2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.datamodel;
23 import static org.testng.AssertJUnit.assertEquals;
24 import static org.testng.AssertJUnit.assertFalse;
25 import static org.testng.AssertJUnit.assertNotNull;
26 import static org.testng.AssertJUnit.assertNotSame;
27 import static org.testng.AssertJUnit.assertNull;
28 import static org.testng.AssertJUnit.assertSame;
29 import static org.testng.AssertJUnit.assertTrue;
31 import jalview.analysis.AlignmentGenerator;
32 import jalview.commands.EditCommand;
33 import jalview.commands.EditCommand.Action;
34 import jalview.datamodel.PDBEntry.Type;
35 import jalview.gui.JvOptionPane;
36 import jalview.util.MapList;
37 import jalview.ws.params.InvalidArgumentException;
40 import java.util.ArrayList;
41 import java.util.Arrays;
42 import java.util.BitSet;
43 import java.util.Iterator;
44 import java.util.List;
45 import java.util.Vector;
47 import org.testng.Assert;
48 import org.testng.annotations.BeforeClass;
49 import org.testng.annotations.BeforeMethod;
50 import org.testng.annotations.Test;
52 import junit.extensions.PA;
54 public class SequenceTest
56 @BeforeClass(alwaysRun = true)
57 public void setUpJvOptionPane()
59 JvOptionPane.setInteractiveMode(false);
60 JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
65 @BeforeMethod(alwaysRun = true)
68 seq = new Sequence("FER1", "AKPNGVL");
71 @Test(groups = { "Functional" })
72 public void testInsertGapsAndGapmaps()
74 SequenceI aseq = seq.deriveSequence();
75 aseq.insertCharAt(2, 3, '-');
76 aseq.insertCharAt(6, 3, '-');
77 assertEquals("Gap insertions not correct", "AK---P---NGVL",
78 aseq.getSequenceAsString());
79 List<int[]> gapInt = aseq.getInsertions();
80 assertEquals("Gap interval 1 start wrong", 2, gapInt.get(0)[0]);
81 assertEquals("Gap interval 1 end wrong", 4, gapInt.get(0)[1]);
82 assertEquals("Gap interval 2 start wrong", 6, gapInt.get(1)[0]);
83 assertEquals("Gap interval 2 end wrong", 8, gapInt.get(1)[1]);
85 BitSet gapfield = aseq.getInsertionsAsBits();
86 BitSet expectedgaps = new BitSet();
87 expectedgaps.set(2, 5);
88 expectedgaps.set(6, 9);
90 assertEquals(6, expectedgaps.cardinality());
92 assertEquals("getInsertionsAsBits didn't mark expected number of gaps",
93 6, gapfield.cardinality());
95 assertEquals("getInsertionsAsBits not correct.", expectedgaps, gapfield);
98 @Test(groups = ("Functional"))
99 public void testIsProtein()
102 assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
104 assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
106 SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
107 assertFalse(sq.isProtein());
108 // change sequence, should trigger an update of cached result
109 sq.setSequence("ASDFASDFADSF");
110 assertTrue(sq.isProtein());
113 @Test(groups = { "Functional" })
114 public void testGetAnnotation()
116 // initial state returns null not an empty array
117 assertNull(seq.getAnnotation());
118 AlignmentAnnotation ann = addAnnotation("label1", "desc1", "calcId1",
120 AlignmentAnnotation[] anns = seq.getAnnotation();
121 assertEquals(1, anns.length);
122 assertSame(ann, anns[0]);
124 // removing all annotations reverts array to null
125 seq.removeAlignmentAnnotation(ann);
126 assertNull(seq.getAnnotation());
129 @Test(groups = { "Functional" })
130 public void testGetAnnotation_forLabel()
132 AlignmentAnnotation ann1 = addAnnotation("label1", "desc1", "calcId1",
134 addAnnotation("label2", "desc2", "calcId2", 1f);
135 AlignmentAnnotation ann3 = addAnnotation("label1", "desc3", "calcId3",
137 AlignmentAnnotation[] anns = seq.getAnnotation("label1");
138 assertEquals(2, anns.length);
139 assertSame(ann1, anns[0]);
140 assertSame(ann3, anns[1]);
143 private AlignmentAnnotation addAnnotation(String label,
144 String description, String calcId, float value)
146 final AlignmentAnnotation annotation = new AlignmentAnnotation(label,
148 annotation.setCalcId(calcId);
149 seq.addAlignmentAnnotation(annotation);
153 @Test(groups = { "Functional" })
154 public void testGetAlignmentAnnotations_forCalcIdAndLabel()
156 addAnnotation("label1", "desc1", "calcId1", 1f);
157 AlignmentAnnotation ann2 = addAnnotation("label2", "desc2", "calcId2",
159 addAnnotation("label2", "desc3", "calcId3", 1f);
160 AlignmentAnnotation ann4 = addAnnotation("label2", "desc3", "calcId2",
162 addAnnotation("label5", "desc3", null, 1f);
163 addAnnotation(null, "desc3", "calcId3", 1f);
165 List<AlignmentAnnotation> anns = seq.getAlignmentAnnotations("calcId2",
167 assertEquals(2, anns.size());
168 assertSame(ann2, anns.get(0));
169 assertSame(ann4, anns.get(1));
171 assertTrue(seq.getAlignmentAnnotations("calcId2", "label3").isEmpty());
172 assertTrue(seq.getAlignmentAnnotations("calcId3", "label5").isEmpty());
173 assertTrue(seq.getAlignmentAnnotations("calcId2", null).isEmpty());
174 assertTrue(seq.getAlignmentAnnotations(null, "label3").isEmpty());
175 assertTrue(seq.getAlignmentAnnotations(null, null).isEmpty());
179 * Tests for addAlignmentAnnotation. Note this method has the side-effect of
180 * setting the sequenceRef on the annotation. Adding the same annotation twice
183 @Test(groups = { "Functional" })
184 public void testAddAlignmentAnnotation()
186 assertNull(seq.getAnnotation());
187 final AlignmentAnnotation annotation = new AlignmentAnnotation("a",
189 assertNull(annotation.sequenceRef);
190 seq.addAlignmentAnnotation(annotation);
191 assertSame(seq, annotation.sequenceRef);
192 AlignmentAnnotation[] anns = seq.getAnnotation();
193 assertEquals(1, anns.length);
194 assertSame(annotation, anns[0]);
196 // re-adding does nothing
197 seq.addAlignmentAnnotation(annotation);
198 anns = seq.getAnnotation();
199 assertEquals(1, anns.length);
200 assertSame(annotation, anns[0]);
202 // an identical but different annotation can be added
203 final AlignmentAnnotation annotation2 = new AlignmentAnnotation("a",
205 seq.addAlignmentAnnotation(annotation2);
206 anns = seq.getAnnotation();
207 assertEquals(2, anns.length);
208 assertSame(annotation, anns[0]);
209 assertSame(annotation2, anns[1]);
212 @Test(groups = { "Functional" })
213 public void testGetStartGetEnd()
215 SequenceI sq = new Sequence("test", "ABCDEF");
216 assertEquals(1, sq.getStart());
217 assertEquals(6, sq.getEnd());
219 sq = new Sequence("test", "--AB-C-DEF--");
220 assertEquals(1, sq.getStart());
221 assertEquals(6, sq.getEnd());
223 sq = new Sequence("test", "----");
224 assertEquals(1, sq.getStart());
225 assertEquals(0, sq.getEnd()); // ??
229 * Tests for the method that returns an alignment column position (base 1) for
230 * a given sequence position (base 1).
232 @Test(groups = { "Functional" })
233 public void testFindIndex()
236 * call sequenceChanged() after each test to invalidate any cursor,
237 * forcing the 1-arg findIndex to be executed
239 SequenceI sq = new Sequence("test", "ABCDEF");
240 assertEquals(0, sq.findIndex(0));
241 sq.sequenceChanged();
242 assertEquals(1, sq.findIndex(1));
243 sq.sequenceChanged();
244 assertEquals(5, sq.findIndex(5));
245 sq.sequenceChanged();
246 assertEquals(6, sq.findIndex(6));
247 sq.sequenceChanged();
248 assertEquals(6, sq.findIndex(9));
250 final String aligned = "-A--B-C-D-E-F--";
251 assertEquals(15, aligned.length());
252 sq = new Sequence("test/8-13", aligned);
253 assertEquals(2, sq.findIndex(8));
254 sq.sequenceChanged();
255 assertEquals(5, sq.findIndex(9));
256 sq.sequenceChanged();
257 assertEquals(7, sq.findIndex(10));
259 // before start returns 0
260 sq.sequenceChanged();
261 assertEquals(0, sq.findIndex(0));
262 sq.sequenceChanged();
263 assertEquals(0, sq.findIndex(-1));
265 // beyond end returns last residue column
266 sq.sequenceChanged();
267 assertEquals(13, sq.findIndex(99));
270 * residue before sequence 'end' but beyond end of sequence returns
271 * length of sequence (last column) (rightly or wrongly!)
273 sq = new Sequence("test/8-15", "A-B-C-"); // trailing gap case
274 assertEquals(6, sq.getLength());
275 sq.sequenceChanged();
276 assertEquals(sq.getLength(), sq.findIndex(14));
277 sq = new Sequence("test/8-99", "-A--B-C-D"); // trailing residue case
278 sq.sequenceChanged();
279 assertEquals(sq.getLength(), sq.findIndex(65));
282 * residue after sequence 'start' but before first residue returns
283 * zero (before first column) (rightly or wrongly!)
