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;
39 import java.util.ArrayList;
40 import java.util.Arrays;
41 import java.util.BitSet;
42 import java.util.Iterator;
43 import java.util.List;
44 import java.util.Vector;
46 import org.testng.Assert;
47 import org.testng.annotations.BeforeClass;
48 import org.testng.annotations.BeforeMethod;
49 import org.testng.annotations.Test;
51 import junit.extensions.PA;
53 public class SequenceTest
55 @BeforeClass(alwaysRun = true)
56 public void setUpJvOptionPane()
58 JvOptionPane.setInteractiveMode(false);
59 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
64 @BeforeMethod(alwaysRun = true)
67 seq = new Sequence("FER1", "AKPNGVL");
70 @Test(groups = { "Functional" })
71 public void testInsertGapsAndGapmaps()
73 SequenceI aseq = seq.deriveSequence();
74 aseq.insertCharAt(2, 3, '-');
75 aseq.insertCharAt(6, 3, '-');
76 assertEquals("Gap insertions not correct", "AK---P---NGVL",
77 aseq.getSequenceAsString());
78 List<int[]> gapInt = aseq.getInsertions();
79 assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
80 assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
81 assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
82 assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
84 BitSet gapfield = aseq.getInsertionsAsBits();
85 BitSet expectedgaps = new BitSet();
86 expectedgaps.set(2, 5);
87 expectedgaps.set(6, 9);
89 assertEquals(6, expectedgaps.cardinality());
91 assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
92 6, gapfield.cardinality());
94 assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
97 @Test(groups = ("Functional"))
98 public void testIsProtein()
101 assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
103 assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
105 SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
106 assertFalse(sq.isProtein());
107 // change sequence, should trigger an update of cached result
108 sq.setSequence("ASDFASDFADSF");
109 assertTrue(sq.isProtein());
112 @Test(groups = { "Functional" })
113 public void testGetAnnotation()
115 // initial state returns null not an empty array
116 assertNull(seq.getAnnotation());
117 AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
119 AlignmentAnnotation[] anns = seq.getAnnotation();
120 assertEquals(1, anns.length);
121 assertSame(ann, anns[0]);
123 // removing all annotations reverts array to null
124 seq.removeAlignmentAnnotation(ann);
125 assertNull(seq.getAnnotation());
128 @Test(groups = { "Functional" })
129 public void testGetAnnotation_forLabel()
131 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
133 addAnnotation("label2", "desc2", "calcId2", 1f);
134 AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
136 AlignmentAnnotation[] anns = seq.getAnnotation("label1");
137 assertEquals(2, anns.length);
138 assertSame(ann1, anns[0]);
139 assertSame(ann3, anns[1]);
142 private AlignmentAnnotation addAnnotation(String label,
143 String description, String calcId, float value)
145 final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
147 annotation.setCalcId(calcId);
148 seq.addAlignmentAnnotation(annotation);
152 @Test(groups = { "Functional" })
153 public void testGetAlignmentAnnotations_forCalcIdAndLabel()
155 addAnnotation("label1", "desc1", "calcId1", 1f);
156 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
158 addAnnotation("label2", "desc3", "calcId3", 1f);
159 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
161 addAnnotation("label5", "desc3", null, 1f);
162 addAnnotation(null, "desc3", "calcId3", 1f);
164 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
166 assertEquals(2, anns.size());
167 assertSame(ann2, anns.get(0));
168 assertSame(ann4, anns.get(1));
170 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
171 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
172 assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
173 assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
174 assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
178 * Tests for addAlignmentAnnotation. Note this method has the side-effect of
179 * setting the sequenceRef on the annotation. Adding the same annotation twice
182 @Test(groups = { "Functional" })
183 public void testAddAlignmentAnnotation()
185 assertNull(seq.getAnnotation());
186 final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
188 assertNull(annotation.sequenceRef);
189 seq.addAlignmentAnnotation(annotation);
190 assertSame(seq, annotation.sequenceRef);
191 AlignmentAnnotation[] anns = seq.getAnnotation();
192 assertEquals(1, anns.length);
193 assertSame(annotation, anns[0]);
195 // re-adding does nothing
196 seq.addAlignmentAnnotation(annotation);
197 anns = seq.getAnnotation();
198 assertEquals(1, anns.length);
199 assertSame(annotation, anns[0]);
201 // an identical but different annotation can be added
202 final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
204 seq.addAlignmentAnnotation(annotation2);
205 anns = seq.getAnnotation();
206 assertEquals(2, anns.length);
207 assertSame(annotation, anns[0]);
208 assertSame(annotation2, anns[1]);
211 @Test(groups = { "Functional" })
212 public void testGetStartGetEnd()
214 SequenceI sq = new Sequence("test", "ABCDEF");
215 assertEquals(1, sq.getStart());
216 assertEquals(6, sq.getEnd());
218 sq = new Sequence("test", "--AB-C-DEF--");
219 assertEquals(1, sq.getStart());
220 assertEquals(6, sq.getEnd());
222 sq = new Sequence("test", "----");
223 assertEquals(1, sq.getStart());
224 assertEquals(0, sq.getEnd()); // ??
228 * Tests for the method that returns an alignment column position (base 1) for
229 * a given sequence position (base 1).
231 @Test(groups = { "Functional" })
232 public void testFindIndex()
235 * call sequenceChanged() after each test to invalidate any cursor,
236 * forcing the 1-arg findIndex to be executed
238 SequenceI sq = new Sequence("test", "ABCDEF");
239 assertEquals(0, sq.findIndex(0));
240 sq.sequenceChanged();
241 assertEquals(1, sq.findIndex(1));
242 sq.sequenceChanged();
243 assertEquals(5, sq.findIndex(5));
244 sq.sequenceChanged();
245 assertEquals(6, sq.findIndex(6));
246 sq.sequenceChanged();
247 assertEquals(6, sq.findIndex(9));
249 final String aligned = "-A--B-C-D-E-F--";
250 assertEquals(15, aligned.length());
251 sq = new Sequence("test/8-13", aligned);
252 assertEquals(2, sq.findIndex(8));
253 sq.sequenceChanged();
254 assertEquals(5, sq.findIndex(9));
255 sq.sequenceChanged();
256 assertEquals(7, sq.findIndex(10));
258 // before start returns 0
259 sq.sequenceChanged();
260 assertEquals(0, sq.findIndex(0));
261 sq.sequenceChanged();
262 assertEquals(0, sq.findIndex(-1));
264 // beyond end returns last residue column
265 sq.sequenceChanged();
266 assertEquals(13, sq.findIndex(99));
269 * residue before sequence 'end' but beyond end of sequence returns
270 * length of sequence (last column) (rightly or wrongly!)
272 sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case
273 assertEquals(6, sq.getLength());
274 sq.sequenceChanged();
275 assertEquals(sq.getLength(), sq.findIndex(14));
276 sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case
277 sq.sequenceChanged();
278 assertEquals(sq.getLength(), sq.findIndex(65));
281 * residue after sequence 'start' but before first residue returns
282 * zero (before first column) (rightly or wrongly!)
284 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
285 sq.sequenceChanged();
286 assertEquals(0, sq.findIndex(3));
287 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
288 sq.sequenceChanged();
289 assertEquals(0, sq.findIndex(2));
292 @Test(groups = { "Functional" })
293 public void testFindPositions()
295 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
300 assertNull(sq.findPositions(6, 5));
305 assertNull(sq.findPositions(1, 1)); // 1-based columns
306 assertNull(sq.findPositions(5, 5));
307 assertNull(sq.findPositions(5, 6));
308 assertNull(sq.findPositions(5, 7));
311 * all ungapped ranges
313 assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
314 assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
315 assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
316 assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
319 * gap to ungapped range
321 assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
322 assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
325 * ungapped to gapped range
327 assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
328 assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
331 * ungapped to ungapped enclosing gaps
333 assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
334 assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
337 * gapped to gapped enclosing ungapped
339 assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
340 assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
341 assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
342 assertEquals(new Range(8, 13), sq.findPositions(1, 99));
345 * now try on a sequence with no gaps
347 sq.createDatasetSequence();
348 assertEquals(new Range(8, 13),
349 sq.getDatasetSequence().findPositions(1, 99));
350 assertEquals(new Range(8, 13),
351 sq.getDatasetSequence().findPositions(0, 99));
356 * Tests for the method that returns a dataset sequence position (start..) for
357 * an aligned column position (base 0).
