476 assertFalse(pdbe6.fakedPDBId());
1477 assertSame(pdbe6,seq.getAllPDBEntries().get(4));
1478 assertEquals("C",pdbe6.getChainCode());
1479 assertEquals(realId, pdbe6.getId());
1483 groups = { "Functional" },
1484 expectedExceptions = { IllegalArgumentException.class })
1485 public void testSetDatasetSequence_toSelf()
1487 seq.setDatasetSequence(seq);
1491 groups = { "Functional" },
1492 expectedExceptions = { IllegalArgumentException.class })
1493 public void testSetDatasetSequence_cascading()
1495 SequenceI seq2 = new Sequence("Seq2", "xyz");
1496 seq2.createDatasetSequence();
1497 seq.setDatasetSequence(seq2);
1500 @Test(groups = { "Functional" })
1501 public void testFindFeatures()
1503 SequenceI sq = new Sequence("test/8-16", "-ABC--DEF--GHI--");
1504 sq.createDatasetSequence();
1506 assertTrue(sq.findFeatures(1, 99).isEmpty());
1508 // add non-positional feature
1509 SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f,
1511 sq.addSequenceFeature(sf0);
1512 // add feature on BCD
1513 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
1515 sq.addSequenceFeature(sfBCD);
1516 // add feature on DE
1517 SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
1519 sq.addSequenceFeature(sfDE);
1520 // add contact feature at [B, H]
1521 SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
1522 "desc", 9, 15, 2f, null);
1523 sq.addSequenceFeature(sfContactBH);
1524 // add contact feature at [F, G]
1525 SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
1526 "desc", 13, 14, 2f, null);
1527 sq.addSequenceFeature(sfContactFG);
1528 // add single position feature at [I]
1529 SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
1530 "desc", 16, 16, null);
1531 sq.addSequenceFeature(sfI);
1533 // no features in columns 1-2 (-A)
1534 List<SequenceFeature> found = sq.findFeatures(1, 2);
1535 assertTrue(found.isEmpty());
1537 // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
1538 found = sq.findFeatures(1, 6);
1539 assertEquals(2, found.size());
1540 assertTrue(found.contains(sfBCD));
1541 assertTrue(found.contains(sfContactBH));
1543 // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
1544 found = sq.findFeatures(5, 6);
1545 assertEquals(1, found.size());
1546 assertTrue(found.contains(sfBCD));
1548 // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
1549 found = sq.findFeatures(7, 10);
1550 assertEquals(3, found.size());
1551 assertTrue(found.contains(sfBCD));
1552 assertTrue(found.contains(sfDE));
1553 assertTrue(found.contains(sfContactFG));
1555 // columns 10-11 (--) should find nothing
1556 found = sq.findFeatures(10, 11);
1557 assertEquals(0, found.size());
1559 // columns 14-14 (I) should find variant feature
1560 found = sq.findFeatures(14, 14);
1561 assertEquals(1, found.size());
1562 assertTrue(found.contains(sfI));
1565 @Test(groups = { "Functional" })
1566 public void testFindIndex_withCursor()
1568 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1569 final int tok = (int) PA.getValue(sq, "changeCount");
1570 assertEquals(1, tok);
1572 // find F given A, check cursor is now at the found position
1573 assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, tok)));
1574 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1575 assertEquals(13, cursor.residuePosition);
1576 assertEquals(10, cursor.columnPosition);
1579 assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, tok)));
1580 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1581 assertEquals(8, cursor.residuePosition);
1582 assertEquals(2, cursor.columnPosition);
1584 // find C given C (no cursor update is done for this case)
1585 assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, tok)));
1586 SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1587 assertSame(cursor2, cursor);
1590 * sequence 'end' beyond end of sequence returns length of sequence
1591 * (for compatibility with pre-cursor code)
1592 * - also verify the cursor is left in a valid state
1594 sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
1595 assertEquals(7, sq.findIndex(10)); // establishes a cursor
1596 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1597 assertEquals(10, cursor.residuePosition);
1598 assertEquals(7, cursor.columnPosition);
1599 assertEquals(sq.getLength(), sq.findIndex(65));
1600 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1601 assertSame(cursor, cursor2); // not updated for this case!