285 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
286 sq.sequenceChanged();
287 assertEquals(0, sq.findIndex(3));
288 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
289 sq.sequenceChanged();
290 assertEquals(0, sq.findIndex(2));
293 @Test(groups = { "Functional" })
294 public void testFindPositions()
296 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
301 assertNull(sq.findPositions(6, 5));
302 assertNull(sq.findPositions(0, 5));
303 assertNull(sq.findPositions(-1, 5));
308 assertNull(sq.findPositions(1, 1)); // 1-based columns
309 assertNull(sq.findPositions(5, 5));
310 assertNull(sq.findPositions(5, 6));
311 assertNull(sq.findPositions(5, 7));
314 * all ungapped ranges
316 assertEquals(new Range(8, 8), sq.findPositions(2, 2)); // A
317 assertEquals(new Range(8, 9), sq.findPositions(2, 3)); // AB
318 assertEquals(new Range(8, 10), sq.findPositions(2, 4)); // ABC
319 assertEquals(new Range(9, 10), sq.findPositions(3, 4)); // BC
322 * gap to ungapped range
324 assertEquals(new Range(8, 10), sq.findPositions(1, 4)); // ABC
325 assertEquals(new Range(11, 12), sq.findPositions(6, 9)); // DE
328 * ungapped to gapped range
330 assertEquals(new Range(10, 10), sq.findPositions(4, 5)); // C
331 assertEquals(new Range(9, 13), sq.findPositions(3, 11)); // BCDEF
334 * ungapped to ungapped enclosing gaps
336 assertEquals(new Range(10, 11), sq.findPositions(4, 8)); // CD
337 assertEquals(new Range(8, 13), sq.findPositions(2, 11)); // ABCDEF
340 * gapped to gapped enclosing ungapped
342 assertEquals(new Range(8, 10), sq.findPositions(1, 5)); // ABC
343 assertEquals(new Range(11, 12), sq.findPositions(5, 10)); // DE
344 assertEquals(new Range(8, 13), sq.findPositions(1, 13)); // the lot
345 assertEquals(new Range(8, 13), sq.findPositions(1, 99));
349 * Tests for the method that returns a dataset sequence position (start..) for
350 * an aligned column position (base 0).
352 @Test(groups = { "Functional" })
353 public void testFindPosition()
356 * call sequenceChanged() after each test to invalidate any cursor,
357 * forcing the 1-arg findPosition to be executed
359 SequenceI sq = new Sequence("test/8-13", "ABCDEF");
360 assertEquals(8, sq.findPosition(0));
361 // Sequence should now hold a cursor at [8, 0]
362 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0",
363 PA.getValue(sq, "cursor").toString());
364 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
365 int token = (int) PA.getValue(sq, "changeCount");
366 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
368 sq.sequenceChanged();
371 * find F13 at column offset 5, cursor should update to [13, 6]
372 * endColumn is found and saved in cursor
374 assertEquals(13, sq.findPosition(5));
375 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
376 assertEquals(++token, (int) PA.getValue(sq, "changeCount"));
377 assertEquals(new SequenceCursor(sq, 13, 6, token), cursor);
378 assertEquals("test:Pos13:Col6:startCol1:endCol6:tok1",
379 PA.getValue(sq, "cursor").toString());
381 // assertEquals(-1, seq.findPosition(6)); // fails
383 sq = new Sequence("test/8-11", "AB-C-D--");
384 token = (int) PA.getValue(sq, "changeCount"); // 0
385 assertEquals(8, sq.findPosition(0));
386 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
387 assertEquals(new SequenceCursor(sq, 8, 1, token), cursor);
388 assertEquals("test:Pos8:Col1:startCol1:endCol0:tok0",
389 PA.getValue(sq, "cursor").toString());
391 sq.sequenceChanged();
392 assertEquals(9, sq.findPosition(1));
393 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
394 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
395 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok1",
396 PA.getValue(sq, "cursor").toString());
398 sq.sequenceChanged();
399 // gap position 'finds' residue to the right (not the left as per javadoc)
400 // cursor is set to the last residue position found [B 2]
401 assertEquals(10, sq.findPosition(2));
402 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
403 assertEquals(new SequenceCursor(sq, 9, 2, ++token), cursor);
404 assertEquals("test:Pos9:Col2:startCol1:endCol0:tok2",
405 PA.getValue(sq, "cursor").toString());
407 sq.sequenceChanged();
408 assertEquals(10, sq.findPosition(3));
409 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
410 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
411 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok3",
412 PA.getValue(sq, "cursor").toString());
414 sq.sequenceChanged();
415 // column[4] is the gap after C - returns D11
416 // cursor is set to [C 4]
417 assertEquals(11, sq.findPosition(4));
418 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
419 assertEquals(new SequenceCursor(sq, 10, 4, ++token), cursor);
420 assertEquals("test:Pos10:Col4:startCol1:endCol0:tok4",
421 PA.getValue(sq, "cursor").toString());
423 sq.sequenceChanged();
424 assertEquals(11, sq.findPosition(5)); // D
425 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
426 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
427 // lastCol has been found and saved in the cursor
428 assertEquals("test:Pos11:Col6:startCol1:endCol6:tok5",
429 PA.getValue(sq, "cursor").toString());
431 sq.sequenceChanged();
432 // returns 1 more than sequence length if off the end ?!?
433 assertEquals(12, sq.findPosition(6));
435 sq.sequenceChanged();
436 assertEquals(12, sq.findPosition(7));
439 * first findPosition should also set firstResCol in cursor
441 sq = new Sequence("test/8-13", "--AB-C-DEF--");
442 assertEquals(8, sq.findPosition(0));
443 assertNull(PA.getValue(sq, "cursor"));
445 sq.sequenceChanged();
446 assertEquals(8, sq.findPosition(1));
447 assertNull(PA.getValue(sq, "cursor"));
449 sq.sequenceChanged();
450 assertEquals(8, sq.findPosition(2));
451 assertEquals("test:Pos8:Col3:startCol3:endCol0:tok2",
452 PA.getValue(sq, "cursor").toString());
454 sq.sequenceChanged();
455 assertEquals(9, sq.findPosition(3));
456 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok3",
457 PA.getValue(sq, "cursor").toString());
459 sq.sequenceChanged();
460 // column[4] is a gap, returns next residue pos (C10)
461 // cursor is set to last residue found [B]
462 assertEquals(10, sq.findPosition(4));
463 assertEquals("test:Pos9:Col4:startCol3:endCol0:tok4",
464 PA.getValue(sq, "cursor").toString());
466 sq.sequenceChanged();
467 assertEquals(10, sq.findPosition(5));
468 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok5",
469 PA.getValue(sq, "cursor").toString());
471 sq.sequenceChanged();
472 // column[6] is a gap, returns next residue pos (D11)
473 // cursor is set to last residue found [C]
474 assertEquals(11, sq.findPosition(6));
475 assertEquals("test:Pos10:Col6:startCol3:endCol0:tok6",
476 PA.getValue(sq, "cursor").toString());
478 sq.sequenceChanged();
479 assertEquals(11, sq.findPosition(7));
480 assertEquals("test:Pos11:Col8:startCol3:endCol0:tok7",
481 PA.getValue(sq, "cursor").toString());
483 sq.sequenceChanged();
484 assertEquals(12, sq.findPosition(8));
485 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok8",
486 PA.getValue(sq, "cursor").toString());
489 * when the last residue column is found, it is set in the cursor
491 sq.sequenceChanged();
492 assertEquals(13, sq.findPosition(9));
493 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok9",
494 PA.getValue(sq, "cursor").toString());
496 sq.sequenceChanged();
497 assertEquals(14, sq.findPosition(10));
498 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok10",
499 PA.getValue(sq, "cursor").toString());
502 * findPosition for column beyond sequence length
503 * returns 1 more than last residue position
505 sq.sequenceChanged();
506 assertEquals(14, sq.findPosition(11));
507 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok11",
508 PA.getValue(sq, "cursor").toString());
510 sq.sequenceChanged();
511 assertEquals(14, sq.findPosition(99));
512 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok12",
513 PA.getValue(sq, "cursor").toString());
516 * gapped sequence ending in non-gap
518 sq = new Sequence("test/8-13", "--AB-C-DEF");
519 assertEquals(13, sq.findPosition(9));
520 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok0",
521 PA.getValue(sq, "cursor").toString());
522 sq.sequenceChanged();
523 assertEquals(12, sq.findPosition(8)); // E12
524 // sequenceChanged() invalidates cursor.lastResidueColumn
525 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
526 assertEquals("test:Pos12:Col9:startCol3:endCol0:tok1",
528 // findPosition with cursor accepts base 1 column values
529 assertEquals(13, ((Sequence) sq).findPosition(10, cursor));
530 assertEquals(13, sq.findPosition(9)); // F13
531 // lastResidueColumn has now been found and saved in cursor
532 assertEquals("test:Pos13:Col10:startCol3:endCol10:tok1",
533 PA.getValue(sq, "cursor").toString());
536 @Test(groups = { "Functional" })
537 public void testDeleteChars()
542 SequenceI sq = new Sequence("test", "ABCDEF");
543 assertNull(PA.getValue(sq, "datasetSequence"));
544 assertEquals(1, sq.getStart());
545 assertEquals(6, sq.getEnd());
546 sq.deleteChars(2, 3);
547 assertEquals("ABDEF", sq.getSequenceAsString());
548 assertEquals(1, sq.getStart());
549 assertEquals(5, sq.getEnd());
550 assertNull(PA.getValue(sq, "datasetSequence"));
555 sq = new Sequence("test", "ABCDEF");
556 sq.deleteChars(0, 2);
557 assertEquals("CDEF", sq.getSequenceAsString());
558 assertEquals(3, sq.getStart());
559 assertEquals(6, sq.getEnd());
560 assertNull(PA.getValue(sq, "datasetSequence"));
562 sq = new Sequence("test", "ABCDE");
563 sq.deleteChars(0, 3);
564 assertEquals("DE", sq.getSequenceAsString());
565 assertEquals(4, sq.getStart());
566 assertEquals(5, sq.getEnd());
567 assertNull(PA.getValue(sq, "datasetSequence"));
572 sq = new Sequence("test", "ABCDEF");
573 sq.deleteChars(4, 6);
574 assertEquals("ABCD", sq.getSequenceAsString());
575 assertEquals(1, sq.getStart());
576 assertEquals(4, sq.getEnd());
577 assertNull(PA.getValue(sq, "datasetSequence"));
580 * delete more positions than there are
582 sq = new Sequence("test/8-11", "ABCD");
583 sq.deleteChars(0, 99);
584 assertEquals("", sq.getSequenceAsString());
585 assertEquals(12, sq.getStart()); // = findPosition(99) ?!?
