Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
SequenceI	41	6	3	1.0100%	Show methods

Class SequenceI

Class SequenceI	Line # 41	Total Statements 6	Complexity 3	TOTAL Coverage 1.0100%
getRootDatasetSequence() : SequenceI   getRootDatasetSequence() : SequenceI	409409	6.06	3.03	1.0 1.0100%

 

Contributing tests

Contributing tests

Select all

	Test contribution	Test	Result	Actions
	0.8181818	jalview.datamodel.SequenceTest.testGetRootDatasetSequence_nestedDatasets_returnLastDatasetjalview.datamodel.SequenceTest.testGetRootDatasetSequence_nestedDatasets_returnLastDataset	1PASS
	0.6363636	jalview.datamodel.SequenceTest.testGetRootDatasetSequence_datasetImplicit_returnDatasetjalview.datamodel.SequenceTest.testGetRootDatasetSequence_datasetImplicit_returnDataset	1PASS
	0.6363636	jalview.datamodel.SequenceTest.testGetRootDatasetSequence_datasetExplicit_returnDatasetjalview.datamodel.SequenceTest.testGetRootDatasetSequence_datasetExplicit_returnDataset	1PASS
	0.36363637	jalview.datamodel.SequenceTest.testGetRootDatasetSequence_datasetIsNull_returnNulljalview.datamodel.SequenceTest.testGetRootDatasetSequence_datasetIsNull_returnNull	1PASS

 