1603 sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
1604 sq.findIndex(10); // establishes a cursor
1605 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1606 assertEquals(sq.getLength(), sq.findIndex(65));
1607 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1608 assertSame(cursor, cursor2); // not updated for this case!
1611 * residue after sequence 'start' but before first residue should return
1612 * zero (for compatibility with pre-cursor code)
1614 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
1615 sq.findIndex(10); // establishes a cursor
1616 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1617 assertEquals(0, sq.findIndex(3));
1618 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1619 assertSame(cursor, cursor2); // not updated for this case!
1621 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
1622 sq.findIndex(10); // establishes a cursor
1623 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1624 assertEquals(0, sq.findIndex(2));
1625 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1626 assertSame(cursor, cursor2); // not updated for this case!
1629 @Test(groups = { "Functional" })
1630 public void testFindPosition_withCursor()
1632 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1633 final int tok = (int) PA.getValue(sq, "changeCount");
1634 assertEquals(1, tok);
1636 // find F pos given A - lastCol gets set in cursor
1638 sq.findPosition(10, new SequenceCursor(sq, 8, 2, tok)));
1639 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1640 PA.getValue(sq, "cursor").toString());
1642 // find A pos given F - first residue column is saved in cursor
1644 sq.findPosition(2, new SequenceCursor(sq, 13, 10, tok)));
1645 assertEquals("test:Pos8:Col2:startCol2:endCol10:tok1",
1646 PA.getValue(sq, "cursor").toString());
1648 // find C pos given C (neither startCol nor endCol is set)
1650 sq.findPosition(6, new SequenceCursor(sq, 10, 6, tok)));
1651 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1",
1652 PA.getValue(sq, "cursor").toString());
1654 // now the grey area - what residue position for a gapped column? JAL-2562
1656 // find 'residue' for column 3 given cursor for D (so working left)
1657 // returns B9; cursor is updated to [B 5]
1658 assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, tok)));
1659 assertEquals("test:Pos9:Col5:startCol0:endCol0:tok1",
1660 PA.getValue(sq, "cursor").toString());
1662 // find 'residue' for column 8 given cursor for D (so working right)
1663 // returns E12; cursor is updated to [D 7]
1665 sq.findPosition(8, new SequenceCursor(sq, 11, 7, tok)));
1666 assertEquals("test:Pos11:Col7:startCol0:endCol0:tok1",
1667 PA.getValue(sq, "cursor").toString());
1669 // find 'residue' for column 12 given cursor for B
1670 // returns 1 more than last residue position; cursor is updated to [F 10]
1671 // lastCol position is saved in cursor
1673 sq.findPosition(12, new SequenceCursor(sq, 9, 5, tok)));
1674 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1675 PA.getValue(sq, "cursor").toString());
1678 * findPosition for column beyond length of sequence
1679 * returns 1 more than the last residue position
1680 * cursor is set to last real residue position [F 10]
1683 sq.findPosition(99, new SequenceCursor(sq, 8, 2, tok)));
1684 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1685 PA.getValue(sq, "cursor").toString());
1688 * and the case without a trailing gap
1690 sq = new Sequence("test/8-13", "-A--BCD-EF");
1691 // first find C from A
1692 assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, tok)));
1693 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1694 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok1",
1696 // now 'find' 99 from C