359 @Test(groups = { "Functional" })
360 public void testFindPosition()
363 * call sequenceChanged() after each test to invalidate any cursor,
364 * forcing the 1-arg findPosition to be executed
366 SequenceI sq = new Sequence("test/8-13", "ABCDEF");
367 assertEquals(8, sq.findPosition(0));
368 // Sequence should now hold a cursor at [8, 0]
369 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0",
370 PA.getValue(sq, "cursor").toString());
371 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
372 int token = (int) PA.getValue(sq, "changeCount");
373 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
375 sq.sequenceChanged();
378 * find F13 at column offset 5, cursor should update to [13, 6]
379 * endColumn is found and saved in cursor
381 assertEquals(13, sq.findPosition(5));
382 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
383 assertEquals(++token, (int) PA.getValue(sq, "changeCount"));
384 assertEquals(new SequenceCursor(sq, 13, 6, token), cursor);
385 assertEquals("test:Pos13:Col6:startCol1:endCol6:tok1",
386 PA.getValue(sq, "cursor").toString());
388 // assertEquals(-1, seq.findPosition(6)); // fails
390 sq = new Sequence("test/8-11", "AB-C-D--");
391 token = (int) PA.getValue(sq, "changeCount"); // 0
392 assertEquals(8, sq.findPosition(0));
393 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
394 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
395 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0",
396 PA.getValue(sq, "cursor").toString());
398 sq.sequenceChanged();
399 assertEquals(9, sq.findPosition(1));
400 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
401 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
402 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok1",
403 PA.getValue(sq, "cursor").toString());
405 sq.sequenceChanged();
406 // gap position 'finds' residue to the right (not the left as per javadoc)
407 // cursor is set to the last residue position found [B 2]
408 assertEquals(10, sq.findPosition(2));
409 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
410 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
411 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2",
412 PA.getValue(sq, "cursor").toString());
414 sq.sequenceChanged();
415 assertEquals(10, sq.findPosition(3));
416 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
417 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
418 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok3",
419 PA.getValue(sq, "cursor").toString());
421 sq.sequenceChanged();
422 // column[4] is the gap after C - returns D11
423 // cursor is set to [C 4]
424 assertEquals(11, sq.findPosition(4));
425 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
426 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
427 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4",
428 PA.getValue(sq, "cursor").toString());
430 sq.sequenceChanged();
431 assertEquals(11, sq.findPosition(5)); // D
432 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
433 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
434 // lastCol has been found and saved in the cursor
435 assertEquals("test:Pos11:Col6:startCol1:endCol6:tok5",
436 PA.getValue(sq, "cursor").toString());
438 sq.sequenceChanged();
439 // returns 1 more than sequence length if off the end ?!?
440 assertEquals(12, sq.findPosition(6));
442 sq.sequenceChanged();
443 assertEquals(12, sq.findPosition(7));
446 * first findPosition should also set firstResCol in cursor
448 sq = new Sequence("test/8-13", "--AB-C-DEF--");
449 assertEquals(8, sq.findPosition(0));
450 assertNull(PA.getValue(sq, "cursor"));
452 sq.sequenceChanged();
453 assertEquals(8, sq.findPosition(1));
454 assertNull(PA.getValue(sq, "cursor"));
456 sq.sequenceChanged();
457 assertEquals(8, sq.findPosition(2));
458 assertEquals("test:Pos8:Col3:startCol3:endCol0:tok2",
459 PA.getValue(sq, "cursor").toString());
461 sq.sequenceChanged();
462 assertEquals(9, sq.findPosition(3));
463 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok3",
464 PA.getValue(sq, "cursor").toString());
466 sq.sequenceChanged();
467 // column[4] is a gap, returns next residue pos (C10)
468 // cursor is set to last residue found [B]
469 assertEquals(10, sq.findPosition(4));
470 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4",
471 PA.getValue(sq, "cursor").toString());
473 sq.sequenceChanged();
474 assertEquals(10, sq.findPosition(5));
475 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok5",
476 PA.getValue(sq, "cursor").toString());
478 sq.sequenceChanged();
479 // column[6] is a gap, returns next residue pos (D11)
480 // cursor is set to last residue found [C]
481 assertEquals(11, sq.findPosition(6));
482 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6",
483 PA.getValue(sq, "cursor").toString());
485 sq.sequenceChanged();
486 assertEquals(11, sq.findPosition(7));
487 assertEquals("test:Pos11:Col8:startCol3:endCol0:tok7",
488 PA.getValue(sq, "cursor").toString());
490 sq.sequenceChanged();
491 assertEquals(12, sq.findPosition(8));
492 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok8",
493 PA.getValue(sq, "cursor").toString());
496 * when the last residue column is found, it is set in the cursor
498 sq.sequenceChanged();
499 assertEquals(13, sq.findPosition(9));
500 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok9",
501 PA.getValue(sq, "cursor").toString());
503 sq.sequenceChanged();
504 assertEquals(14, sq.findPosition(10));
505 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10",
506 PA.getValue(sq, "cursor").toString());
509 * findPosition for column beyond sequence length
510 * returns 1 more than last residue position
512 sq.sequenceChanged();
513 assertEquals(14, sq.findPosition(11));
514 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11",
515 PA.getValue(sq, "cursor").toString());
517 sq.sequenceChanged();
518 assertEquals(14, sq.findPosition(99));
519 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12",
520 PA.getValue(sq, "cursor").toString());
523 * gapped sequence ending in non-gap
525 sq = new Sequence("test/8-13", "--AB-C-DEF");
526 assertEquals(13, sq.findPosition(9));
527 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0",
528 PA.getValue(sq, "cursor").toString());
529 sq.sequenceChanged();
530 assertEquals(12, sq.findPosition(8)); // E12
531 // sequenceChanged() invalidates cursor.lastResidueColumn
532 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
533 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1",
535 // findPosition with cursor accepts base 1 column values
536 assertEquals(13, ((Sequence) sq).findPosition(10, cursor));
537 assertEquals(13, sq.findPosition(9)); // F13
538 // lastResidueColumn has now been found and saved in cursor
539 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1",
540 PA.getValue(sq, "cursor").toString());
543 @Test(groups = { "Functional" })
544 public void testDeleteChars()
549 SequenceI sq = new Sequence("test", "ABCDEF");
550 assertNull(PA.getValue(sq, "datasetSequence"));
551 assertEquals(1, sq.getStart());
552 assertEquals(6, sq.getEnd());
553 sq.deleteChars(2, 3);
554 assertEquals("ABDEF", sq.getSequenceAsString());
555 assertEquals(1, sq.getStart());
556 assertEquals(5, sq.getEnd());
557 assertNull(PA.getValue(sq, "datasetSequence"));
562 sq = new Sequence("test", "ABCDEF");
563 sq.deleteChars(0, 2);
564 assertEquals("CDEF", sq.getSequenceAsString());
565 assertEquals(3, sq.getStart());
566 assertEquals(6, sq.getEnd());
567 assertNull(PA.getValue(sq, "datasetSequence"));
569 sq = new Sequence("test", "ABCDE");
570 sq.deleteChars(0, 3);
571 assertEquals("DE", sq.getSequenceAsString());
572 assertEquals(4, sq.getStart());
573 assertEquals(5, sq.getEnd());
574 assertNull(PA.getValue(sq, "datasetSequence"));
579 sq = new Sequence("test", "ABCDEF");
580 sq.deleteChars(4, 6);
581 assertEquals("ABCD", sq.getSequenceAsString());
582 assertEquals(1, sq.getStart());
583 assertEquals(4, sq.getEnd());
584 assertNull(PA.getValue(sq, "datasetSequence"));
587 * delete more positions than there are
589 sq = new Sequence("test/8-11", "ABCD");
590 sq.deleteChars(0, 99);
591 assertEquals("", sq.getSequenceAsString());
592 assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
593 assertEquals(11, sq.getEnd());
595 sq = new Sequence("test/8-11", "----");
596 sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
597 assertEquals("", sq.getSequenceAsString());
598 assertEquals(8, sq.getStart());
599 assertEquals(11, sq.getEnd());
602 @Test(groups = { "Functional" })
603 public void testDeleteChars_withDbRefsAndFeatures()
606 * internal delete - new dataset sequence created
607 * gets a copy of any dbrefs
609 SequenceI sq = new Sequence("test", "ABCDEF");
610 sq.createDatasetSequence();