Source view

1		/*
2		* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3		* Copyright (C) $$Year-Rel$$ The Jalview Authors
4		*
5		* This file is part of Jalview.
6		*
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.
11		*
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.
16		*
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.
20		*/
21		package jalview.datamodel;
22
23		import java.util.BitSet;
24		import java.util.Iterator;
25		import java.util.List;
26		import java.util.Vector;
27
28		import fr.orsay.lri.varna.models.rna.RNA;
29		import jalview.datamodel.Sequence.DBModList;
30		import jalview.datamodel.features.SequenceFeaturesI;
31		import jalview.util.MapList;
32		import jalview.ws.params.InvalidArgumentException;
33
34		/**
35		* Methods for manipulating a sequence, its metadata and related annotation in
36		* an alignment or dataset.
37		*
38		* @author $author$
39		* @version $Revision$
40		*/
		100% Uncovered Elements: 0 (11) Complexity: 3 Complexity Density: 0.5
41		public interface SequenceI extends ASequenceI, ContactMapHolderI
42		{
43		/**
44		* Set the display name for the sequence
45		*
46		* @param name
47		*/
48		public void setName(String name);
49
50		public HiddenMarkovModel getHMM();
51
52		public void setHMM(HiddenMarkovModel hmm);
53		/**
54		* Get the display name
55		*/
56		public String getName();
57
58		/**
59		* Set start position of first non-gapped symbol in sequence
60		*
61		* @param start
62		* new start position
63		*/
64		public void setStart(int start);
65
66		/**
67		* get start position of first non-gapped residue in sequence
68		*
69		* @return
70		*/
71		public int getStart();
72
73		/**
74		* get the displayed id of the sequence
75		*
76		* @return true means the id will be returned in the form
77		* DisplayName/Start-End
78		*/
79		public String getDisplayId(boolean jvsuffix);
80
81		/**
82		* set end position for last residue in sequence
83		*
84		* @param end
85		*/
86		public void setEnd(int end);
87
88		/**
89		* get end position for last residue in sequence getEnd()>getStart() unless
90		* sequence only consists of gap characters
91		*
92		* @return
93		*/
94		public int getEnd();
95
96		/**
97		* @return length of sequence including gaps
98		*
99		*/
100		public int getLength();
101
102		/**
103		* Replace the sequence with the given characters
104		*
105		* @param sequence
106		* new sequence characters
107		*/
108		public void setSequence(char[] sequence);
109
110		/**
111		* Replace the sequence with the given string
112		*
113		* @param sequence
114		* new sequence string
115		*/
116		public void setSequence(String sequence);
117
118		/**
119		* @return sequence as string
120		*/
121		public String getSequenceAsString();
122
123		/**
124		* get a range on the sequence as a string
125		*
126		* @param start
127		* (inclusive) position relative to start of sequence including gaps
128		* (from 0)
129		* @param end
130		* (exclusive) position relative to start of sequence including gaps
131		* (from 0)
132		*
133		* @return String containing all gap and symbols in specified range
134		*/
135		public String getSequenceAsString(int start, int end);
136
137		/**
138		* Answers a copy of the sequence as a character array
139		*
140		* @return
141		*/
142		public char[] getSequence();
143
144		/**
145		* get stretch of sequence characters in an array
146		*
147		* @param start
148		* absolute index into getSequence()
149		* @param end
150		* exclusive index of last position in segment to be returned.
151		*
152		* @return char[max(0,end-start)];
153		*/
154		public char[] getSequence(int start, int end);
155
156		/**
157		* create a new sequence object with a subsequence of this one but sharing the
158		* same dataset sequence
159		*
160		* @param start
161		* int index for start position (base 0, inclusive)
162		* @param end
163		* int index for end position (base 0, exclusive)
164		*
165		* @return SequenceI
166		* @note implementations may use getSequence to get the sequence data
167		*/
168		public SequenceI getSubSequence(int start, int end);
169
170		/**
171		* get the i'th character in this sequence's local reference frame (ie from
172		* 0-number of characters lying from start-end)
173		*
174		* @param i
175		* index
176		* @return character or ' '
177		*/
178		public char getCharAt(int i);
179
180		/**
181		* DOCUMENT ME!
182		*
183		* @param desc
184		* DOCUMENT ME!
185		*/
186		public void setDescription(String desc);
187
188		/**
189		* DOCUMENT ME!
190		*
191		* @return DOCUMENT ME!
192		*/
193		public String getDescription();
194
195		/**
196		* Return the alignment column (from 1..) for a sequence position
197		*
198		* @param pos
199		* lying from start to end
200		*
201		* @return aligned column for residue (0 if residue is upstream from
202		* alignment, -1 if residue is downstream from alignment) note.
203		* Sequence object returns sequence.getEnd() for positions upstream
204		* currently. TODO: change sequence for
205		* assert(findIndex(seq.getEnd()+1)==-1) and fix incremental bugs
206		*
207		*/
208		public int findIndex(int pos);
209
210		/**
211		* Returns the sequence position for an alignment (column) position. If at a
212		* gap, returns the position of the next residue to the right. If beyond the
213		* end of the sequence, returns 1 more than the last residue position.
214		*
215		* @param i
216		* column index in alignment (from 0..<length)
217		*
218		* @return
219		*/
220		public int findPosition(int i);
221
222		/**
223		* Returns the sequence positions for first and last residues lying within the
224		* given column positions [fromColum,toColumn] (where columns are numbered
225		* from 1), or null if no residues are included in the range
226		*
227		* @param fromColum
228		* - first column base 1. (0 and negative positions are rounded up)
229		* @param toColumn
230		* - last column, base 1
231		* @return null if fromColum>toColumn
232		*/
233		public ContiguousI findPositions(int fromColum, int toColumn);
234
235		/**
236		* Returns an int array where indices correspond to each residue in the
237		* sequence and the element value gives its position in the alignment
238		*
239		* @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no
240		* residues in SequenceI object
241		*/
242		public int[] gapMap();
243
244		/**
245		* Build a bitset corresponding to sequence gaps
246		*
247		* @return a BitSet where set values correspond to gaps in the sequence
248		*/
249		public BitSet gapBitset();
250
251		/**
252		* Returns an int array where indices correspond to each position in sequence
253		* char array and the element value gives the result of findPosition for that
254		* index in the sequence.
255		*
256		* @return int[SequenceI.getLength()]
257		*/
258		public int[] findPositionMap();
259
260		/**
261		* Answers true if the sequence is composed of amino acid characters. Note
262		* that implementations may use heuristic methods which are not guaranteed to
263		* give the biologically 'right' answer.
264		*
265		* @return
266		*/
267		public boolean isProtein();
268
269		/**