1697 // cursor is set to [F 10] and saved lastCol
1698 assertEquals(14, sq.findPosition(99, cursor));
1699 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok1",
1700 PA.getValue(sq, "cursor").toString());
1704 public void testIsValidCursor()
1706 Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
1707 assertFalse(sq.isValidCursor(null));
1710 * cursor is valid if it has valid sequence ref and changeCount token
1711 * and positions within the range of the sequence
1713 int changeCount = (int) PA.getValue(sq, "changeCount");
1714 SequenceCursor cursor = new SequenceCursor(sq, 13, 1, changeCount);
1715 assertTrue(sq.isValidCursor(cursor));
1718 * column position outside [0 - length] is rejected
1720 cursor = new SequenceCursor(sq, 13, -1, changeCount);
1721 assertFalse(sq.isValidCursor(cursor));
1722 cursor = new SequenceCursor(sq, 13, 10, changeCount);
1723 assertFalse(sq.isValidCursor(cursor));
1724 cursor = new SequenceCursor(sq, 7, 8, changeCount);
1725 assertFalse(sq.isValidCursor(cursor));
1726 cursor = new SequenceCursor(sq, 14, 2, changeCount);
1727 assertFalse(sq.isValidCursor(cursor));
1730 * wrong sequence is rejected
1732 cursor = new SequenceCursor(null, 13, 1, changeCount);
1733 assertFalse(sq.isValidCursor(cursor));
1734 cursor = new SequenceCursor(new Sequence("Seq", "abc"), 13, 1,
1736 assertFalse(sq.isValidCursor(cursor));
1739 * wrong token value is rejected
1741 cursor = new SequenceCursor(sq, 13, 1, changeCount + 1);
1742 assertFalse(sq.isValidCursor(cursor));
1743 cursor = new SequenceCursor(sq, 13, 1, changeCount - 1);
1744 assertFalse(sq.isValidCursor(cursor));
1747 @Test(groups = { "Functional" })
1748 public void testFindPosition_withCursorAndEdits()
1750 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1752 // find F pos given A
1753 assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
1754 int token = (int) PA.getValue(sq, "changeCount"); // 0
1755 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1756 assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
1759 * setSequence should invalidate the cursor cached by the sequence
1761 sq.setSequence("-A-BCD-EF---"); // one gap removed
1762 assertEquals(8, sq.getStart()); // sanity check
1763 assertEquals(11, sq.findPosition(5)); // D11
1764 // cursor should now be at [D 6]
1765 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1766 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
1767 assertEquals(0, cursor.lastColumnPosition); // not yet found
1768 assertEquals(13, sq.findPosition(8)); // E13
1769 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1770 assertEquals(9, cursor.lastColumnPosition); // found
1773 * deleteChars should invalidate the cached cursor
1775 sq.deleteChars(2, 5); // delete -BC
1776 assertEquals("-AD-EF---", sq.getSequenceAsString());
1777 assertEquals(8, sq.getStart()); // sanity check
1778 assertEquals(10, sq.findPosition(4)); // E10
1779 // cursor should now be at [E 5]
1780 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1781 assertEquals(new SequenceCursor(sq, 10, 5, ++token), cursor);
1784 * Edit to insert gaps should invalidate the cached cursor
1785 * insert 2 gaps at column[3] to make -AD---EF---
1787 SequenceI[] seqs = new SequenceI[] { sq };
1788 AlignmentI al = new Alignment(seqs);
1789 new EditCommand().appendEdit(Action.INSERT_GAP, seqs, 3, 2, al, true);
1790 assertEquals("-AD---EF---", sq.getSequenceAsString());
1791 assertEquals(10, sq.findPosition(4)); // E10
1792 // cursor should now be at [D 3]
1793 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1794 assertEquals(new SequenceCursor(sq, 9, 3, ++token), cursor);
1797 * insertCharAt should invalidate the cached cursor
1798 * insert CC at column[4] to make -AD-CC--EF---