586 assertEquals(11, sq.getEnd());
588 sq = new Sequence("test/8-11", "----");
589 sq.deleteChars(0, 99); // ArrayIndexOutOfBoundsException <= 2.10.2
590 assertEquals("", sq.getSequenceAsString());
591 assertEquals(8, sq.getStart());
592 assertEquals(11, sq.getEnd());
595 @Test(groups = { "Functional" })
596 public void testDeleteChars_withDbRefsAndFeatures()
599 * internal delete - new dataset sequence created
600 * gets a copy of any dbrefs
602 SequenceI sq = new Sequence("test", "ABCDEF");
603 sq.createDatasetSequence();
604 DBRefEntry dbr1 = new DBRefEntry("Uniprot", "0", "a123");
606 Object ds = PA.getValue(sq, "datasetSequence");
608 assertEquals(1, sq.getStart());
609 assertEquals(6, sq.getEnd());
610 sq.deleteChars(2, 3);
611 assertEquals("ABDEF", sq.getSequenceAsString());
612 assertEquals(1, sq.getStart());
613 assertEquals(5, sq.getEnd());
614 Object newDs = PA.getValue(sq, "datasetSequence");
615 assertNotNull(newDs);
616 assertNotSame(ds, newDs);
617 assertNotNull(sq.getDBRefs());
618 assertEquals(1, sq.getDBRefs().size());
619 assertNotSame(dbr1, sq.getDBRefs().get(0));
620 assertEquals(dbr1, sq.getDBRefs().get(0));
623 * internal delete with sequence features
624 * (failure case for JAL-2541)
626 sq = new Sequence("test", "ABCDEF");
627 sq.createDatasetSequence();
628 SequenceFeature sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
630 sq.addSequenceFeature(sf1);
631 ds = PA.getValue(sq, "datasetSequence");
633 assertEquals(1, sq.getStart());
634 assertEquals(6, sq.getEnd());
635 sq.deleteChars(2, 4);
636 assertEquals("ABEF", sq.getSequenceAsString());
637 assertEquals(1, sq.getStart());
638 assertEquals(4, sq.getEnd());
639 newDs = PA.getValue(sq, "datasetSequence");
640 assertNotNull(newDs);
641 assertNotSame(ds, newDs);
642 List<SequenceFeature> sfs = sq.getSequenceFeatures();
643 assertEquals(1, sfs.size());
644 assertNotSame(sf1, sfs.get(0));
645 assertEquals(sf1, sfs.get(0));
648 * delete at start - no new dataset sequence created
649 * any sequence features remain as before
651 sq = new Sequence("test", "ABCDEF");
652 sq.createDatasetSequence();
653 ds = PA.getValue(sq, "datasetSequence");
654 sf1 = new SequenceFeature("Cath", "desc", 2, 4, 2f, "CathGroup");
655 sq.addSequenceFeature(sf1);
656 sq.deleteChars(0, 2);
657 assertEquals("CDEF", sq.getSequenceAsString());
658 assertEquals(3, sq.getStart());
659 assertEquals(6, sq.getEnd());
660 assertSame(ds, PA.getValue(sq, "datasetSequence"));
661 sfs = sq.getSequenceFeatures();
663 assertEquals(1, sfs.size());
664 assertSame(sf1, sfs.get(0));
667 * delete at end - no new dataset sequence created
668 * any dbrefs remain as before
670 sq = new Sequence("test", "ABCDEF");
671 sq.createDatasetSequence();
672 ds = PA.getValue(sq, "datasetSequence");
673 dbr1 = new DBRefEntry("Uniprot", "0", "a123");
675 sq.deleteChars(4, 6);
676 assertEquals("ABCD", sq.getSequenceAsString());
677 assertEquals(1, sq.getStart());
678 assertEquals(4, sq.getEnd());
679 assertSame(ds, PA.getValue(sq, "datasetSequence"));
680 assertNotNull(sq.getDBRefs());
681 assertEquals(1, sq.getDBRefs().size());
682 assertSame(dbr1, sq.getDBRefs().get(0));
685 @Test(groups = { "Functional" })
686 public void testInsertCharAt()
688 // non-static methods:
689 SequenceI sq = new Sequence("test", "ABCDEF");
690 sq.insertCharAt(0, 'z');
691 assertEquals("zABCDEF", sq.getSequenceAsString());
692 sq.insertCharAt(2, 2, 'x');
693 assertEquals("zAxxBCDEF", sq.getSequenceAsString());
695 // for static method see StringUtilsTest
699 * Test the method that returns an array of aligned sequence positions where
700 * the array index is the data sequence position (both base 0).
702 @Test(groups = { "Functional" })
703 public void testGapMap()
705 SequenceI sq = new Sequence("test", "-A--B-CD-E--F-");
706 sq.createDatasetSequence();
707 assertEquals("[1, 4, 6, 7, 9, 12]", Arrays.toString(sq.gapMap()));
711 * Test the method that gets sequence features, either from the sequence or
714 @Test(groups = { "Functional" })
715 public void testGetSequenceFeatures()
717 SequenceI sq = new Sequence("test", "GATCAT");
718 sq.createDatasetSequence();
720 assertTrue(sq.getSequenceFeatures().isEmpty());
723 * SequenceFeature on sequence
725 SequenceFeature sf = new SequenceFeature("Cath", "desc", 2, 4, 2f, null);
726 sq.addSequenceFeature(sf);
727 List<SequenceFeature> sfs = sq.getSequenceFeatures();
728 assertEquals(1, sfs.size());
729 assertSame(sf, sfs.get(0));
732 * SequenceFeature on sequence and dataset sequence; returns that on
735 * Note JAL-2046: spurious: we have no use case for this at the moment.
736 * This test also buggy - as sf2.equals(sf), no new feature is added
738 SequenceFeature sf2 = new SequenceFeature("Cath", "desc", 2, 4, 2f,
740 sq.getDatasetSequence().addSequenceFeature(sf2);
741 sfs = sq.getSequenceFeatures();
742 assertEquals(1, sfs.size());
743 assertSame(sf, sfs.get(0));
746 * SequenceFeature on dataset sequence only
747 * Note JAL-2046: spurious: we have no use case for setting a non-dataset sequence's feature array to null at the moment.
749 sq.setSequenceFeatures(null);
750 assertTrue(sq.getDatasetSequence().getSequenceFeatures().isEmpty());
753 * Corrupt case - no SequenceFeature, dataset's dataset is the original
754 * sequence. Test shows no infinite loop results.
756 sq.getDatasetSequence().setSequenceFeatures(null);
758 * is there a usecase for this ? setDatasetSequence should throw an error if
759 * this actually occurs.
763 sq.getDatasetSequence().setDatasetSequence(sq); // loop!
764 Assert.fail("Expected Error to be raised when calling setDatasetSequence with self reference");
765 } catch (IllegalArgumentException e)
767 // TODO Jalview error/exception class for raising implementation errors
768 assertTrue(e.getMessage().toLowerCase()
769 .contains("implementation error"));
771 assertTrue(sq.getSequenceFeatures().isEmpty());
775 * Test the method that returns an array, indexed by sequence position, whose
776 * entries are the residue positions at the sequence position (or to the right
779 @Test(groups = { "Functional" })
780 public void testFindPositionMap()
783 * Note: Javadoc for findPosition says it returns the residue position to
784 * the left of a gapped position; in fact it returns the position to the
785 * right. Also it returns a non-existent residue position for a gap beyond
788 Sequence sq = new Sequence("TestSeq", "AB.C-D E.");
789 int[] map = sq.findPositionMap();
790 assertEquals(Arrays.toString(new int[] { 1, 2, 3, 3, 4, 4, 5, 5, 6 }),
791 Arrays.toString(map));
795 * Test for getSubsequence
797 @Test(groups = { "Functional" })
798 public void testGetSubsequence()
800 SequenceI sq = new Sequence("TestSeq", "ABCDEFG");
801 sq.createDatasetSequence();
803 // positions are base 0, end position is exclusive
804 SequenceI subseq = sq.getSubSequence(2, 4);
806 assertEquals("CD", subseq.getSequenceAsString());
807 // start/end are base 1 positions
808 assertEquals(3, subseq.getStart());
809 assertEquals(4, subseq.getEnd());
810 // subsequence shares the full dataset sequence
811 assertSame(sq.getDatasetSequence(), subseq.getDatasetSequence());
815 * test createDatasetSequence behaves to doc
817 @Test(groups = { "Functional" })
818 public void testCreateDatasetSequence()
820 SequenceI sq = new Sequence("my", "ASDASD");
821 sq.addSequenceFeature(new SequenceFeature("type", "desc", 1, 10, 1f,
823 sq.addDBRef(new DBRefEntry("source", "version", "accession"));
824 assertNull(sq.getDatasetSequence());
825 assertNotNull(PA.getValue(sq, "sequenceFeatureStore"));
826 assertNotNull(PA.getValue(sq, "dbrefs"));
828 SequenceI rds = sq.createDatasetSequence();
830 assertNull(rds.getDatasetSequence());
831 assertSame(sq.getDatasetSequence(), rds);
833 // sequence features and dbrefs transferred to dataset sequence
834 assertNull(PA.getValue(sq, "sequenceFeatureStore"));
835 assertNull(PA.getValue(sq, "dbrefs"));
836 assertNotNull(PA.getValue(rds, "sequenceFeatureStore"));
837 assertNotNull(PA.getValue(rds, "dbrefs"));
841 * Test for deriveSequence applied to a sequence with a dataset
843 @Test(groups = { "Functional" })
844 public void testDeriveSequence_existingDataset()
846 Sequence sq = new Sequence("Seq1", "CD");
847 sq.setDatasetSequence(new Sequence("Seq1", "ABCDEF"));
848 sq.getDatasetSequence().addSequenceFeature(
849 new SequenceFeature("", "", 1, 2, 0f, null));
853 sq.setDescription("Test sequence description..");
854 sq.setVamsasId("TestVamsasId");
855 sq.addDBRef(new DBRefEntry("PDB", "version0", "1TST"));