611 DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
613 Object ds = PA.getValue(sq, "datasetSequence");
615 assertEquals(1, sq.getStart());
616 assertEquals(6, sq.getEnd());
617 sq.deleteChars(2, 3);
618 assertEquals("ABDEF", sq.getSequenceAsString());
619 assertEquals(1, sq.getStart());
620 assertEquals(5, sq.getEnd());
621 Object newDs = PA.getValue(sq, "datasetSequence");
622 assertNotNull(newDs);
623 assertNotSame(ds, newDs);
624 assertNotNull(sq.getDBRefs());
625 assertEquals(1, sq.getDBRefs().length);
626 assertNotSame(dbr1, sq.getDBRefs()[0]);
627 assertEquals(dbr1, sq.getDBRefs()[0]);
630 * internal delete with sequence features
631 * (failure case for JAL-2541)
633 sq = new Sequence("test", "ABCDEF");
634 sq.createDatasetSequence();
635 SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
637 sq.addSequenceFeature(sf1);
638 ds = PA.getValue(sq, "datasetSequence");
640 assertEquals(1, sq.getStart());
641 assertEquals(6, sq.getEnd());
642 sq.deleteChars(2, 4);
643 assertEquals("ABEF", sq.getSequenceAsString());
644 assertEquals(1, sq.getStart());
645 assertEquals(4, sq.getEnd());
646 newDs = PA.getValue(sq, "datasetSequence");
647 assertNotNull(newDs);
648 assertNotSame(ds, newDs);
649 List<SequenceFeature> sfs = sq.getSequenceFeatures();
650 assertEquals(1, sfs.size());
651 assertNotSame(sf1, sfs.get(0));
652 assertEquals(sf1, sfs.get(0));
655 * delete at start - no new dataset sequence created
656 * any sequence features remain as before
658 sq = new Sequence("test", "ABCDEF");
659 sq.createDatasetSequence();
660 ds = PA.getValue(sq, "datasetSequence");
661 sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
662 sq.addSequenceFeature(sf1);
663 sq.deleteChars(0, 2);
664 assertEquals("CDEF", sq.getSequenceAsString());
665 assertEquals(3, sq.getStart());
666 assertEquals(6, sq.getEnd());
667 assertSame(ds, PA.getValue(sq, "datasetSequence"));
668 sfs = sq.getSequenceFeatures();
670 assertEquals(1, sfs.size());
671 assertSame(sf1, sfs.get(0));
674 * delete at end - no new dataset sequence created
675 * any dbrefs remain as before
677 sq = new Sequence("test", "ABCDEF");
678 sq.createDatasetSequence();
679 ds = PA.getValue(sq, "datasetSequence");
680 dbr1 = new DBRefEntry("Uniprot", "0", "a123");
682 sq.deleteChars(4, 6);
683 assertEquals("ABCD", sq.getSequenceAsString());
684 assertEquals(1, sq.getStart());
685 assertEquals(4, sq.getEnd());
686 assertSame(ds, PA.getValue(sq, "datasetSequence"));
687 assertNotNull(sq.getDBRefs());
688 assertEquals(1, sq.getDBRefs().length);
689 assertSame(dbr1, sq.getDBRefs()[0]);
692 @Test(groups = { "Functional" })
693 public void testInsertCharAt()
695 // non-static methods:
696 SequenceI sq = new Sequence("test", "ABCDEF");
697 sq.insertCharAt(0, 'z');
698 assertEquals("zABCDEF", sq.getSequenceAsString());
699 sq.insertCharAt(2, 2, 'x');
700 assertEquals("zAxxBCDEF", sq.getSequenceAsString());
702 // for static method see StringUtilsTest
706 * Test the method that returns an array of aligned sequence positions where
707 * the array index is the data sequence position (both base 0).
709 @Test(groups = { "Functional" })
710 public void testGapMap()
712 SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
713 sq.createDatasetSequence();
714 assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
718 * Test the method that gets sequence features, either from the sequence or
721 @Test(groups = { "Functional" })
722 public void testGetSequenceFeatures()
724 SequenceI sq = new Sequence("test", "GATCAT");
725 sq.createDatasetSequence();
727 assertTrue(sq.getSequenceFeatures().isEmpty());
730 * SequenceFeature on sequence
732 SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
733 sq.addSequenceFeature(sf);
734 List<SequenceFeature> sfs = sq.getSequenceFeatures();
735 assertEquals(1, sfs.size());
736 assertSame(sf, sfs.get(0));
739 * SequenceFeature on sequence and dataset sequence; returns that on
742 * Note JAL-2046: spurious: we have no use case for this at the moment.
743 * This test also buggy - as sf2.equals(sf), no new feature is added
745 SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
747 sq.getDatasetSequence().addSequenceFeature(sf2);
748 sfs = sq.getSequenceFeatures();
749 assertEquals(1, sfs.size());
750 assertSame(sf, sfs.get(0));
753 * SequenceFeature on dataset sequence only
754 * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
756 sq.setSequenceFeatures(null);
757 assertTrue(sq.getDatasetSequence().getSequenceFeatures().isEmpty());
760 * Corrupt case - no SequenceFeature, dataset's dataset is the original
761 * sequence. Test shows no infinite loop results.
763 sq.getDatasetSequence().setSequenceFeatures(null);
765 * is there a usecase for this ? setDatasetSequence should throw an error if
766 * this actually occurs.
770 sq.getDatasetSequence().setDatasetSequence(sq); // loop!
771 Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
772 } catch (IllegalArgumentException e)
774 // TODO Jalview error/exception class for raising implementation errors
775 assertTrue(e.getMessage().toLowerCase()
776 .contains("implementation error"));
778 assertTrue(sq.getSequenceFeatures().isEmpty());
782 * Test the method that returns an array, indexed by sequence position, whose
783 * entries are the residue positions at the sequence position (or to the right
786 @Test(groups = { "Functional" })
787 public void testFindPositionMap()
790 * Note: Javadoc for findPosition says it returns the residue position to
791 * the left of a gapped position; in fact it returns the position to the
792 * right. Also it returns a non-existent residue position for a gap beyond
795 Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
796 int[] map = sq.findPositionMap();
797 assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
798 Arrays.toString(map));
802 * Test for getSubsequence
804 @Test(groups = { "Functional" })
805 public void testGetSubsequence()
807 SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
808 sq.createDatasetSequence();
810 // positions are base 0, end position is exclusive
811 SequenceI subseq = sq.getSubSequence(2, 4);
813 assertEquals("CD", subseq.getSequenceAsString());
814 // start/end are base 1 positions
815 assertEquals(3, subseq.getStart());
816 assertEquals(4, subseq.getEnd());
817 // subsequence shares the full dataset sequence
818 assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
822 * test createDatasetSequence behaves to doc
824 @Test(groups = { "Functional" })
825 public void testCreateDatasetSequence()
827 SequenceI sq = new Sequence("my", "ASDASD");
828 sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
830 sq.addDBRef(new DBRefEntry("source", "version", "accession"));
831 assertNull(sq.getDatasetSequence());
832 assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
833 assertNotNull(PA.getValue(sq, "dbrefs"));
835 SequenceI rds = sq.createDatasetSequence();
837 assertNull(rds.getDatasetSequence());
838 assertSame(sq.getDatasetSequence(), rds);
840 // sequence features and dbrefs transferred to dataset sequence
841 assertNull(PA.getValue(sq, "sequenceFeatureStore"));
842 assertNull(PA.getValue(sq, "dbrefs"));
843 assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
844 assertNotNull(PA.getValue(rds, "dbrefs"));
848 * Test for deriveSequence applied to a sequence with a dataset
850 @Test(groups = { "Functional" })
851 public void testDeriveSequence_existingDataset()
853 Sequence sq = new Sequence("Seq1", "CD");
854 sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
855 sq.getDatasetSequence().addSequenceFeature(
856 new SequenceFeature("", "", 1, 2, 0f, null));
860 sq.setDescription("Test sequence description..");
861 sq.setVamsasId("TestVamsasId");
862 sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
864 sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
865 sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
866 sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
867 sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
869 sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
870 sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
871 sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
872 sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
874 // these are the same as ones already added
875 DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
876 DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
878 List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
881 sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
882 sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
883 sq.getDatasetSequence().addDBRef(
884 new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
885 sq.getDatasetSequence().addDBRef(
886 new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