1800 sq.insertCharAt(4, 2, 'C');
1801 assertEquals("-AD-CC--EF---", sq.getSequenceAsString());
1802 assertEquals(13, sq.findPosition(9)); // F13
1803 // cursor should now be at [F 10]
1804 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1805 assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
1808 * changing sequence start should invalidate cursor
1810 sq = new Sequence("test/8-13", "-A--BCD-EF--");
1811 assertEquals(8, sq.getStart());
1812 assertEquals(9, sq.findPosition(4)); // B(9)
1814 assertEquals(8, sq.findPosition(4)); // is now B(8)
1816 assertEquals(11, sq.findPosition(4)); // is now B(11)
1819 @Test(groups = { "Functional" })
1820 public void testGetSequence()
1822 String seqstring = "-A--BCD-EF--";
1823 Sequence sq = new Sequence("test/8-13", seqstring);
1824 sq.createDatasetSequence();
1825 assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray()));
1826 assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(),
1827 "ABCDEF".toCharArray()));
1829 // verify a copy of the sequence array is returned
1830 char[] theSeq = (char[]) PA.getValue(sq, "sequence");
1831 assertNotSame(theSeq, sq.getSequence());
1832 theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence");
1833 assertNotSame(theSeq, sq.getDatasetSequence().getSequence());
1836 @Test(groups = { "Functional" })
1837 public void testReplace()
1839 String seqstring = "-A--BCD-EF--";
1840 SequenceI sq = new Sequence("test/8-13", seqstring);
1841 // changeCount is incremented for setStart
1842 assertEquals(1, PA.getValue(sq, "changeCount"));
1844 assertEquals(0, sq.replace('A', 'A')); // same char
1845 assertEquals(seqstring, sq.getSequenceAsString());
1846 assertEquals(1, PA.getValue(sq, "changeCount"));
1848 assertEquals(0, sq.replace('X', 'Y')); // not there
1849 assertEquals(seqstring, sq.getSequenceAsString());
1850 assertEquals(1, PA.getValue(sq, "changeCount"));
1852 assertEquals(1, sq.replace('A', 'K'));
1853 assertEquals("-K--BCD-EF--", sq.getSequenceAsString());
1854 assertEquals(2, PA.getValue(sq, "changeCount"));
1856 assertEquals(6, sq.replace('-', '.'));
1857 assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
1858 assertEquals(3, PA.getValue(sq, "changeCount"));
1861 @Test(groups = { "Functional" })
1862 public void testGapBitset()
1864 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
1865 BitSet bs = sq.gapBitset();
1866 BitSet expected = new BitSet();
1870 expected.set(11, 13);
1872 assertTrue(bs.equals(expected));
1876 public void testFindFeatures_largeEndPos()
1879 * imitate a PDB sequence where end is larger than end position
1881 SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
1882 sq.createDatasetSequence();
1884 assertTrue(sq.findFeatures(1, 9).isEmpty());
1885 // should be no array bounds exception - JAL-2772
1886 assertTrue(sq.findFeatures(1, 15).isEmpty());
1888 // add feature on BCD
1889 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
1891 sq.addSequenceFeature(sfBCD);
1893 // no features in columns 1-2 (-A)
1894 List<SequenceFeature> found = sq.findFeatures(1, 2);
1895 assertTrue(found.isEmpty());
1897 // columns 1-6 (-ABC--) includes BCD
1898 found = sq.findFeatures(1, 6);
1899 assertEquals(1, found.size());
1900 assertTrue(found.contains(sfBCD));
1902 // columns 10-11 (--) should find nothing
1903 found = sq.findFeatures(10, 11);
1904 assertEquals(0, found.size());
1907 @Test(groups = { "Functional" })
1908 public void testSetName()
1910 SequenceI sq = new Sequence("test", "-ABC---DE-F--");
1911 assertEquals("test", sq.getName());
1912 assertEquals(1, sq.getStart());
1913 assertEquals(6, sq.getEnd());
1915 sq.setName("testing");
1916 assertEquals("testing", sq.getName());
1918 sq.setName("test/8-10");