857 sq.addDBRef(new DBRefEntry("PDB", "version1", "1PDB"));
858 sq.addDBRef(new DBRefEntry("PDB", "version2", "2PDB"));
859 sq.addDBRef(new DBRefEntry("PDB", "version3", "3PDB"));
860 sq.addDBRef(new DBRefEntry("PDB", "version4", "4PDB"));
862 sq.addPDBId(new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1"));
863 sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
864 sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
865 sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
867 // these are the same as ones already added
868 DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
869 DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
871 List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
874 sq.getDatasetSequence().addDBRef(pdb1pdb); // should do nothing
875 sq.getDatasetSequence().addDBRef(pdb2pdb); // should do nothing
876 sq.getDatasetSequence().addDBRef(
877 new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
878 sq.getDatasetSequence().addDBRef(
879 new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
881 PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
882 PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
883 PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
885 PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
887 sq.getDatasetSequence().addPDBId(pdbe1a);
888 sq.getDatasetSequence().addPDBId(pdbe1b);
889 sq.getDatasetSequence().addPDBId(pdbe2a);
890 sq.getDatasetSequence().addPDBId(pdbe2b);
893 * test we added pdb entries to the dataset sequence
895 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries(), Arrays
896 .asList(new PDBEntry[] { pdbe1a, pdbe1b, pdbe2a, pdbe2b }),
897 "PDB Entries were not found on dataset sequence.");
900 * we should recover a pdb entry that is on the dataset sequence via PDBEntry
902 Assert.assertEquals(pdbe1a,
903 sq.getDatasetSequence().getPDBEntry("1PDB"),
904 "PDB Entry '1PDB' not found on dataset sequence via getPDBEntry.");
905 ArrayList<Annotation> annotsList = new ArrayList<>();
906 System.out.println(">>>>>> " + sq.getSequenceAsString().length());
907 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
908 annotsList.add(new Annotation("A", "A", 'X', 0.1f));
909 Annotation[] annots = annotsList.toArray(new Annotation[0]);
910 sq.addAlignmentAnnotation(new AlignmentAnnotation("Test annot",
911 "Test annot description", annots));
912 sq.getDatasetSequence().addAlignmentAnnotation(
913 new AlignmentAnnotation("Test annot", "Test annot description",
915 Assert.assertEquals(sq.getDescription(), "Test sequence description..");
916 Assert.assertEquals(sq.getDBRefs().size(), 5); // DBRefs are on dataset
918 Assert.assertEquals(sq.getAllPDBEntries().size(), 4);
919 Assert.assertNotNull(sq.getAnnotation());
920 Assert.assertEquals(sq.getAnnotation()[0].annotations.length, 2);
921 Assert.assertEquals(sq.getDatasetSequence().getDBRefs().size(), 5); // same
924 Assert.assertEquals(sq.getDatasetSequence().getAllPDBEntries().size(),
926 Assert.assertNotNull(sq.getDatasetSequence().getAnnotation());
928 Sequence derived = (Sequence) sq.deriveSequence();
930 Assert.assertEquals(derived.getDescription(),
931 "Test sequence description..");
932 Assert.assertEquals(derived.getDBRefs().size(), 5); // come from dataset
933 Assert.assertEquals(derived.getAllPDBEntries().size(), 4);
934 Assert.assertNotNull(derived.getAnnotation());
935 Assert.assertEquals(derived.getAnnotation()[0].annotations.length, 2);
936 Assert.assertEquals(derived.getDatasetSequence().getDBRefs().size(), 5);
937 Assert.assertEquals(derived.getDatasetSequence().getAllPDBEntries()
939 Assert.assertNotNull(derived.getDatasetSequence().getAnnotation());
941 assertEquals("CD", derived.getSequenceAsString());
942 assertSame(sq.getDatasetSequence(), derived.getDatasetSequence());
944 // derived sequence should access dataset sequence features
945 assertNotNull(sq.getSequenceFeatures());
946 assertEquals(sq.getSequenceFeatures(), derived.getSequenceFeatures());
949 * verify we have primary db refs *just* for PDB IDs with associated
953 assertEquals(primRefs, sq.getPrimaryDBRefs());
954 assertEquals(primRefs, sq.getDatasetSequence().getPrimaryDBRefs());
956 assertEquals(sq.getPrimaryDBRefs(), derived.getPrimaryDBRefs());
961 * Test for deriveSequence applied to an ungapped sequence with no dataset
963 @Test(groups = { "Functional" })
964 public void testDeriveSequence_noDatasetUngapped()
966 SequenceI sq = new Sequence("Seq1", "ABCDEF");
967 assertEquals(1, sq.getStart());
968 assertEquals(6, sq.getEnd());
969 SequenceI derived = sq.deriveSequence();
970 assertEquals("ABCDEF", derived.getSequenceAsString());
971 assertEquals("ABCDEF", derived.getDatasetSequence()
972 .getSequenceAsString());
976 * Test for deriveSequence applied to a gapped sequence with no dataset
978 @Test(groups = { "Functional" })
979 public void testDeriveSequence_noDatasetGapped()
981 SequenceI sq = new Sequence("Seq1", "AB-C.D EF");
982 assertEquals(1, sq.getStart());
983 assertEquals(6, sq.getEnd());
984 assertNull(sq.getDatasetSequence());
985 SequenceI derived = sq.deriveSequence();
986 assertEquals("AB-C.D EF", derived.getSequenceAsString());
987 assertEquals("ABCDEF", derived.getDatasetSequence()
988 .getSequenceAsString());
991 @Test(groups = { "Functional" })
992 public void testCopyConstructor_noDataset()
994 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
995 seq1.setDescription("description");
996 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
998 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1000 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1001 seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
1003 SequenceI copy = new Sequence(seq1);
1005 assertNull(copy.getDatasetSequence());
1007 verifyCopiedSequence(seq1, copy);
1009 // copy has a copy of the DBRefEntry
1010 // this is murky - DBrefs are only copied for dataset sequences
1011 // where the test for 'dataset sequence' is 'dataset is null'
1012 // but that doesn't distinguish it from an aligned sequence
1013 // which has not yet generated a dataset sequence
1014 // NB getDBRef looks inside dataset sequence if not null
1015 List<DBRefEntry> dbrefs = copy.getDBRefs();
1016 assertEquals(1, dbrefs.size());
1017 assertFalse(dbrefs.get(0) == seq1.getDBRefs().get(0));
1018 assertTrue(dbrefs.get(0).equals(seq1.getDBRefs().get(0)));
1021 @Test(groups = { "Functional" })
1022 public void testCopyConstructor_withDataset()
1024 SequenceI seq1 = new Sequence("Seq1", "AB-C.D EF");
1025 seq1.createDatasetSequence();
1026 seq1.setDescription("description");
1027 seq1.addAlignmentAnnotation(new AlignmentAnnotation("label", "desc",
1029 // JAL-2046 - what is the contract for using a derived sequence's
1030 // addSequenceFeature ?
1031 seq1.addSequenceFeature(new SequenceFeature("type", "desc", 22, 33,
1033 seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
1034 // here we add DBRef to the dataset sequence:
1035 seq1.getDatasetSequence().addDBRef(
1036 new DBRefEntry("EMBL", "1.2", "AZ12345"));
1038 SequenceI copy = new Sequence(seq1);
1040 assertNotNull(copy.getDatasetSequence());
1041 assertSame(copy.getDatasetSequence(), seq1.getDatasetSequence());
1043 verifyCopiedSequence(seq1, copy);
1045 // getDBRef looks inside dataset sequence and this is shared,
1046 // so holds the same dbref objects
1047 List<DBRefEntry> dbrefs = copy.getDBRefs();
1048 assertEquals(1, dbrefs.size());
1049 assertSame(dbrefs.get(0), seq1.getDBRefs().get(0));
1053 * Helper to make assertions about a copied sequence
1058 protected void verifyCopiedSequence(SequenceI seq1, SequenceI copy)
1060 // verify basic properties:
1061 assertEquals(copy.getName(), seq1.getName());
1062 assertEquals(copy.getDescription(), seq1.getDescription());
1063 assertEquals(copy.getStart(), seq1.getStart());
1064 assertEquals(copy.getEnd(), seq1.getEnd());
1065 assertEquals(copy.getSequenceAsString(), seq1.getSequenceAsString());
1067 // copy has a copy of the annotation:
1068 AlignmentAnnotation[] anns = copy.getAnnotation();
1069 assertEquals(1, anns.length);
1070 assertFalse(anns[0] == seq1.getAnnotation()[0]);
1071 assertEquals(anns[0].label, seq1.getAnnotation()[0].label);
1072 assertEquals(anns[0].description, seq1.getAnnotation()[0].description);
1073 assertEquals(anns[0].score, seq1.getAnnotation()[0].score);
1075 // copy has a copy of the sequence feature:
1076 List<SequenceFeature> sfs = copy.getSequenceFeatures();
1077 assertEquals(1, sfs.size());
1078 if (seq1.getDatasetSequence() != null