888 PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
889 PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
890 PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
892 PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
894 sq.getDatasetSequence().addPDBId(pdbe1a);
895 sq.getDatasetSequence().addPDBId(pdbe1b);
896 sq.getDatasetSequence().addPDBId(pdbe2a);
897 sq.getDatasetSequence().addPDBId(pdbe2b);
900 * test we added pdb entries to the dataset sequence
902 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
903 .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
904 "PDB Entries were not found on dataset sequence.");
907 * we should recover a pdb entry that is on the dataset sequence via PDBEntry
909 Assert.assertEquals(pdbe1a,
910 sq.getDatasetSequence().getPDBEntry("1PDB"),
911 "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
912 ArrayList<Annotation> annotsList = new ArrayList<>();
913 System.out.println(">>>>>> " + sq.getSequenceAsString().length());
914 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
915 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
916 Annotation[] annots = annotsList.toArray(new Annotation[0]);
917 sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
918 "Test annot description", annots));
919 sq.getDatasetSequence().addAlignmentAnnotation(
920 new AlignmentAnnotation("Test annot", "Test annot description",
922 Assert.assertEquals(sq.getDescription(), "Test sequence description..");
923 Assert.assertEquals(sq.getDBRefs().length, 5); // DBRefs are on dataset
925 Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
926 Assert.assertNotNull(sq.getAnnotation());
927 Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
928 Assert.assertEquals(sq.getDatasetSequence().getDBRefs().length, 5); // same
931 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
933 Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
935 Sequence derived = (Sequence) sq.deriveSequence();
937 Assert.assertEquals(derived.getDescription(),
938 "Test sequence description..");
939 Assert.assertEquals(derived.getDBRefs().length, 5); // come from dataset
940 Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
941 Assert.assertNotNull(derived.getAnnotation());
942 Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
943 Assert.assertEquals(derived.getDatasetSequence().getDBRefs().length, 5);
944 Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
946 Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
948 assertEquals("CD", derived.getSequenceAsString());
949 assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
951 // derived sequence should access dataset sequence features
952 assertNotNull(sq.getSequenceFeatures());
953 assertEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures());
956 * verify we have primary db refs *just* for PDB IDs with associated
960 assertEquals(primRefs, sq.getPrimaryDBRefs());
961 assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
963 assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
968 * Test for deriveSequence applied to an ungapped sequence with no dataset
970 @Test(groups = { "Functional" })
971 public void testDeriveSequence_noDatasetUngapped()
973 SequenceI sq = new Sequence("Seq1", "ABCDEF");
974 assertEquals(1, sq.getStart());
975 assertEquals(6, sq.getEnd());
976 SequenceI derived = sq.deriveSequence();
977 assertEquals("ABCDEF", derived.getSequenceAsString());
978 assertEquals("ABCDEF", derived.getDatasetSequence()
979 .getSequenceAsString());
983 * Test for deriveSequence applied to a gapped sequence with no dataset
985 @Test(groups = { "Functional" })
986 public void testDeriveSequence_noDatasetGapped()
988 SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
989 assertEquals(1, sq.getStart());
990 assertEquals(6, sq.getEnd());
991 assertNull(sq.getDatasetSequence());
992 SequenceI derived = sq.deriveSequence();
993 assertEquals("AB-C.D EF", derived.getSequenceAsString());
994 assertEquals("ABCDEF", derived.getDatasetSequence()
995 .getSequenceAsString());
998 @Test(groups = { "Functional" })
999 public void testCopyConstructor_noDataset()
1001 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1002 seq1.setDescription("description");
1003 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1005 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1007 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1008 seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
1010 SequenceI copy = new Sequence(seq1);
1012 assertNull(copy.getDatasetSequence());
1014 verifyCopiedSequence(seq1, copy);
1016 // copy has a copy of the DBRefEntry
1017 // this is murky - DBrefs are only copied for dataset sequences
1018 // where the test for 'dataset sequence' is 'dataset is null'
1019 // but that doesn't distinguish it from an aligned sequence
1020 // which has not yet generated a dataset sequence
1021 // NB getDBRef looks inside dataset sequence if not null
1022 DBRefEntry[] dbrefs = copy.getDBRefs();
1023 assertEquals(1, dbrefs.length);
1024 assertFalse(dbrefs[0] == seq1.getDBRefs()[0]);
1025 assertTrue(dbrefs[0].equals(seq1.getDBRefs()[0]));
1028 @Test(groups = { "Functional" })
1029 public void testCopyConstructor_withDataset()
1031 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1032 seq1.createDatasetSequence();
1033 seq1.setDescription("description");
1034 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1036 // JAL-2046 - what is the contract for using a derived sequence's
1037 // addSequenceFeature ?
1038 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1040 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1041 // here we add DBRef to the dataset sequence:
1042 seq1.getDatasetSequence().addDBRef(
1043 new DBRefEntry("EMBL", "1.2", "AZ12345"));
1045 SequenceI copy = new Sequence(seq1);
1047 assertNotNull(copy.getDatasetSequence());
1048 assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
1050 verifyCopiedSequence(seq1, copy);
1052 // getDBRef looks inside dataset sequence and this is shared,
1053 // so holds the same dbref objects
1054 DBRefEntry[] dbrefs = copy.getDBRefs();
1055 assertEquals(1, dbrefs.length);
1056 assertSame(dbrefs[0], seq1.getDBRefs()[0]);
1060 * Helper to make assertions about a copied sequence
1065 protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
1067 // verify basic properties:
1068 assertEquals(copy.getName(), seq1.getName());
1069 assertEquals(copy.getDescription(), seq1.getDescription());
1070 assertEquals(copy.getStart(), seq1.getStart());
1071 assertEquals(copy.getEnd(), seq1.getEnd());
1072 assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
1074 // copy has a copy of the annotation:
1075 AlignmentAnnotation[] anns = copy.getAnnotation();
1076 assertEquals(1, anns.length);
1077 assertFalse(anns[0] == seq1.getAnnotation()[0]);
1078 assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
1079 assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
1080 assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
1082 // copy has a copy of the sequence feature:
1083 List<SequenceFeature> sfs = copy.getSequenceFeatures();
1084 assertEquals(1, sfs.size());
1085 if (seq1.getDatasetSequence() != null
1086 && copy.getDatasetSequence() == seq1.getDatasetSequence())
1088 assertSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1092 assertNotSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1094 assertEquals(sfs.get(0), seq1.getSequenceFeatures().get(0));
1096 // copy has a copy of the PDB entry
1097 Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
1098 assertEquals(1, pdbs.size());
1099 assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
1100 assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
1103 @Test(groups = "Functional")
1104 public void testGetCharAt()
1106 SequenceI sq = new Sequence("", "abcde");
1107 assertEquals('a', sq.getCharAt(0));
1108 assertEquals('e', sq.getCharAt(4));
1109 assertEquals(' ', sq.getCharAt(5));
1110 assertEquals(' ', sq.getCharAt(-1));
1113 @Test(groups = { "Functional" })
1114 public void testAddSequenceFeatures()
1116 SequenceI sq = new Sequence("", "abcde");
1117 // type may not be null
1118 assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
1120 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1122 // can't add a duplicate feature
1123 assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
1125 // can add a different feature
1126 assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
1127 8, 0f, null))); // different type
1128 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
1129 "description", 4, 8, 0f, null)));// different description
1130 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
1131 8, 0f, null))); // different start position