1919 assertEquals("test", sq.getName());
1920 assertEquals(8, sq.getStart());
1921 assertEquals(13, sq.getEnd()); // note end is recomputed
1923 sq.setName("testing/7-99");
1924 assertEquals("testing", sq.getName());
1925 assertEquals(7, sq.getStart());
1926 assertEquals(99, sq.getEnd()); // end may be beyond physical end
1929 assertEquals("", sq.getName());
1930 assertEquals(2, sq.getStart());
1931 assertEquals(7, sq.getEnd());
1933 sq.setName("test/"); // invalid
1934 assertEquals("test/", sq.getName());
1935 assertEquals(2, sq.getStart());
1936 assertEquals(7, sq.getEnd());
1938 sq.setName("test/6-13/7-99");
1939 assertEquals("test/6-13", sq.getName());
1940 assertEquals(7, sq.getStart());
1941 assertEquals(99, sq.getEnd());
1943 sq.setName("test/0-5"); // 0 is invalid - ignored
1944 assertEquals("test/0-5", sq.getName());
1945 assertEquals(7, sq.getStart());
1946 assertEquals(99, sq.getEnd());
1948 sq.setName("test/a-5"); // a is invalid - ignored
1949 assertEquals("test/a-5", sq.getName());
1950 assertEquals(7, sq.getStart());
1951 assertEquals(99, sq.getEnd());
1953 sq.setName("test/6-5"); // start > end is invalid - ignored
1954 assertEquals("test/6-5", sq.getName());
1955 assertEquals(7, sq.getStart());
1956 assertEquals(99, sq.getEnd());
1958 sq.setName("test/5"); // invalid - ignored
1959 assertEquals("test/5", sq.getName());
1960 assertEquals(7, sq.getStart());
1961 assertEquals(99, sq.getEnd());
1963 sq.setName("test/-5"); // invalid - ignored
1964 assertEquals("test/-5", sq.getName());
1965 assertEquals(7, sq.getStart());
1966 assertEquals(99, sq.getEnd());
1968 sq.setName("test/5-"); // invalid - ignored
1969 assertEquals("test/5-", sq.getName());
1970 assertEquals(7, sq.getStart());
1971 assertEquals(99, sq.getEnd());
1973 sq.setName("test/5-6-7"); // invalid - ignored
1974 assertEquals("test/5-6-7", sq.getName());
1975 assertEquals(7, sq.getStart());
1976 assertEquals(99, sq.getEnd());
1978 sq.setName(null); // invalid, gets converted to space
1979 assertEquals("", sq.getName());
1980 assertEquals(7, sq.getStart());
1981 assertEquals(99, sq.getEnd());
1984 @Test(groups = { "Functional" })
1985 public void testCheckValidRange()
1987 Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
1988 assertEquals(7, sq.getStart());
1989 assertEquals(12, sq.getEnd());
1992 * checkValidRange ensures end is at least the last residue position
1994 PA.setValue(sq, "end", 2);
1995 sq.checkValidRange();
1996 assertEquals(12, sq.getEnd());
1999 * end may be beyond the last residue position
2001 PA.setValue(sq, "end", 22);
2002 sq.checkValidRange();
2003 assertEquals(22, sq.getEnd());
2006 @Test(groups = { "Functional" })
2007 public void testDeleteChars_withGaps()
2012 SequenceI sq = new Sequence("test/8-10", "A-B-C");
2013 sq.createDatasetSequence();
2014 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2015 sq.deleteChars(1, 2); // delete first gap
2016 assertEquals("AB-C", sq.getSequenceAsString());
2017 assertEquals(8, sq.getStart());
2018 assertEquals(10, sq.getEnd());
2019 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2022 * delete gaps and residues at start (no new dataset sequence)
2024 sq = new Sequence("test/8-10", "A-B-C");
2025 sq.createDatasetSequence();
2026 sq.deleteChars(0, 3); // delete A-B
2027 assertEquals("-C", sq.getSequenceAsString());
2028 assertEquals(10, sq.getStart());
2029 assertEquals(10, sq.getEnd());
2030 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2033 * delete gaps and residues at end (no new dataset sequence)
2035 sq = new Sequence("test/8-10", "A-B-C");
2036 sq.createDatasetSequence();
2037 sq.deleteChars(2, 5); // delete B-C
2038 assertEquals("A-", sq.getSequenceAsString());
2039 assertEquals(8, sq.getStart());