1079 && copy.getDatasetSequence() == seq1.getDatasetSequence())
1081 assertSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1085 assertNotSame(sfs.get(0), seq1.getSequenceFeatures().get(0));
1087 assertEquals(sfs.get(0), seq1.getSequenceFeatures().get(0));
1089 // copy has a copy of the PDB entry
1090 Vector<PDBEntry> pdbs = copy.getAllPDBEntries();
1091 assertEquals(1, pdbs.size());
1092 assertFalse(pdbs.get(0) == seq1.getAllPDBEntries().get(0));
1093 assertTrue(pdbs.get(0).equals(seq1.getAllPDBEntries().get(0)));
1096 @Test(groups = "Functional")
1097 public void testGetCharAt()
1099 SequenceI sq = new Sequence("", "abcde");
1100 assertEquals('a', sq.getCharAt(0));
1101 assertEquals('e', sq.getCharAt(4));
1102 assertEquals(' ', sq.getCharAt(5));
1103 assertEquals(' ', sq.getCharAt(-1));
1106 @Test(groups = { "Functional" })
1107 public void testAddSequenceFeatures()
1109 SequenceI sq = new Sequence("", "abcde");
1110 // type may not be null
1111 assertFalse(sq.addSequenceFeature(new SequenceFeature(null, "desc", 4,
1113 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1115 // can't add a duplicate feature
1116 assertFalse(sq.addSequenceFeature(new SequenceFeature("Cath", "desc",
1118 // can add a different feature
1119 assertTrue(sq.addSequenceFeature(new SequenceFeature("Scop", "desc", 4,
1120 8, 0f, null))); // different type
1121 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath",
1122 "description", 4, 8, 0f, null)));// different description
1123 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 3,
1124 8, 0f, null))); // different start position
1125 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1126 9, 0f, null))); // different end position
1127 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1128 8, 1f, null))); // different score
1129 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1130 8, Float.NaN, null))); // score NaN
1131 assertTrue(sq.addSequenceFeature(new SequenceFeature("Cath", "desc", 4,
1132 8, 0f, "Metal"))); // different group
1133 assertEquals(8, sq.getFeatures().getAllFeatures().size());
1137 * Tests for adding (or updating) dbrefs
1139 * @see DBRefEntry#updateFrom(DBRefEntry)
1141 @Test(groups = { "Functional" })
1142 public void testAddDBRef()
1144 SequenceI sq = new Sequence("", "abcde");
1145 assertNull(sq.getDBRefs());
1146 DBRefEntry dbref = new DBRefEntry("Uniprot", "1", "P00340");
1148 assertEquals(1, sq.getDBRefs().size());
1149 assertSame(dbref, sq.getDBRefs().get(0));
1152 * change of version - new entry
1154 DBRefEntry dbref2 = new DBRefEntry("Uniprot", "2", "P00340");
1155 sq.addDBRef(dbref2);
1156 assertEquals(2, sq.getDBRefs().size());
1157 assertSame(dbref, sq.getDBRefs().get(0));
1158 assertSame(dbref2, sq.getDBRefs().get(1));
1161 * matches existing entry - not added
1163 sq.addDBRef(new DBRefEntry("UNIPROT", "1", "p00340"));
1164 assertEquals(2, sq.getDBRefs().size());
1167 * different source = new entry
1169 DBRefEntry dbref3 = new DBRefEntry("UniRef", "1", "p00340");
1170 sq.addDBRef(dbref3);
1171 assertEquals(3, sq.getDBRefs().size());
1172 assertSame(dbref3, sq.getDBRefs().get(2));
1175 * different ref = new entry
1177 DBRefEntry dbref4 = new DBRefEntry("UniRef", "1", "p00341");
1178 sq.addDBRef(dbref4);
1179 assertEquals(4, sq.getDBRefs().size());
1180 assertSame(dbref4, sq.getDBRefs().get(3));
1183 * matching ref with a mapping - map updated
1185 DBRefEntry dbref5 = new DBRefEntry("UniRef", "1", "p00341");
1186 Mapping map = new Mapping(new MapList(new int[] { 1, 3 }, new int[] {
1189 sq.addDBRef(dbref5);
1190 assertEquals(4, sq.getDBRefs().size());
1191 assertSame(dbref4, sq.getDBRefs().get(3));
1192 assertSame(map, dbref4.getMap());
1195 * 'real' version replaces "0" version
1197 dbref2.setVersion("0");
1198 DBRefEntry dbref6 = new DBRefEntry(dbref2.getSource(), "3",
1199 dbref2.getAccessionId());
1200 sq.addDBRef(dbref6);
1201 assertEquals(4, sq.getDBRefs().size());
1202 assertSame(dbref2, sq.getDBRefs().get(1));
1203 assertEquals("3", dbref2.getVersion());
1206 * 'real' version replaces "source:0" version
1208 dbref3.setVersion("Uniprot:0");
1209 DBRefEntry dbref7 = new DBRefEntry(dbref3.getSource(), "3",
1210 dbref3.getAccessionId());
1211 sq.addDBRef(dbref7);
1212 assertEquals(4, sq.getDBRefs().size());
1213 assertSame(dbref3, sq.getDBRefs().get(2));
1214 assertEquals("3", dbref2.getVersion());
1217 @Test(groups = { "Functional" })
1218 public void testGetPrimaryDBRefs_peptide()
1220 SequenceI sq = new Sequence("aseq", "ASDFKYLMQPRST", 10, 22);
1223 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1224 assertTrue(primaryDBRefs.isEmpty());
1228 primaryDBRefs = sq.getPrimaryDBRefs();
1229 assertTrue(primaryDBRefs.isEmpty());
1231 // primary - uniprot
1232 DBRefEntry upentry1 = new DBRefEntry("UNIPROT", "0", "Q04760");
1233 sq.addDBRef(upentry1);
1235 // primary - uniprot with congruent map
1236 DBRefEntry upentry2 = new DBRefEntry("UNIPROT", "0", "Q04762");
1237 upentry2.setMap(new Mapping(null, new MapList(new int[] { 10, 22 },
1238 new int[] { 10, 22 }, 1, 1)));
1239 sq.addDBRef(upentry2);
1241 // primary - uniprot with map of enclosing sequence
1242 DBRefEntry upentry3 = new DBRefEntry("UNIPROT", "0", "Q04763");
1243 upentry3.setMap(new Mapping(null, new MapList(new int[] { 8, 24 },
1244 new int[] { 8, 24 }, 1, 1)));
1245 sq.addDBRef(upentry3);
1247 // not primary - uniprot with map of sub-sequence (5')
1248 DBRefEntry upentry4 = new DBRefEntry("UNIPROT", "0", "Q04764");
1249 upentry4.setMap(new Mapping(null, new MapList(new int[] { 10, 18 },
1250 new int[] { 10, 18 }, 1, 1)));
1251 sq.addDBRef(upentry4);
1253 // not primary - uniprot with map that overlaps 3'
1254 DBRefEntry upentry5 = new DBRefEntry("UNIPROT", "0", "Q04765");
1255 upentry5.setMap(new Mapping(null, new MapList(new int[] { 12, 22 },
1256 new int[] { 12, 22 }, 1, 1)));
1257 sq.addDBRef(upentry5);
1259 // not primary - uniprot with map to different coordinates frame
1260 DBRefEntry upentry6 = new DBRefEntry("UNIPROT", "0", "Q04766");
1261 upentry6.setMap(new Mapping(null, new MapList(new int[] { 12, 18 },
1262 new int[] { 112, 118 }, 1, 1)));
1263 sq.addDBRef(upentry6);
1265 // not primary - dbref to 'non-core' database
1266 DBRefEntry upentry7 = new DBRefEntry("Pfam", "0", "PF00903");
1267 sq.addDBRef(upentry7);
1269 // primary - type is PDB
1270 DBRefEntry pdbentry = new DBRefEntry("PDB", "0", "1qip");
1271 sq.addDBRef(pdbentry);
1273 // not primary - PDBEntry has no file
1274 sq.addDBRef(new DBRefEntry("PDB", "0", "1AAA"));
1276 // not primary - no PDBEntry
1277 sq.addDBRef(new DBRefEntry("PDB", "0", "1DDD"));
1279 // add corroborating PDB entry for primary DBref -
1280 // needs to have a file as well as matching ID
1281 // note PDB ID is not treated as case sensitive
1282 sq.addPDBId(new PDBEntry("1QIP", null, Type.PDB, new File("/blah")
1285 // not valid DBRef - no file..
1286 sq.addPDBId(new PDBEntry("1AAA", null, null, null));
1288 primaryDBRefs = sq.getPrimaryDBRefs();
1289 assertEquals(4, primaryDBRefs.size());
1290 assertTrue("Couldn't find simple primary reference (UNIPROT)",
1291 primaryDBRefs.contains(upentry1));
1292 assertTrue("Couldn't find mapped primary reference (UNIPROT)",
1293 primaryDBRefs.contains(upentry2));
1294 assertTrue("Couldn't find mapped context reference (UNIPROT)",
1295 primaryDBRefs.contains(upentry3));
1296 assertTrue("Couldn't find expected PDB primary reference",
1297 primaryDBRefs.contains(pdbentry));
1300 @Test(groups = { "Functional" })
1301 public void testGetPrimaryDBRefs_nucleotide()
1303 SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
1305 // primary - Ensembl
1306 DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
1309 // not primary - Ensembl 'transcript' mapping of sub-sequence
1310 DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
1311 dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
1312 new int[] { 1, 11 }, 1, 1)));
1315 // primary - EMBL with congruent map
1316 DBRefEntry dbr3 = new DBRefEntry("EMBL", "0", "J1234");
1317 dbr3.setMap(new Mapping(null, new MapList(new int[] { 10, 34 },
1318 new int[] { 10, 34 }, 1, 1)));
1321 // not primary - to non-core database
1322 DBRefEntry dbr4 = new DBRefEntry("CCDS", "0", "J1234");
1325 // not primary - to protein
1326 DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
1329 List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
1330 assertEquals(2, primaryDBRefs.size());
1331 assertTrue(primaryDBRefs.contains(dbr1));
1332 assertTrue(primaryDBRefs.contains(dbr3));