1132 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1133 9, 0f, null))); // different end position
1134 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1135 8, 1f, null))); // different score
1136 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1137 8, Float.NaN, null))); // score NaN
1138 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1139 8, 0f, "Metal"))); // different group
1140 assertEquals(8, sq.getFeatures().getAllFeatures().size());
1144 * Tests for adding (or updating) dbrefs
1146 * @see DBRefEntry#updateFrom(DBRefEntry)
1148 @Test(groups = { "Functional" })
1149 public void testAddDBRef()
1151 SequenceI sq = new Sequence("", "abcde");
1152 assertNull(sq.getDBRefs());
1153 DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
1155 assertEquals(1, sq.getDBRefs().length);
1156 assertSame(dbref, sq.getDBRefs()[0]);
1159 * change of version - new entry
1161 DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
1162 sq.addDBRef(dbref2);
1163 assertEquals(2, sq.getDBRefs().length);
1164 assertSame(dbref, sq.getDBRefs()[0]);
1165 assertSame(dbref2, sq.getDBRefs()[1]);
1168 * matches existing entry - not added
1170 sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
1171 assertEquals(2, sq.getDBRefs().length);
1174 * different source = new entry
1176 DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
1177 sq.addDBRef(dbref3);
1178 assertEquals(3, sq.getDBRefs().length);
1179 assertSame(dbref3, sq.getDBRefs()[2]);
1182 * different ref = new entry
1184 DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
1185 sq.addDBRef(dbref4);
1186 assertEquals(4, sq.getDBRefs().length);
1187 assertSame(dbref4, sq.getDBRefs()[3]);
1190 * matching ref with a mapping - map updated
1192 DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
1193 Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
1196 sq.addDBRef(dbref5);
1197 assertEquals(4, sq.getDBRefs().length);
1198 assertSame(dbref4, sq.getDBRefs()[3]);
1199 assertSame(map, dbref4.getMap());
1202 * 'real' version replaces "0" version
1204 dbref2.setVersion("0");
1205 DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
1206 dbref2.getAccessionId());
1207 sq.addDBRef(dbref6);
1208 assertEquals(4, sq.getDBRefs().length);
1209 assertSame(dbref2, sq.getDBRefs()[1]);
1210 assertEquals("3", dbref2.getVersion());
1213 * 'real' version replaces "source:0" version
1215 dbref3.setVersion("Uniprot:0");
1216 DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
1217 dbref3.getAccessionId());
1218 sq.addDBRef(dbref7);
1219 assertEquals(4, sq.getDBRefs().length);
1220 assertSame(dbref3, sq.getDBRefs()[2]);
1221 assertEquals("3", dbref2.getVersion());
1224 @Test(groups = { "Functional" })
1225 public void testGetPrimaryDBRefs_peptide()
1227 SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22);
1230 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1231 assertTrue(primaryDBRefs.isEmpty());
1234 sq.setDBRefs(new DBRefEntry[] {});
1235 primaryDBRefs = sq.getPrimaryDBRefs();
1236 assertTrue(primaryDBRefs.isEmpty());
1238 // primary - uniprot
1239 DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760");
1240 sq.addDBRef(upentry1);
1242 // primary - uniprot with congruent map
1243 DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
1244 upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
1245 new int[] { 10, 22 }, 1, 1)));
1246 sq.addDBRef(upentry2);
1248 // primary - uniprot with map of enclosing sequence
1249 DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
1250 upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
1251 new int[] { 8, 24 }, 1, 1)));
1252 sq.addDBRef(upentry3);
1254 // not primary - uniprot with map of sub-sequence (5')
1255 DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
1256 upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
1257 new int[] { 10, 18 }, 1, 1)));
1258 sq.addDBRef(upentry4);
1260 // not primary - uniprot with map that overlaps 3'
1261 DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
1262 upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
1263 new int[] { 12, 22 }, 1, 1)));
1264 sq.addDBRef(upentry5);
1266 // not primary - uniprot with map to different coordinates frame
1267 DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
1268 upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
1269 new int[] { 112, 118 }, 1, 1)));
1270 sq.addDBRef(upentry6);
1272 // not primary - dbref to 'non-core' database
1273 DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903");
1274 sq.addDBRef(upentry7);
1276 // primary - type is PDB
1277 DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
1278 sq.addDBRef(pdbentry);
1280 // not primary - PDBEntry has no file
1281 sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
1283 // not primary - no PDBEntry
1284 sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
1286 // add corroborating PDB entry for primary DBref -
1287 // needs to have a file as well as matching ID
1288 // note PDB ID is not treated as case sensitive
1289 sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
1292 // not valid DBRef - no file..
1293 sq.addPDBId(new PDBEntry("1AAA", null, null, null));
1295 primaryDBRefs = sq.getPrimaryDBRefs();
1296 assertEquals(4, primaryDBRefs.size());
1297 assertTrue("Couldn't find simple primary reference (UNIPROT)",
1298 primaryDBRefs.contains(upentry1));
1299 assertTrue("Couldn't find mapped primary reference (UNIPROT)",
1300 primaryDBRefs.contains(upentry2));
1301 assertTrue("Couldn't find mapped context reference (UNIPROT)",
1302 primaryDBRefs.contains(upentry3));
1303 assertTrue("Couldn't find expected PDB primary reference",
1304 primaryDBRefs.contains(pdbentry));
1307 @Test(groups = { "Functional" })
1308 public void testGetPrimaryDBRefs_nucleotide()
1310 SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
1312 // primary - Ensembl
1313 DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
1316 // not primary - Ensembl 'transcript' mapping of sub-sequence
1317 DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
1318 dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
1319 new int[] { 1, 11 }, 1, 1)));
1322 // primary - EMBL with congruent map
1323 DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
1324 dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
1325 new int[] { 10, 34 }, 1, 1)));
1328 // not primary - to non-core database
1329 DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234");
1332 // not primary - to protein
1333 DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
1336 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1337 assertEquals(2, primaryDBRefs.size());
1338 assertTrue(primaryDBRefs.contains(dbr1));
1339 assertTrue(primaryDBRefs.contains(dbr3));
1343 * Test the method that updates the list of PDBEntry from any new DBRefEntry
1346 @Test(groups = { "Functional" })
1347 public void testUpdatePDBIds()
1349 PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
1350 seq.addPDBId(pdbe1);
1351 seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
1352 seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
1353 seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
1354 seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
1355 // 7 is not a valid chain code:
1356 seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
1359 List<PDBEntry> pdbIds = seq.getAllPDBEntries();
1360 assertEquals(4, pdbIds.size());
1361 assertSame(pdbe1, pdbIds.get(0));
1362 // chain code got added to 3A6S:
1363 assertEquals("B", pdbe1.getChainCode());
1364 assertEquals("1A70", pdbIds.get(1).getId());
1365 // 4BQGA is parsed into id + chain
1366 assertEquals("4BQG", pdbIds.get(2).getId());
1367 assertEquals("a", pdbIds.get(2).getChainCode());
1368 assertEquals("2GIS7", pdbIds.get(3).getId());
1369 assertNull(pdbIds.get(3).getChainCode());
1373 * Test the method that either adds a pdbid or updates an existing one
1375 @Test(groups = { "Functional" })
1376 public void testAddPDBId()
1378 PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
1380 assertEquals(1, seq.getAllPDBEntries().size());
1381 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1382 assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
1384 // add the same entry
1386 assertEquals(1, seq.getAllPDBEntries().size());
1387 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1389 // add an identical entry
1390 seq.addPDBId(new PDBEntry("3A6S", null, null, null));
1391 assertEquals(1, seq.getAllPDBEntries().size());
1392 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1394 // add a different entry
1395 PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
1396 seq.addPDBId(pdbe2);
1397 assertEquals(2, seq.getAllPDBEntries().size());
1398 assertSame(pdbe, seq.getAllPDBEntries().get(0));