2040 assertEquals(8, sq.getEnd());
2041 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
2044 * delete gaps and residues internally (new dataset sequence)
2045 * first delete from gap to residue
2047 sq = new Sequence("test/8-10", "A-B-C");
2048 sq.createDatasetSequence();
2049 sq.deleteChars(1, 3); // delete -B
2050 assertEquals("A-C", sq.getSequenceAsString());
2051 assertEquals(8, sq.getStart());
2052 assertEquals(9, sq.getEnd());
2053 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2054 assertEquals(8, sq.getDatasetSequence().getStart());
2055 assertEquals(9, sq.getDatasetSequence().getEnd());
2058 * internal delete from gap to gap
2060 sq = new Sequence("test/8-10", "A-B-C");
2061 sq.createDatasetSequence();
2062 sq.deleteChars(1, 4); // delete -B-
2063 assertEquals("AC", sq.getSequenceAsString());
2064 assertEquals(8, sq.getStart());
2065 assertEquals(9, sq.getEnd());
2066 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2067 assertEquals(8, sq.getDatasetSequence().getStart());
2068 assertEquals(9, sq.getDatasetSequence().getEnd());
2071 * internal delete from residue to residue
2073 sq = new Sequence("test/8-10", "A-B-C");
2074 sq.createDatasetSequence();
2075 sq.deleteChars(2, 3); // delete B
2076 assertEquals("A--C", sq.getSequenceAsString());
2077 assertEquals(8, sq.getStart());
2078 assertEquals(9, sq.getEnd());
2079 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2080 assertEquals(8, sq.getDatasetSequence().getStart());
2081 assertEquals(9, sq.getDatasetSequence().getEnd());
2085 * Test the code used to locate the reference sequence ruler origin
2087 @Test(groups = { "Functional" })
2088 public void testLocateVisibleStartofSequence()
2090 // create random alignment
2091 AlignmentGenerator gen = new AlignmentGenerator(false);
2092 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
2094 HiddenColumns cs = al.getHiddenColumns();
2095 ColumnSelection colsel = new ColumnSelection();
2097 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
2098 assertEquals(2, seq.findIndex(seq.getStart()));
2100 // no hidden columns
2101 assertEquals(seq.findIndex(seq.getStart()) - 1,
2102 seq.firstResidueOutsideIterator(cs.iterator()));
2104 // hidden column on gap after end of sequence - should not affect bounds
2105 colsel.hideSelectedColumns(13, al.getHiddenColumns());
2106 assertEquals(seq.findIndex(seq.getStart()) - 1,
2107 seq.firstResidueOutsideIterator(cs.iterator()));
2109 cs.revealAllHiddenColumns(colsel);
2110 // hidden column on gap before beginning of sequence - should vis bounds by
2112 colsel.hideSelectedColumns(0, al.getHiddenColumns());
2113 assertEquals(seq.findIndex(seq.getStart()) - 2,
2114 cs.absoluteToVisibleColumn(
2115 seq.firstResidueOutsideIterator(cs.iterator())));
2117 cs.revealAllHiddenColumns(colsel);
2118 // hide columns around most of sequence - leave one residue remaining
2119 cs.hideColumns(1, 3);
2120 cs.hideColumns(6, 11);
2122 Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
2124 assertEquals("-D", seq.getSequenceStringFromIterator(it));
2125 // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
2128 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2129 cs.revealAllHiddenColumns(colsel);
2131 // hide whole sequence - should just get location of hidden region
2132 // containing sequence
2133 cs.hideColumns(1, 11);
2134 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2136 cs.revealAllHiddenColumns(colsel);
2137 cs.hideColumns(0, 15);
2138 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2140 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
2142 cs.revealAllHiddenColumns(colsel);
2143 cs.hideColumns(7, 17);
2144 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2146 cs.revealAllHiddenColumns(colsel);