1336 * Test the method that updates the list of PDBEntry from any new DBRefEntry
1339 @Test(groups = { "Functional" })
1340 public void testUpdatePDBIds()
1342 PDBEntry pdbe1 = new PDBEntry("3A6S", null, null, null);
1343 seq.addPDBId(pdbe1);
1344 seq.addDBRef(new DBRefEntry("Ensembl", "8", "ENST1234"));
1345 seq.addDBRef(new DBRefEntry("PDB", "0", "1A70"));
1346 seq.addDBRef(new DBRefEntry("PDB", "0", "4BQGa"));
1347 seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
1348 // 7 is not a valid chain code:
1349 seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
1352 List<PDBEntry> pdbIds = seq.getAllPDBEntries();
1353 assertEquals(4, pdbIds.size());
1354 assertSame(pdbe1, pdbIds.get(0));
1355 // chain code got added to 3A6S:
1356 assertEquals("B", pdbe1.getChainCode());
1357 assertEquals("1A70", pdbIds.get(1).getId());
1358 // 4BQGA is parsed into id + chain
1359 assertEquals("4BQG", pdbIds.get(2).getId());
1360 assertEquals("a", pdbIds.get(2).getChainCode());
1361 assertEquals("2GIS7", pdbIds.get(3).getId());
1362 assertNull(pdbIds.get(3).getChainCode());
1366 * Test the method that either adds a pdbid or updates an existing one
1368 @Test(groups = { "Functional" })
1369 public void testAddPDBId()
1371 PDBEntry pdbe = new PDBEntry("3A6S", null, null, null);
1373 assertEquals(1, seq.getAllPDBEntries().size());
1374 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1375 assertSame(pdbe, seq.getPDBEntry("3a6s")); // case-insensitive
1377 // add the same entry
1379 assertEquals(1, seq.getAllPDBEntries().size());
1380 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1382 // add an identical entry
1383 seq.addPDBId(new PDBEntry("3A6S", null, null, null));
1384 assertEquals(1, seq.getAllPDBEntries().size());
1385 assertSame(pdbe, seq.getPDBEntry("3A6S"));
1387 // add a different entry
1388 PDBEntry pdbe2 = new PDBEntry("1A70", null, null, null);
1389 seq.addPDBId(pdbe2);
1390 assertEquals(2, seq.getAllPDBEntries().size());
1391 assertSame(pdbe, seq.getAllPDBEntries().get(0));
1392 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1394 // update pdbe with chain code, file, type
1395 PDBEntry pdbe3 = new PDBEntry("3a6s", "A", Type.PDB, "filepath");
1396 seq.addPDBId(pdbe3);
1397 assertEquals(2, seq.getAllPDBEntries().size());
1398 assertSame(pdbe, seq.getAllPDBEntries().get(0)); // updated in situ
1399 assertEquals("3A6S", pdbe.getId()); // unchanged
1400 assertEquals("A", pdbe.getChainCode()); // updated
1401 assertEquals(Type.PDB.toString(), pdbe.getType()); // updated
1402 assertEquals("filepath", pdbe.getFile()); // updated
1403 assertSame(pdbe2, seq.getAllPDBEntries().get(1));
1405 // add with a different file path
1406 PDBEntry pdbe4 = new PDBEntry("3a6s", "A", Type.PDB, "filepath2");
1407 seq.addPDBId(pdbe4);
1408 assertEquals(3, seq.getAllPDBEntries().size());
1409 assertSame(pdbe4, seq.getAllPDBEntries().get(2));
1411 // add with a different chain code
1412 PDBEntry pdbe5 = new PDBEntry("3a6s", "B", Type.PDB, "filepath");
1413 seq.addPDBId(pdbe5);
1414 assertEquals(4, seq.getAllPDBEntries().size());
1415 assertSame(pdbe5, seq.getAllPDBEntries().get(3));
1419 groups = { "Functional" },
1420 expectedExceptions = { IllegalArgumentException.class })
1421 public void testSetDatasetSequence_toSelf()
1423 seq.setDatasetSequence(seq);
1427 groups = { "Functional" },
1428 expectedExceptions = { IllegalArgumentException.class })
1429 public void testSetDatasetSequence_cascading()
1431 SequenceI seq2 = new Sequence("Seq2", "xyz");
1432 seq2.createDatasetSequence();
1433 seq.setDatasetSequence(seq2);
1436 @Test(groups = { "Functional" })
1437 public void testFindFeatures()
1439 SequenceI sq = new Sequence("test/8-16", "-ABC--DEF--GHI--");
1440 sq.createDatasetSequence();
1442 assertTrue(sq.findFeatures(1, 99).isEmpty());
1444 // add non-positional feature
1445 SequenceFeature sf0 = new SequenceFeature("Cath", "desc", 0, 0, 2f,
1447 sq.addSequenceFeature(sf0);
1448 // add feature on BCD
1449 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 9, 11, 2f,
1451 sq.addSequenceFeature(sfBCD);
1452 // add feature on DE
1453 SequenceFeature sfDE = new SequenceFeature("Cath", "desc", 11, 12, 2f,
1455 sq.addSequenceFeature(sfDE);
1456 // add contact feature at [B, H]
1457 SequenceFeature sfContactBH = new SequenceFeature("Disulphide bond",
1458 "desc", 9, 15, 2f, null);
1459 sq.addSequenceFeature(sfContactBH);
1460 // add contact feature at [F, G]
1461 SequenceFeature sfContactFG = new SequenceFeature("Disulfide Bond",
1462 "desc", 13, 14, 2f, null);
1463 sq.addSequenceFeature(sfContactFG);
1464 // add single position feature at [I]
1465 SequenceFeature sfI = new SequenceFeature("Disulfide Bond",
1466 "desc", 16, 16, null);
1467 sq.addSequenceFeature(sfI);
1469 // no features in columns 1-2 (-A)
1470 List<SequenceFeature> found = sq.findFeatures(1, 2);
1471 assertTrue(found.isEmpty());
1473 // columns 1-6 (-ABC--) includes BCD and B/H feature but not DE
1474 found = sq.findFeatures(1, 6);
1475 assertEquals(2, found.size());
1476 assertTrue(found.contains(sfBCD));
1477 assertTrue(found.contains(sfContactBH));
1479 // columns 5-6 (--) includes (enclosing) BCD but not (contact) B/H feature
1480 found = sq.findFeatures(5, 6);
1481 assertEquals(1, found.size());
1482 assertTrue(found.contains(sfBCD));
1484 // columns 7-10 (DEF-) includes BCD, DE, F/G but not B/H feature
1485 found = sq.findFeatures(7, 10);
1486 assertEquals(3, found.size());
1487 assertTrue(found.contains(sfBCD));
1488 assertTrue(found.contains(sfDE));
1489 assertTrue(found.contains(sfContactFG));
1491 // columns 10-11 (--) should find nothing
1492 found = sq.findFeatures(10, 11);
1493 assertEquals(0, found.size());
1495 // columns 14-14 (I) should find variant feature
1496 found = sq.findFeatures(14, 14);
1497 assertEquals(1, found.size());
1498 assertTrue(found.contains(sfI));
1501 @Test(groups = { "Functional" })
1502 public void testFindIndex_withCursor()
1504 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1506 // find F given A, check cursor is now at the found position
1507 assertEquals(10, sq.findIndex(13, new SequenceCursor(sq, 8, 2, 0)));
1508 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1509 assertEquals(13, cursor.residuePosition);
1510 assertEquals(10, cursor.columnPosition);
1513 assertEquals(2, sq.findIndex(8, new SequenceCursor(sq, 13, 10, 0)));
1514 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1515 assertEquals(8, cursor.residuePosition);
1516 assertEquals(2, cursor.columnPosition);
1518 // find C given C (no cursor update is done for this case)
1519 assertEquals(6, sq.findIndex(10, new SequenceCursor(sq, 10, 6, 0)));
1520 SequenceCursor cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1521 assertSame(cursor2, cursor);
1524 * sequence 'end' beyond end of sequence returns length of sequence
1525 * (for compatibility with pre-cursor code)
1526 * - also verify the cursor is left in a valid state
1528 sq = new Sequence("test/8-99", "-A--B-C-D-E-F--"); // trailing gap case
1529 assertEquals(7, sq.findIndex(10)); // establishes a cursor
1530 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1531 assertEquals(10, cursor.residuePosition);
1532 assertEquals(7, cursor.columnPosition);
1533 assertEquals(sq.getLength(), sq.findIndex(65));
1534 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1535 assertSame(cursor, cursor2); // not updated for this case!
1537 sq = new Sequence("test/8-99", "-A--B-C-D-E-F"); // trailing residue case
1538 sq.findIndex(10); // establishes a cursor
1539 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1540 assertEquals(sq.getLength(), sq.findIndex(65));
1541 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1542 assertSame(cursor, cursor2); // not updated for this case!
1545 * residue after sequence 'start' but before first residue should return
1546 * zero (for compatibility with pre-cursor code)
1548 sq = new Sequence("test/8-15", "-A-B-C-"); // leading gap case
1549 sq.findIndex(10); // establishes a cursor
1550 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1551 assertEquals(0, sq.findIndex(3));
1552 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1553 assertSame(cursor, cursor2); // not updated for this case!
1555 sq = new Sequence("test/8-15", "A-B-C-"); // leading residue case
1556 sq.findIndex(10); // establishes a cursor
1557 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1558 assertEquals(0, sq.findIndex(2));
1559 cursor2 = (SequenceCursor) PA.getValue(sq, "cursor");
1560 assertSame(cursor, cursor2); // not updated for this case!