1399 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1401 // update pdbe with chain code, file, type
1402 PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
1403 seq.addPDBId(pdbe3);
1404 assertEquals(2, seq.getAllPDBEntries().size());
1405 assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
1406 assertEquals("3A6S", pdbe.getId()); // unchanged
1407 assertEquals("A", pdbe.getChainCode()); // updated
1408 assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
1409 assertEquals("filepath", pdbe.getFile()); // updated
1410 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1412 // add with a different file path
1413 PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
1414 seq.addPDBId(pdbe4);
1415 assertEquals(3, seq.getAllPDBEntries().size());
1416 assertSame(pdbe4, seq.getAllPDBEntries().get(2));
1418 // add with a different chain code
1419 PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
1420 seq.addPDBId(pdbe5);
1421 assertEquals(4, seq.getAllPDBEntries().size());
1422 assertSame(pdbe5, seq.getAllPDBEntries().get(3));
1426 groups = { "Functional" },
1427 expectedExceptions = { IllegalArgumentException.class })
1428 public void testSetDatasetSequence_toSelf()
1430 seq.setDatasetSequence(seq);
1434 groups = { "Functional" },
1435 expectedExceptions = { IllegalArgumentException.class })
1436 public void testSetDatasetSequence_cascading()
1438 SequenceI seq2 = new Sequence("Seq2", "xyz");
1439 seq2.createDatasetSequence();
1440 seq.setDatasetSequence(seq2);
1443 @Test(groups = { "Functional" })
1444 public void testFindFeatures()
1446 SequenceI sq = new Sequence("test/8-16", "-ABC--DEF--GHI--");
1447 sq.createDatasetSequence();
1449 assertTrue(sq.findFeatures(1, 99).isEmpty());
1451 // add non-positional feature
1452 SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f,
1454 sq.addSequenceFeature(sf0);
1455 // add feature on BCD
1456 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
1458 sq.addSequenceFeature(sfBCD);
1459 // add feature on DE
1460 SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
1462 sq.addSequenceFeature(sfDE);
1463 // add contact feature at [B, H]
1464 SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
1465 "desc", 9, 15, 2f, null);
1466 sq.addSequenceFeature(sfContactBH);
1467 // add contact feature at [F, G]
1468 SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
1469 "desc", 13, 14, 2f, null);
1470 sq.addSequenceFeature(sfContactFG);
1471 // add single position feature at [I]
1472 SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
1473 "desc", 16, 16, null);
1474 sq.addSequenceFeature(sfI);
1476 // no features in columns 1-2 (-A)
1477 List<SequenceFeature> found = sq.findFeatures(1, 2);
1478 assertTrue(found.isEmpty());
1480 // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
1481 found = sq.findFeatures(1, 6);
1482 assertEquals(2, found.size());
1483 assertTrue(found.contains(sfBCD));
1484 assertTrue(found.contains(sfContactBH));
1486 // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
1487 found = sq.findFeatures(5, 6);
1488 assertEquals(1, found.size());
1489 assertTrue(found.contains(sfBCD));
1491 // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
1492 found = sq.findFeatures(7, 10);
1493 assertEquals(3, found.size());
1494 assertTrue(found.contains(sfBCD));
1495 assertTrue(found.contains(sfDE));
1496 assertTrue(found.contains(sfContactFG));
1498 // columns 10-11 (--) should find nothing
1499 found = sq.findFeatures(10, 11);
1500 assertEquals(0, found.size());
1502 // columns 14-14 (I) should find variant feature
1503 found = sq.findFeatures(14, 14);
1504 assertEquals(1, found.size());
1505 assertTrue(found.contains(sfI));
1508 @Test(groups = { "Functional" })
1509 public void testFindIndex_withCursor()
1511 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1513 // find F given A, check cursor is now at the found position
1514 assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0)));
1515 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1516 assertEquals(13, cursor.residuePosition);
1517 assertEquals(10, cursor.columnPosition);
1520 assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0)));
1521 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1522 assertEquals(8, cursor.residuePosition);
1523 assertEquals(2, cursor.columnPosition);
1525 // find C given C (no cursor update is done for this case)
1526 assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
1527 SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1528 assertSame(cursor2, cursor);
1531 * sequence 'end' beyond end of sequence returns length of sequence
1532 * (for compatibility with pre-cursor code)
1533 * - also verify the cursor is left in a valid state
1535 sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
1536 assertEquals(7, sq.findIndex(10)); // establishes a cursor
1537 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1538 assertEquals(10, cursor.residuePosition);
1539 assertEquals(7, cursor.columnPosition);
1540 assertEquals(sq.getLength(), sq.findIndex(65));
1541 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1542 assertSame(cursor, cursor2); // not updated for this case!
1544 sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
1545 sq.findIndex(10); // establishes a cursor
1546 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1547 assertEquals(sq.getLength(), sq.findIndex(65));
1548 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1549 assertSame(cursor, cursor2); // not updated for this case!
1552 * residue after sequence 'start' but before first residue should return
1553 * zero (for compatibility with pre-cursor code)
1555 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
1556 sq.findIndex(10); // establishes a cursor
1557 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1558 assertEquals(0, sq.findIndex(3));
1559 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1560 assertSame(cursor, cursor2); // not updated for this case!
1562 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
1563 sq.findIndex(10); // establishes a cursor
1564 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1565 assertEquals(0, sq.findIndex(2));
1566 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1567 assertSame(cursor, cursor2); // not updated for this case!
1570 @Test(groups = { "Functional" })
1571 public void testFindPosition_withCursor()
1573 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1575 // find F pos given A - lastCol gets set in cursor
1576 assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
1577 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1578 PA.getValue(sq, "cursor").toString());
1580 // find A pos given F - first residue column is saved in cursor
1581 assertEquals(8, sq.findPosition(2, new SequenceCursor(sq, 13, 10, 0)));
1582 assertEquals("test:Pos8:Col2:startCol2:endCol10:tok0",
1583 PA.getValue(sq, "cursor").toString());
1585 // find C pos given C (neither startCol nor endCol is set)
1586 assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 10, 6, 0)));
1587 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0",
1588 PA.getValue(sq, "cursor").toString());
1590 // now the grey area - what residue position for a gapped column? JAL-2562
1592 // find 'residue' for column 3 given cursor for D (so working left)
1593 // returns B9; cursor is updated to [B 5]
1594 assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, 0)));
1595 assertEquals("test:Pos9:Col5:startCol0:endCol0:tok0",
1596 PA.getValue(sq, "cursor").toString());
1598 // find 'residue' for column 8 given cursor for D (so working right)
1599 // returns E12; cursor is updated to [D 7]
1600 assertEquals(12, sq.findPosition(8, new SequenceCursor(sq, 11, 7, 0)));
1601 assertEquals("test:Pos11:Col7:startCol0:endCol0:tok0",
1602 PA.getValue(sq, "cursor").toString());
1604 // find 'residue' for column 12 given cursor for B
1605 // returns 1 more than last residue position; cursor is updated to [F 10]
1606 // lastCol position is saved in cursor
1607 assertEquals(14, sq.findPosition(12, new SequenceCursor(sq, 9, 5, 0)));
1608 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1609 PA.getValue(sq, "cursor").toString());
1612 * findPosition for column beyond length of sequence
1613 * returns 1 more than the last residue position
1614 * cursor is set to last real residue position [F 10]
1616 assertEquals(14, sq.findPosition(99, new SequenceCursor(sq, 8, 2, 0)));
1617 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1618 PA.getValue(sq, "cursor").toString());
1621 * and the case without a trailing gap
1623 sq = new Sequence("test/8-13", "-A--BCD-EF");
1624 // first find C from A
1625 assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, 0)));