2147 cs.hideColumns(3, 17);
2148 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2150 cs.revealAllHiddenColumns(colsel);
2151 cs.hideColumns(3, 19);
2152 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2154 cs.revealAllHiddenColumns(colsel);
2155 cs.hideColumns(0, 0);
2156 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2158 cs.revealAllHiddenColumns(colsel);
2159 cs.hideColumns(0, 1);
2160 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2162 cs.revealAllHiddenColumns(colsel);
2163 cs.hideColumns(0, 2);
2164 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2166 cs.revealAllHiddenColumns(colsel);
2167 cs.hideColumns(1, 1);
2168 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2170 cs.revealAllHiddenColumns(colsel);
2171 cs.hideColumns(1, 2);
2172 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2174 cs.revealAllHiddenColumns(colsel);
2175 cs.hideColumns(1, 3);
2176 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2178 cs.revealAllHiddenColumns(colsel);
2179 cs.hideColumns(0, 2);
2180 cs.hideColumns(5, 6);
2181 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2183 cs.revealAllHiddenColumns(colsel);
2184 cs.hideColumns(0, 2);
2185 cs.hideColumns(5, 6);
2186 cs.hideColumns(9, 10);
2187 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2189 cs.revealAllHiddenColumns(colsel);
2190 cs.hideColumns(0, 2);
2191 cs.hideColumns(7, 11);
2192 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2194 cs.revealAllHiddenColumns(colsel);
2195 cs.hideColumns(2, 4);
2196 cs.hideColumns(7, 11);
2197 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2199 cs.revealAllHiddenColumns(colsel);
2200 cs.hideColumns(2, 4);
2201 cs.hideColumns(7, 12);
2202 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2204 cs.revealAllHiddenColumns(colsel);
2205 cs.hideColumns(1, 11);
2206 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2208 cs.revealAllHiddenColumns(colsel);
2209 cs.hideColumns(0, 12);
2210 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2212 cs.revealAllHiddenColumns(colsel);
2213 cs.hideColumns(0, 4);
2214 cs.hideColumns(6, 12);
2215 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2217 cs.revealAllHiddenColumns(colsel);
2218 cs.hideColumns(0, 1);
2219 cs.hideColumns(3, 12);
2220 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2222 cs.revealAllHiddenColumns(colsel);
2223 cs.hideColumns(3, 14);
2224 cs.hideColumns(17, 19);
2225 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2227 cs.revealAllHiddenColumns(colsel);
2228 cs.hideColumns(3, 7);
2229 cs.hideColumns(9, 14);
2230 cs.hideColumns(17, 19);
2231 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2233 cs.revealAllHiddenColumns(colsel);
2234 cs.hideColumns(0, 1);
2235 cs.hideColumns(3, 4);
2236 cs.hideColumns(6, 8);
2237 cs.hideColumns(10, 12);
2238 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2241 @Test(groups= {"Functional"})
2242 public void testTransferAnnotation() {
2243 Sequence origSeq = new Sequence("MYSEQ","THISISASEQ");
2244 Sequence toSeq = new Sequence("MYSEQ","THISISASEQ");
2245 origSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, true));
2246 toSeq.transferAnnotation(origSeq, null);
2247 assertTrue(toSeq.getDBRefs().size()==1);
2249 assertTrue(toSeq.getDBRefs().get(0).isCanonical());
2251 // check for promotion of non-canonical
2252 // to canonical (e.g. fetch-db-refs on a jalview project pre 2.11.2)
2253 toSeq.setDBRefs(null);
2254 toSeq.addDBRef(new DBRefEntry("UNIPROT", "0", "Q12345", null, false));
2255 toSeq.transferAnnotation(origSeq, null);
2256 assertTrue(toSeq.getDBRefs().size()==1);
2258 assertTrue("Promotion of non-canonical DBRefEntry failed",toSeq.getDBRefs().get(0).isCanonical());