1563 @Test(groups = { "Functional" })
1564 public void testFindPosition_withCursor()
1566 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1568 // find F pos given A - lastCol gets set in cursor
1569 assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
1570 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1571 PA.getValue(sq, "cursor").toString());
1573 // find A pos given F - first residue column is saved in cursor
1574 assertEquals(8, sq.findPosition(2, new SequenceCursor(sq, 13, 10, 0)));
1575 assertEquals("test:Pos8:Col2:startCol2:endCol10:tok0",
1576 PA.getValue(sq, "cursor").toString());
1578 // find C pos given C (neither startCol nor endCol is set)
1579 assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 10, 6, 0)));
1580 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0",
1581 PA.getValue(sq, "cursor").toString());
1583 // now the grey area - what residue position for a gapped column? JAL-2562
1585 // find 'residue' for column 3 given cursor for D (so working left)
1586 // returns B9; cursor is updated to [B 5]
1587 assertEquals(9, sq.findPosition(3, new SequenceCursor(sq, 11, 7, 0)));
1588 assertEquals("test:Pos9:Col5:startCol0:endCol0:tok0",
1589 PA.getValue(sq, "cursor").toString());
1591 // find 'residue' for column 8 given cursor for D (so working right)
1592 // returns E12; cursor is updated to [D 7]
1593 assertEquals(12, sq.findPosition(8, new SequenceCursor(sq, 11, 7, 0)));
1594 assertEquals("test:Pos11:Col7:startCol0:endCol0:tok0",
1595 PA.getValue(sq, "cursor").toString());
1597 // find 'residue' for column 12 given cursor for B
1598 // returns 1 more than last residue position; cursor is updated to [F 10]
1599 // lastCol position is saved in cursor
1600 assertEquals(14, sq.findPosition(12, new SequenceCursor(sq, 9, 5, 0)));
1601 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1602 PA.getValue(sq, "cursor").toString());
1605 * findPosition for column beyond length of sequence
1606 * returns 1 more than the last residue position
1607 * cursor is set to last real residue position [F 10]
1609 assertEquals(14, sq.findPosition(99, new SequenceCursor(sq, 8, 2, 0)));
1610 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1611 PA.getValue(sq, "cursor").toString());
1614 * and the case without a trailing gap
1616 sq = new Sequence("test/8-13", "-A--BCD-EF");
1617 // first find C from A
1618 assertEquals(10, sq.findPosition(6, new SequenceCursor(sq, 8, 2, 0)));
1619 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1620 assertEquals("test:Pos10:Col6:startCol0:endCol0:tok0",
1622 // now 'find' 99 from C
1623 // cursor is set to [F 10] and saved lastCol
1624 assertEquals(14, sq.findPosition(99, cursor));
1625 assertEquals("test:Pos13:Col10:startCol0:endCol10:tok0",
1626 PA.getValue(sq, "cursor").toString());
1630 public void testIsValidCursor()
1632 Sequence sq = new Sequence("Seq", "ABC--DE-F", 8, 13);
1633 assertFalse(sq.isValidCursor(null));
1636 * cursor is valid if it has valid sequence ref and changeCount token
1637 * and positions within the range of the sequence
1639 int changeCount = (int) PA.getValue(sq, "changeCount");
1640 SequenceCursor cursor = new SequenceCursor(sq, 13, 1, changeCount);
1641 assertTrue(sq.isValidCursor(cursor));
1644 * column position outside [0 - length] is rejected
1646 cursor = new SequenceCursor(sq, 13, -1, changeCount);
1647 assertFalse(sq.isValidCursor(cursor));
1648 cursor = new SequenceCursor(sq, 13, 10, changeCount);
1649 assertFalse(sq.isValidCursor(cursor));
1650 cursor = new SequenceCursor(sq, 7, 8, changeCount);
1651 assertFalse(sq.isValidCursor(cursor));
1652 cursor = new SequenceCursor(sq, 14, 2, changeCount);
1653 assertFalse(sq.isValidCursor(cursor));
1656 * wrong sequence is rejected
1658 cursor = new SequenceCursor(null, 13, 1, changeCount);
1659 assertFalse(sq.isValidCursor(cursor));
1660 cursor = new SequenceCursor(new Sequence("Seq", "abc"), 13, 1,
1662 assertFalse(sq.isValidCursor(cursor));
1665 * wrong token value is rejected
1667 cursor = new SequenceCursor(sq, 13, 1, changeCount + 1);
1668 assertFalse(sq.isValidCursor(cursor));
1669 cursor = new SequenceCursor(sq, 13, 1, changeCount - 1);
1670 assertFalse(sq.isValidCursor(cursor));
1673 @Test(groups = { "Functional" })
1674 public void testFindPosition_withCursorAndEdits()
1676 Sequence sq = new Sequence("test/8-13", "-A--BCD-EF--");
1678 // find F pos given A
1679 assertEquals(13, sq.findPosition(10, new SequenceCursor(sq, 8, 2, 0)));
1680 int token = (int) PA.getValue(sq, "changeCount"); // 0
1681 SequenceCursor cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1682 assertEquals(new SequenceCursor(sq, 13, 10, token), cursor);
1685 * setSequence should invalidate the cursor cached by the sequence
1687 sq.setSequence("-A-BCD-EF---"); // one gap removed
1688 assertEquals(8, sq.getStart()); // sanity check
1689 assertEquals(11, sq.findPosition(5)); // D11
1690 // cursor should now be at [D 6]
1691 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1692 assertEquals(new SequenceCursor(sq, 11, 6, ++token), cursor);
1693 assertEquals(0, cursor.lastColumnPosition); // not yet found
1694 assertEquals(13, sq.findPosition(8)); // E13
1695 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1696 assertEquals(9, cursor.lastColumnPosition); // found
1699 * deleteChars should invalidate the cached cursor
1701 sq.deleteChars(2, 5); // delete -BC
1702 assertEquals("-AD-EF---", sq.getSequenceAsString());
1703 assertEquals(8, sq.getStart()); // sanity check
1704 assertEquals(10, sq.findPosition(4)); // E10
1705 // cursor should now be at [E 5]
1706 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1707 assertEquals(new SequenceCursor(sq, 10, 5, ++token), cursor);
1710 * Edit to insert gaps should invalidate the cached cursor
1711 * insert 2 gaps at column[3] to make -AD---EF---
1713 SequenceI[] seqs = new SequenceI[] { sq };
1714 AlignmentI al = new Alignment(seqs);
1715 new EditCommand().appendEdit(Action.INSERT_GAP, seqs, 3, 2, al, true);
1716 assertEquals("-AD---EF---", sq.getSequenceAsString());
1717 assertEquals(10, sq.findPosition(4)); // E10
1718 // cursor should now be at [D 3]
1719 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1720 assertEquals(new SequenceCursor(sq, 9, 3, ++token), cursor);
1723 * insertCharAt should invalidate the cached cursor
1724 * insert CC at column[4] to make -AD-CC--EF---
1726 sq.insertCharAt(4, 2, 'C');
1727 assertEquals("-AD-CC--EF---", sq.getSequenceAsString());
1728 assertEquals(13, sq.findPosition(9)); // F13
1729 // cursor should now be at [F 10]
1730 cursor = (SequenceCursor) PA.getValue(sq, "cursor");
1731 assertEquals(new SequenceCursor(sq, 13, 10, ++token), cursor);
1734 @Test(groups = { "Functional" })
1735 public void testGetSequence()
1737 String seqstring = "-A--BCD-EF--";
1738 Sequence sq = new Sequence("test/8-13", seqstring);
1739 sq.createDatasetSequence();
1740 assertTrue(Arrays.equals(sq.getSequence(), seqstring.toCharArray()));
1741 assertTrue(Arrays.equals(sq.getDatasetSequence().getSequence(),
1742 "ABCDEF".toCharArray()));
1744 // verify a copy of the sequence array is returned
1745 char[] theSeq = (char[]) PA.getValue(sq, "sequence");
1746 assertNotSame(theSeq, sq.getSequence());
1747 theSeq = (char[]) PA.getValue(sq.getDatasetSequence(), "sequence");
1748 assertNotSame(theSeq, sq.getDatasetSequence().getSequence());
1751 @Test(groups = { "Functional" })
1752 public void testReplace()
1754 String seqstring = "-A--BCD-EF--";
1755 SequenceI sq = new Sequence("test/8-13", seqstring);
1756 assertEquals(0, PA.getValue(sq, "changeCount"));
1758 assertEquals(0, sq.replace('A', 'A')); // same char
1759 assertEquals(seqstring, sq.getSequenceAsString());
1760 assertEquals(0, PA.getValue(sq, "changeCount"));
1762 assertEquals(0, sq.replace('X', 'Y')); // not there
1763 assertEquals(seqstring, sq.getSequenceAsString());
1764 assertEquals(0, PA.getValue(sq, "changeCount"));
1766 assertEquals(1, sq.replace('A', 'K'));
1767 assertEquals("-K--BCD-EF--", sq.getSequenceAsString());
1768 assertEquals(1, PA.getValue(sq, "changeCount"));
1770 assertEquals(6, sq.replace('-', '.'));
1771 assertEquals(".K..BCD.EF..", sq.getSequenceAsString());
1772 assertEquals(2, PA.getValue(sq, "changeCount"));
1775 @Test(groups = { "Functional" })
1776 public void testGapBitset()
1778 SequenceI sq = new Sequence("test/8-13", "-ABC---DE-F--");
1779 BitSet bs = sq.gapBitset();
1780 BitSet expected = new BitSet();
1784 expected.set(11, 13);
1786 assertTrue(bs.equals(expected));
1790 public void testFindFeatures_largeEndPos()
1793 * imitate a PDB sequence where end is larger than end position
1795 SequenceI sq = new Sequence("test", "-ABC--DEF--", 1, 20);
1796 sq.createDatasetSequence();
1798 assertTrue(sq.findFeatures(1, 9).isEmpty());
1799 // should be no array bounds exception - JAL-2772
1800 assertTrue(sq.findFeatures(1, 15).isEmpty());
1802 // add feature on BCD
1803 SequenceFeature sfBCD = new SequenceFeature("Cath", "desc", 2, 4, 2f,
1805 sq.addSequenceFeature(sfBCD);
1807 // no features in columns 1-2 (-A)
1808 List<SequenceFeature> found = sq.findFeatures(1, 2);
1809 assertTrue(found.isEmpty());
1811 // columns 1-6 (-ABC--) includes BCD
1812 found = sq.findFeatures(1, 6);
1813 assertEquals(1, found.size());
1814 assertTrue(found.contains(sfBCD));
1816 // columns 10-11 (--) should find nothing
1817 found = sq.findFeatures(10, 11);
1818 assertEquals(0, found.size());
1821 @Test(groups = { "Functional" })
1822 public void testSetName()
1824 SequenceI sq = new Sequence("test", "-ABC---DE-F--");
1825 assertEquals("test", sq.getName());
1826 assertEquals(1, sq.getStart());
1827 assertEquals(6, sq.getEnd());
1829 sq.setName("testing");
1830 assertEquals("testing", sq.getName());
1832 sq.setName("test/8-10");
1833 assertEquals("test", sq.getName());
1834 assertEquals(8, sq.getStart());
1835 assertEquals(13, sq.getEnd()); // note end is recomputed
1837 sq.setName("testing/7-99");
1838 assertEquals("testing", sq.getName());
1839 assertEquals(7, sq.getStart());
1840 assertEquals(99, sq.getEnd()); // end may be beyond physical end
1843 assertEquals("", sq.getName());