1626 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1627 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0",
1629 // now 'find' 99 from C
1630 // cursor is set to [F 10] and saved lastCol
1631 assertEquals(14, sq.findPosition(99, cursor));
1632 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1633 PA.getValue(sq, "cursor").toString());
1637 public void testIsValidCursor()
1639 Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
1640 assertFalse(sq.isValidCursor(null));
1643 * cursor is valid if it has valid sequence ref and changeCount token
1644 * and positions within the range of the sequence
1646 int changeCount = (int) PA.getValue(sq, "changeCount");
1647 SequenceCursor cursor = new SequenceCursor(sq, 13, 1, changeCount);
1648 assertTrue(sq.isValidCursor(cursor));
1651 * column position outside [0 - length] is rejected
1653 cursor = new SequenceCursor(sq, 13, -1, changeCount);
1654 assertFalse(sq.isValidCursor(cursor));
1655 cursor = new SequenceCursor(sq, 13, 10, changeCount);
1656 assertFalse(sq.isValidCursor(cursor));
1657 cursor = new SequenceCursor(sq, 7, 8, changeCount);
1658 assertFalse(sq.isValidCursor(cursor));
1659 cursor = new SequenceCursor(sq, 14, 2, changeCount);
1660 assertFalse(sq.isValidCursor(cursor));
1663 * wrong sequence is rejected
1665 cursor = new SequenceCursor(null, 13, 1, changeCount);
1666 assertFalse(sq.isValidCursor(cursor));
1667 cursor = new SequenceCursor(new Sequence("Seq", "abc"), 13, 1,
1669 assertFalse(sq.isValidCursor(cursor));
1672 * wrong token value is rejected
1674 cursor = new SequenceCursor(sq, 13, 1, changeCount + 1);
1675 assertFalse(sq.isValidCursor(cursor));
1676 cursor = new SequenceCursor(sq, 13, 1, changeCount - 1);
1677 assertFalse(sq.isValidCursor(cursor));
1680 @Test(groups = { "Functional" })
1681 public void testFindPosition_withCursorAndEdits()
1683 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1685 // find F pos given A
1686 assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
1687 int token = (int) PA.getValue(sq, "changeCount"); // 0
1688 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1689 assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
1692 * setSequence should invalidate the cursor cached by the sequence
1694 sq.setSequence("-A-BCD-EF---"); // one gap removed
1695 assertEquals(8, sq.getStart()); // sanity check
1696 assertEquals(11, sq.findPosition(5)); // D11
1697 // cursor should now be at [D 6]
1698 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1699 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
1700 assertEquals(0, cursor.lastColumnPosition); // not yet found
1701 assertEquals(13, sq.findPosition(8)); // E13
1702 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1703 assertEquals(9, cursor.lastColumnPosition); // found
1706 * deleteChars should invalidate the cached cursor
1708 sq.deleteChars(2, 5); // delete -BC
1709 assertEquals("-AD-EF---", sq.getSequenceAsString());
1710 assertEquals(8, sq.getStart()); // sanity check
1711 assertEquals(10, sq.findPosition(4)); // E10
1712 // cursor should now be at [E 5]
1713 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1714 assertEquals(new SequenceCursor(sq, 10, 5, ++token), cursor);
1717 * Edit to insert gaps should invalidate the cached cursor
1718 * insert 2 gaps at column[3] to make -AD---EF---
1720 SequenceI[] seqs = new SequenceI[] { sq };
1721 AlignmentI al = new Alignment(seqs);
1722 new EditCommand().appendEdit(Action.INSERT_GAP, seqs, 3, 2, al, true);
1723 assertEquals("-AD---EF---", sq.getSequenceAsString());
1724 assertEquals(10, sq.findPosition(4)); // E10
1725 // cursor should now be at [D 3]
1726 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1727 assertEquals(new SequenceCursor(sq, 9, 3, ++token), cursor);
1730 * insertCharAt should invalidate the cached cursor
1731 * insert CC at column[4] to make -AD-CC--EF---
1733 sq.insertCharAt(4, 2, 'C');
1734 assertEquals("-AD-CC--EF---", sq.getSequenceAsString());
1735 assertEquals(13, sq.findPosition(9)); // F13
1736 // cursor should now be at [F 10]
1737 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1738 assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
1741 @Test(groups = { "Functional" })
1742 public void testGetSequence()
1744 String seqstring = "-A--BCD-EF--";
1745 Sequence sq = new Sequence("test/8-13", seqstring);
1746 sq.createDatasetSequence();
1747 assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray()));
1748 assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(),
1749 "ABCDEF".toCharArray()));
1751 // verify a copy of the sequence array is returned
1752 char[] theSeq = (char[]) PA.getValue(sq, "sequence");
1753 assertNotSame(theSeq, sq.getSequence());
1754 theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence");
1755 assertNotSame(theSeq, sq.getDatasetSequence().getSequence());
1758 @Test(groups = { "Functional" })
1759 public void testReplace()
1761 String seqstring = "-A--BCD-EF--";
1762 SequenceI sq = new Sequence("test/8-13", seqstring);
1763 assertEquals(0, PA.getValue(sq, "changeCount"));
1765 assertEquals(0, sq.replace('A', 'A')); // same char
1766 assertEquals(seqstring, sq.getSequenceAsString());
1767 assertEquals(0, PA.getValue(sq, "changeCount"));
1769 assertEquals(0, sq.replace('X', 'Y')); // not there
1770 assertEquals(seqstring, sq.getSequenceAsString());
1771 assertEquals(0, PA.getValue(sq, "changeCount"));
1773 assertEquals(1, sq.replace('A', 'K'));
1774 assertEquals("-K--BCD-EF--", sq.getSequenceAsString());
1775 assertEquals(1, PA.getValue(sq, "changeCount"));
1777 assertEquals(6, sq.replace('-', '.'));
1778 assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
1779 assertEquals(2, PA.getValue(sq, "changeCount"));
1782 @Test(groups = { "Functional" })
1783 public void testGapBitset()
1785 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
1786 BitSet bs = sq.gapBitset();
1787 BitSet expected = new BitSet();
1791 expected.set(11, 13);
1793 assertTrue(bs.equals(expected));
1797 public void testFindFeatures_largeEndPos()
1800 * imitate a PDB sequence where end is larger than end position
1802 SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
1803 sq.createDatasetSequence();
1805 assertTrue(sq.findFeatures(1, 9).isEmpty());
1806 // should be no array bounds exception - JAL-2772
1807 assertTrue(sq.findFeatures(1, 15).isEmpty());
1809 // add feature on BCD
1810 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
1812 sq.addSequenceFeature(sfBCD);
1814 // no features in columns 1-2 (-A)
1815 List<SequenceFeature> found = sq.findFeatures(1, 2);
1816 assertTrue(found.isEmpty());
1818 // columns 1-6 (-ABC--) includes BCD
1819 found = sq.findFeatures(1, 6);
1820 assertEquals(1, found.size());
1821 assertTrue(found.contains(sfBCD));
1823 // columns 10-11 (--) should find nothing
1824 found = sq.findFeatures(10, 11);
1825 assertEquals(0, found.size());
1828 @Test(groups = { "Functional" })
1829 public void testSetName()
1831 SequenceI sq = new Sequence("test", "-ABC---DE-F--");
1832 assertEquals("test", sq.getName());
1833 assertEquals(1, sq.getStart());
1834 assertEquals(6, sq.getEnd());
1836 sq.setName("testing");
1837 assertEquals("testing", sq.getName());
1839 sq.setName("test/8-10");
1840 assertEquals("test", sq.getName());
1841 assertEquals(8, sq.getStart());
1842 assertEquals(13, sq.getEnd()); // note end is recomputed
1844 sq.setName("testing/7-99");
1845 assertEquals("testing", sq.getName());
1846 assertEquals(7, sq.getStart());
1847 assertEquals(99, sq.getEnd()); // end may be beyond physical end
1850 assertEquals("", sq.getName());
1851 assertEquals(2, sq.getStart());
1852 assertEquals(7, sq.getEnd());
1854 sq.setName("test/"); // invalid
1855 assertEquals("test/", sq.getName());
1856 assertEquals(2, sq.getStart());
1857 assertEquals(7, sq.getEnd());
1859 sq.setName("test/6-13/7-99");
1860 assertEquals("test/6-13", sq.getName());
1861 assertEquals(7, sq.getStart());
1862 assertEquals(99, sq.getEnd());
1864 sq.setName("test/0-5"); // 0 is invalid - ignored
1865 assertEquals("test/0-5", sq.getName());
1866 assertEquals(7, sq.getStart());
1867 assertEquals(99, sq.getEnd());
1869 sq.setName("test/a-5"); // a is invalid - ignored
1870 assertEquals("test/a-5", sq.getName());
1871 assertEquals(7, sq.getStart());
1872 assertEquals(99, sq.getEnd());
1874 sq.setName("test/6-5"); // start > end is invalid - ignored
1875 assertEquals("test/6-5", sq.getName());
1876 assertEquals(7, sq.getStart());
1877 assertEquals(99, sq.getEnd());
1879 sq.setName("test/5"); // invalid - ignored
1880 assertEquals("test/5", sq.getName());
1881 assertEquals(7, sq.getStart());
1882 assertEquals(99, sq.getEnd());
1884 sq.setName("test/-5"); // invalid - ignored
1885 assertEquals("test/-5", sq.getName());
1886 assertEquals(7, sq.getStart());
1887 assertEquals(99, sq.getEnd());