1844 assertEquals(2, sq.getStart());
1845 assertEquals(7, sq.getEnd());
1847 sq.setName("test/"); // invalid
1848 assertEquals("test/", sq.getName());
1849 assertEquals(2, sq.getStart());
1850 assertEquals(7, sq.getEnd());
1852 sq.setName("test/6-13/7-99");
1853 assertEquals("test/6-13", sq.getName());
1854 assertEquals(7, sq.getStart());
1855 assertEquals(99, sq.getEnd());
1857 sq.setName("test/0-5"); // 0 is invalid - ignored
1858 assertEquals("test/0-5", sq.getName());
1859 assertEquals(7, sq.getStart());
1860 assertEquals(99, sq.getEnd());
1862 sq.setName("test/a-5"); // a is invalid - ignored
1863 assertEquals("test/a-5", sq.getName());
1864 assertEquals(7, sq.getStart());
1865 assertEquals(99, sq.getEnd());
1867 sq.setName("test/6-5"); // start > end is invalid - ignored
1868 assertEquals("test/6-5", sq.getName());
1869 assertEquals(7, sq.getStart());
1870 assertEquals(99, sq.getEnd());
1872 sq.setName("test/5"); // invalid - ignored
1873 assertEquals("test/5", sq.getName());
1874 assertEquals(7, sq.getStart());
1875 assertEquals(99, sq.getEnd());
1877 sq.setName("test/-5"); // invalid - ignored
1878 assertEquals("test/-5", sq.getName());
1879 assertEquals(7, sq.getStart());
1880 assertEquals(99, sq.getEnd());
1882 sq.setName("test/5-"); // invalid - ignored
1883 assertEquals("test/5-", sq.getName());
1884 assertEquals(7, sq.getStart());
1885 assertEquals(99, sq.getEnd());
1887 sq.setName("test/5-6-7"); // invalid - ignored
1888 assertEquals("test/5-6-7", sq.getName());
1889 assertEquals(7, sq.getStart());
1890 assertEquals(99, sq.getEnd());
1892 sq.setName(null); // invalid, gets converted to space
1893 assertEquals("", sq.getName());
1894 assertEquals(7, sq.getStart());
1895 assertEquals(99, sq.getEnd());
1898 @Test(groups = { "Functional" })
1899 public void testCheckValidRange()
1901 Sequence sq = new Sequence("test/7-12", "-ABC---DE-F--");
1902 assertEquals(7, sq.getStart());
1903 assertEquals(12, sq.getEnd());
1906 * checkValidRange ensures end is at least the last residue position
1908 PA.setValue(sq, "end", 2);
1909 sq.checkValidRange();
1910 assertEquals(12, sq.getEnd());
1913 * end may be beyond the last residue position
1915 PA.setValue(sq, "end", 22);
1916 sq.checkValidRange();
1917 assertEquals(22, sq.getEnd());
1920 @Test(groups = { "Functional" })
1921 public void testDeleteChars_withGaps()
1926 SequenceI sq = new Sequence("test/8-10", "A-B-C");
1927 sq.createDatasetSequence();
1928 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1929 sq.deleteChars(1, 2); // delete first gap
1930 assertEquals("AB-C", sq.getSequenceAsString());
1931 assertEquals(8, sq.getStart());
1932 assertEquals(10, sq.getEnd());
1933 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1936 * delete gaps and residues at start (no new dataset sequence)
1938 sq = new Sequence("test/8-10", "A-B-C");
1939 sq.createDatasetSequence();
1940 sq.deleteChars(0, 3); // delete A-B
1941 assertEquals("-C", sq.getSequenceAsString());
1942 assertEquals(10, sq.getStart());
1943 assertEquals(10, sq.getEnd());
1944 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1947 * delete gaps and residues at end (no new dataset sequence)
1949 sq = new Sequence("test/8-10", "A-B-C");
1950 sq.createDatasetSequence();
1951 sq.deleteChars(2, 5); // delete B-C
1952 assertEquals("A-", sq.getSequenceAsString());
1953 assertEquals(8, sq.getStart());
1954 assertEquals(8, sq.getEnd());
1955 assertEquals("ABC", sq.getDatasetSequence().getSequenceAsString());
1958 * delete gaps and residues internally (new dataset sequence)
1959 * first delete from gap to residue
1961 sq = new Sequence("test/8-10", "A-B-C");
1962 sq.createDatasetSequence();
1963 sq.deleteChars(1, 3); // delete -B
1964 assertEquals("A-C", sq.getSequenceAsString());
1965 assertEquals(8, sq.getStart());
1966 assertEquals(9, sq.getEnd());
1967 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
1968 assertEquals(8, sq.getDatasetSequence().getStart());
1969 assertEquals(9, sq.getDatasetSequence().getEnd());
1972 * internal delete from gap to gap
1974 sq = new Sequence("test/8-10", "A-B-C");
1975 sq.createDatasetSequence();
1976 sq.deleteChars(1, 4); // delete -B-
1977 assertEquals("AC", sq.getSequenceAsString());
1978 assertEquals(8, sq.getStart());
1979 assertEquals(9, sq.getEnd());
1980 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
1981 assertEquals(8, sq.getDatasetSequence().getStart());
1982 assertEquals(9, sq.getDatasetSequence().getEnd());
1985 * internal delete from residue to residue
1987 sq = new Sequence("test/8-10", "A-B-C");
1988 sq.createDatasetSequence();
1989 sq.deleteChars(2, 3); // delete B
1990 assertEquals("A--C", sq.getSequenceAsString());
1991 assertEquals(8, sq.getStart());
1992 assertEquals(9, sq.getEnd());
1993 assertEquals("AC", sq.getDatasetSequence().getSequenceAsString());
1994 assertEquals(8, sq.getDatasetSequence().getStart());
1995 assertEquals(9, sq.getDatasetSequence().getEnd());
1999 * Test the code used to locate the reference sequence ruler origin
2001 @Test(groups = { "Functional" })
2002 public void testLocateVisibleStartofSequence()
2004 // create random alignment
2005 AlignmentGenerator gen = new AlignmentGenerator(false);
2006 AlignmentI al = gen.generate(50, 20, 123, 5, 5);
2008 HiddenColumns cs = al.getHiddenColumns();
2009 ColumnSelection colsel = new ColumnSelection();
2011 SequenceI seq = new Sequence("RefSeq", "-A-SD-ASD--E---");
2012 assertEquals(2, seq.findIndex(seq.getStart()));
2014 // no hidden columns
2015 assertEquals(seq.findIndex(seq.getStart()) - 1,
2016 seq.firstResidueOutsideIterator(cs.iterator()));
2018 // hidden column on gap after end of sequence - should not affect bounds
2019 colsel.hideSelectedColumns(13, al.getHiddenColumns());
2020 assertEquals(seq.findIndex(seq.getStart()) - 1,
2021 seq.firstResidueOutsideIterator(cs.iterator()));
2023 cs.revealAllHiddenColumns(colsel);
2024 // hidden column on gap before beginning of sequence - should vis bounds by
2026 colsel.hideSelectedColumns(0, al.getHiddenColumns());
2027 assertEquals(seq.findIndex(seq.getStart()) - 2,
2028 cs.absoluteToVisibleColumn(
2029 seq.firstResidueOutsideIterator(cs.iterator())));
2031 cs.revealAllHiddenColumns(colsel);
2032 // hide columns around most of sequence - leave one residue remaining
2033 cs.hideColumns(1, 3);
2034 cs.hideColumns(6, 11);
2036 Iterator<int[]> it = cs.getVisContigsIterator(0, 6, false);
2038 assertEquals("-D", seq.getSequenceStringFromIterator(it));
2039 // cs.getVisibleSequenceStrings(0, 5, new SequenceI[]
2042 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2043 cs.revealAllHiddenColumns(colsel);
2045 // hide whole sequence - should just get location of hidden region
2046 // containing sequence
2047 cs.hideColumns(1, 11);
2048 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2050 cs.revealAllHiddenColumns(colsel);
2051 cs.hideColumns(0, 15);
2052 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2054 SequenceI seq2 = new Sequence("RefSeq2", "-------A-SD-ASD--E---");
2056 cs.revealAllHiddenColumns(colsel);
2057 cs.hideColumns(7, 17);
2058 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2060 cs.revealAllHiddenColumns(colsel);
2061 cs.hideColumns(3, 17);
2062 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2064 cs.revealAllHiddenColumns(colsel);
2065 cs.hideColumns(3, 19);
2066 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2068 cs.revealAllHiddenColumns(colsel);
2069 cs.hideColumns(0, 0);
2070 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2072 cs.revealAllHiddenColumns(colsel);
2073 cs.hideColumns(0, 1);
2074 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2076 cs.revealAllHiddenColumns(colsel);
2077 cs.hideColumns(0, 2);
2078 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2080 cs.revealAllHiddenColumns(colsel);
2081 cs.hideColumns(1, 1);
2082 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2084 cs.revealAllHiddenColumns(colsel);
2085 cs.hideColumns(1, 2);
2086 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2088 cs.revealAllHiddenColumns(colsel);
2089 cs.hideColumns(1, 3);
2090 assertEquals(4, seq.firstResidueOutsideIterator(cs.iterator()));
2092 cs.revealAllHiddenColumns(colsel);
2093 cs.hideColumns(0, 2);
2094 cs.hideColumns(5, 6);
2095 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2097 cs.revealAllHiddenColumns(colsel);
2098 cs.hideColumns(0, 2);
2099 cs.hideColumns(5, 6);
2100 cs.hideColumns(9, 10);
2101 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2103 cs.revealAllHiddenColumns(colsel);
2104 cs.hideColumns(0, 2);
2105 cs.hideColumns(7, 11);
2106 assertEquals(3, seq.firstResidueOutsideIterator(cs.iterator()));
2108 cs.revealAllHiddenColumns(colsel);
2109 cs.hideColumns(2, 4);
2110 cs.hideColumns(7, 11);
2111 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2113 cs.revealAllHiddenColumns(colsel);
2114 cs.hideColumns(2, 4);
2115 cs.hideColumns(7, 12);
2116 assertEquals(1, seq.firstResidueOutsideIterator(cs.iterator()));
2118 cs.revealAllHiddenColumns(colsel);
2119 cs.hideColumns(1, 11);
2120 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2122 cs.revealAllHiddenColumns(colsel);
2123 cs.hideColumns(0, 12);
2124 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2126 cs.revealAllHiddenColumns(colsel);
2127 cs.hideColumns(0, 4);
2128 cs.hideColumns(6, 12);
2129 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2131 cs.revealAllHiddenColumns(colsel);
2132 cs.hideColumns(0, 1);
2133 cs.hideColumns(3, 12);
2134 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));
2136 cs.revealAllHiddenColumns(colsel);
2137 cs.hideColumns(3, 14);
2138 cs.hideColumns(17, 19);
2139 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2141 cs.revealAllHiddenColumns(colsel);
2142 cs.hideColumns(3, 7);
2143 cs.hideColumns(9, 14);
2144 cs.hideColumns(17, 19);
2145 assertEquals(0, seq2.firstResidueOutsideIterator(cs.iterator()));
2147 cs.revealAllHiddenColumns(colsel);
2148 cs.hideColumns(0, 1);
2149 cs.hideColumns(3, 4);
2150 cs.hideColumns(6, 8);
2151 cs.hideColumns(10, 12);
2152 assertEquals(0, seq.firstResidueOutsideIterator(cs.iterator()));