1889 sq.setName("test/5-"); // invalid - ignored
1890 assertEquals("test/5-", sq.getName());
1891 assertEquals(7, sq.getStart());
1892 assertEquals(99, sq.getEnd());
1894 sq.setName("test/5-6-7"); // invalid - ignored
1895 assertEquals("test/5-6-7", sq.getName());
1896 assertEquals(7, sq.getStart());
1897 assertEquals(99, sq.getEnd());
1899 sq.setName(null); // invalid, gets converted to space
1900 assertEquals("", sq.getName());
1901 assertEquals(7, sq.getStart());
1902 assertEquals(99, sq.getEnd());
1905 @Test(groups = { "Functional" })
1906 public void testCheckValidRange()
1908 Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
1909 assertEquals(7, sq.getStart());
1910 assertEquals(12, sq.getEnd());
1913 * checkValidRange ensures end is at least the last residue position
1915 PA.setValue(sq, "end", 2);
1916 sq.checkValidRange();
1917 assertEquals(12, sq.getEnd());
1920 * end may be beyond the last residue position
1922 PA.setValue(sq, "end", 22);
1923 sq.checkValidRange();
1924 assertEquals(22, sq.getEnd());
1927 @Test(groups = { "Functional" })
1928 public void testDeleteChars_withGaps()
1933 SequenceI sq = new Sequence("test/8-10", "A-B-C");
1934 sq.createDatasetSequence();
1935 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1936 sq.deleteChars(1, 2); // delete first gap
1937 assertEquals("AB-C", sq.getSequenceAsString());
1938 assertEquals(8, sq.getStart());
1939 assertEquals(10, sq.getEnd());
1940 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1943 * delete gaps and residues at start (no new dataset sequence)
1945 sq = new Sequence("test/8-10", "A-B-C");
1946 sq.createDatasetSequence();
1947 sq.deleteChars(0, 3); // delete A-B
1948 assertEquals("-C", sq.getSequenceAsString());
1949 assertEquals(10, sq.getStart());
1950 assertEquals(10, sq.getEnd());
1951 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1954 * delete gaps and residues at end (no new dataset sequence)
1956 sq = new Sequence("test/8-10", "A-B-C");
1957 sq.createDatasetSequence();
1958 sq.deleteChars(2, 5); // delete B-C
1959 assertEquals("A-", sq.getSequenceAsString());
1960 assertEquals(8, sq.getStart());
1961 assertEquals(8, sq.getEnd());
1962 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1965 * delete gaps and residues internally (new dataset sequence)
1966 * first delete from gap to residue
1968 sq = new Sequence("test/8-10", "A-B-C");
1969 sq.createDatasetSequence();
1970 sq.deleteChars(1, 3); // delete -B
1971 assertEquals("A-C", sq.getSequenceAsString());
1972 assertEquals(8, sq.getStart());
1973 assertEquals(9, sq.getEnd());
1974 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
1975 assertEquals(8, sq.getDatasetSequence().getStart());
1976 assertEquals(9, sq.getDatasetSequence().getEnd());
1979 * internal delete from gap to gap
1981 sq = new Sequence("test/8-10", "A-B-C");
1982 sq.createDatasetSequence();
1983 sq.deleteChars(1, 4); // delete -B-
1984 assertEquals("AC", sq.getSequenceAsString());
1985 assertEquals(8, sq.getStart());
1986 assertEquals(9, sq.getEnd());
1987 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
1988 assertEquals(8, sq.getDatasetSequence().getStart());
1989 assertEquals(9, sq.getDatasetSequence().getEnd());
1992 * internal delete from residue to residue
1994 sq = new Sequence("test/8-10", "A-B-C");
1995 sq.createDatasetSequence();
1996 sq.deleteChars(2, 3); // delete B
1997 assertEquals("A--C", sq.getSequenceAsString());
1998 assertEquals(8, sq.getStart());
1999 assertEquals(9, sq.getEnd());
2000 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
2001 assertEquals(8, sq.getDatasetSequence().getStart());
2002 assertEquals(9, sq.getDatasetSequence().getEnd());
2006 * Test the code used to locate the reference sequence ruler origin
2008 @Test(groups = { "Functional" })
2009 public void testLocateVisibleStartofSequence()
2011 // create random alignment
2012 AlignmentGenerator gen = new AlignmentGenerator(false);
2013 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
2015 HiddenColumns cs = al.getHiddenColumns();
2016 ColumnSelection colsel = new ColumnSelection();
2018 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
2019 assertEquals(2, seq.findIndex(seq.getStart()));
2021 // no hidden columns
2022 assertEquals(seq.findIndex(seq.getStart()) - 1,
2023 seq.firstResidueOutsideIterator(cs.iterator()));
2025 // hidden column on gap after end of sequence - should not affect bounds
2026 colsel.hideSelectedColumns(13, al.getHiddenColumns());
2027 assertEquals(seq.findIndex(seq.getStart()) - 1,
2028 seq.firstResidueOutsideIterator(cs.iterator()));
2030 cs.revealAllHiddenColumns(colsel);
2031 // hidden column on gap before beginning of sequence - should vis bounds by
2033 colsel.hideSelectedColumns(0, al.getHiddenColumns());
2034 assertEquals(seq.findIndex(seq.getStart()) - 2,
2035 cs.absoluteToVisibleColumn(
2036 seq.firstResidueOutsideIterator(cs.iterator())));
2038 cs.revealAllHiddenColumns(colsel);
2039 // hide columns around most of sequence - leave one residue remaining
2040 cs.hideColumns(1, 3);
2041 cs.hideColumns(6, 11);
2043 Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
2045 assertEquals("-D", seq.getSequenceStringFromIterator(it));
2046 // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
2049 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2050 cs.revealAllHiddenColumns(colsel);
2052 // hide whole sequence - should just get location of hidden region
2053 // containing sequence
2054 cs.hideColumns(1, 11);
2055 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2057 cs.revealAllHiddenColumns(colsel);
2058 cs.hideColumns(0, 15);
2059 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2061 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
2063 cs.revealAllHiddenColumns(colsel);
2064 cs.hideColumns(7, 17);
2065 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2067 cs.revealAllHiddenColumns(colsel);
2068 cs.hideColumns(3, 17);
2069 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2071 cs.revealAllHiddenColumns(colsel);
2072 cs.hideColumns(3, 19);
2073 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2075 cs.revealAllHiddenColumns(colsel);
2076 cs.hideColumns(0, 0);
2077 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2079 cs.revealAllHiddenColumns(colsel);
2080 cs.hideColumns(0, 1);
2081 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2083 cs.revealAllHiddenColumns(colsel);
2084 cs.hideColumns(0, 2);
2085 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2087 cs.revealAllHiddenColumns(colsel);
2088 cs.hideColumns(1, 1);
2089 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2091 cs.revealAllHiddenColumns(colsel);
2092 cs.hideColumns(1, 2);
2093 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2095 cs.revealAllHiddenColumns(colsel);
2096 cs.hideColumns(1, 3);
2097 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2099 cs.revealAllHiddenColumns(colsel);
2100 cs.hideColumns(0, 2);
2101 cs.hideColumns(5, 6);
2102 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2104 cs.revealAllHiddenColumns(colsel);
2105 cs.hideColumns(0, 2);
2106 cs.hideColumns(5, 6);
2107 cs.hideColumns(9, 10);
2108 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2110 cs.revealAllHiddenColumns(colsel);
2111 cs.hideColumns(0, 2);
2112 cs.hideColumns(7, 11);
2113 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2115 cs.revealAllHiddenColumns(colsel);
2116 cs.hideColumns(2, 4);
2117 cs.hideColumns(7, 11);
2118 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2120 cs.revealAllHiddenColumns(colsel);
2121 cs.hideColumns(2, 4);
2122 cs.hideColumns(7, 12);
2123 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2125 cs.revealAllHiddenColumns(colsel);
2126 cs.hideColumns(1, 11);
2127 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2129 cs.revealAllHiddenColumns(colsel);
2130 cs.hideColumns(0, 12);
2131 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2133 cs.revealAllHiddenColumns(colsel);
2134 cs.hideColumns(0, 4);
2135 cs.hideColumns(6, 12);
2136 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2138 cs.revealAllHiddenColumns(colsel);
2139 cs.hideColumns(0, 1);
2140 cs.hideColumns(3, 12);
2141 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2143 cs.revealAllHiddenColumns(colsel);
2144 cs.hideColumns(3, 14);
2145 cs.hideColumns(17, 19);
2146 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2148 cs.revealAllHiddenColumns(colsel);
2149 cs.hideColumns(3, 7);
2150 cs.hideColumns(9, 14);
2151 cs.hideColumns(17, 19);
2152 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2154 cs.revealAllHiddenColumns(colsel);
2155 cs.hideColumns(0, 1);
2156 cs.hideColumns(3, 4);
2157 cs.hideColumns(6, 8);
2158 cs.hideColumns(10, 12);
2159 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));