270		* Delete a range of aligned sequence columns, creating a new dataset sequence
271		* if necessary and adjusting start and end positions accordingly.
272		*
273		* @param i
274		* first column in range to delete (inclusive)
275		* @param j
276		* last column in range to delete (exclusive)
277		*/
278		public void deleteChars(int i, int j);
279
280		/**
281		* DOCUMENT ME!
282		*
283		* @param i
284		* alignment column number
285		* @param c
286		* character to insert
287		*/
288		public void insertCharAt(int i, char c);
289
290		/**
291		* insert given character at alignment column position
292		*
293		* @param position
294		* alignment column number
295		* @param count
296		* length of insert
297		* @param ch
298		* character to insert
299		*/
300		public void insertCharAt(int position, int count, char ch);
301
302		/**
303		* Answers a list of all sequence features associated with this sequence. The
304		* list may be held by the sequence's dataset sequence if that is defined.
305		*
306		* @return
307		*/
308		public List<SequenceFeature> getSequenceFeatures();
309
310		/**
311		* Answers the object holding features for the sequence
312		*
313		* @return
314		*/
315		SequenceFeaturesI getFeatures();
316
317		/**
318		* Replaces the sequence features associated with this sequence with the given
319		* features. If this sequence has a dataset sequence, then this method will
320		* update the dataset sequence's features instead.
321		*
322		* @param features
323		*/
324		public void setSequenceFeatures(List<SequenceFeature> features);
325
326		/**
327		* DOCUMENT ME!
328		*
329		* @param id
330		* DOCUMENT ME!
331		*/
332		public void setPDBId(Vector<PDBEntry> ids);
333
334		/**
335		* Returns a list
336		*
337		* @return DOCUMENT ME!
338		*/
339		public Vector<PDBEntry> getAllPDBEntries();
340
341		/**
342		* Adds the entry to the *normalised* list of PDBIds.
343		*
344		* If a PDBEntry is passed with the same entry.getID() string as one already
345		* in the list, or one is added that appears to be the same but has a chain ID
346		* appended, then the existing PDBEntry will be updated with the new
347		* attributes instead, unless the entries have distinct chain codes or
348		* associated structure files.
349		*
350		* @param entry
351		* @return true if the entry was added, false if updated
352		*/
353		public boolean addPDBId(PDBEntry entry);
354
355		/**
356		* update the list of PDBEntrys to include any DBRefEntrys citing structural
357		* databases
358		*
359		* @return true if PDBEntry list was modified
360		*/
361		public boolean updatePDBIds();
362
363		public String getVamsasId();
364
365		public void setVamsasId(String id);
366
367		/**
368		* set the array of Database references for the sequence.
369		*
370		* BH 2019.02.04 changes param to DBModlist
371		*
372		* @param dbs
373		* @deprecated - use is discouraged since side-effects may occur if DBRefEntry
374		* set are not normalised.
375		* @throws InvalidArgumentException if the is not one created by Sequence itself
376		*/
377		@Deprecated
378		public void setDBRefs(DBModList<DBRefEntry> dbs);
379
380		public DBModList<DBRefEntry> getDBRefs();
381
382		/**
383		* add the given entry to the list of DBRefs for this sequence, or replace a
384		* similar one if entry contains a map object and the existing one doesnt.
385		*
386		* @param entry
387		*/
388		public void addDBRef(DBRefEntry entry);
389
390		/**
391		* Adds the given sequence feature and returns true, or returns false if it is
392		* already present on the sequence, or if the feature type is null.
393		*
394		* @param sf
395		* @return
396		*/
397		public boolean addSequenceFeature(SequenceFeature sf);
398
399		public void deleteFeature(SequenceFeature sf);
400
401		public void setDatasetSequence(SequenceI seq);
402
403		public SequenceI getDatasetSequence();
404
405		/**
406		* Returns the top grandparent in the dataset sequences hierarchy
407		* or null if there is no dataset associated with this sequence.
408		*/
		100% Uncovered Elements: 0 (10) Complexity: 3 Complexity Density: 0.5
409	4	public default SequenceI getRootDatasetSequence()...
410		{
411	4	if (getDatasetSequence() == null)
412		{
413	1	return null;
414		}
415	3	var sequence = getDatasetSequence();
416	4	while (sequence.getDatasetSequence() != null)
417		{
418	1	sequence = sequence.getDatasetSequence();
419		}
420	3	return sequence;
421		}
422
423		/**
424		* Returns a new array containing this sequence's annotations, or null.
425		*/
426		public AlignmentAnnotation[] getAnnotation();
427
428		/**
429		* Returns true if this sequence has the given annotation (by object
430		* identity).
431		*/
432		public boolean hasAnnotation(AlignmentAnnotation ann);
433
434		/**
435		* Add the given annotation, if not already added, and set its sequence ref to
436		* be this sequence. Does nothing if this sequence's annotations already
437		* include this annotation (by identical object reference).
438		*/
439		public void addAlignmentAnnotation(AlignmentAnnotation annotation);
440
441		public void removeAlignmentAnnotation(AlignmentAnnotation annotation);
442
443		/**
444		* Derive a sequence (using this one's dataset or as the dataset)
445		*
446		* @return duplicate sequence and any annotation present with valid dataset
447		* sequence
448		*/
449		public SequenceI deriveSequence();
450
451		/**
452		* set the array of associated AlignmentAnnotation for this sequenceI
453		*
454		* @param revealed
455		*/
456		public void setAlignmentAnnotation(AlignmentAnnotation[] annotation);
457
458		/**
459		* Get one or more alignment annotations with a particular label.
460		*
461		* @param label
462		* string which each returned annotation must have as a label.
463		* @return null or array of annotations.
464		*/
465		public AlignmentAnnotation[] getAnnotation(String label);
466
467		/**
468		* Returns a (possibly empty) list of any annotations that match on given
469		* calcId (source) and label (type). Null values do not match.
470		*
471		* @param calcId
472		* @param label
473		*/
474		public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
475		String label);
476
477		/**
478		* Returns a (possibly empty) list of any annotations that match on given
479		* calcId (source), label (type) and description (observation instance).
480		* Null values do not match.
481		*
482		* @param calcId
483		* @param label
484		* @param description
485		*/
486		public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
487		String label, String description);
488		/**
489		* create a new dataset sequence (if necessary) for this sequence and sets
490		* this sequence to refer to it. This call will move any features or
491		* references on the sequence onto the dataset. It will also make a duplicate
492		* of existing annotation rows for the dataset sequence, rather than relocate
493		* them in order to preserve external references (since 2.8.2).
494		*
495		* @return dataset sequence for this sequence
496		*/
497		public SequenceI createDatasetSequence();
498
499		/**
500		* Transfer any database references or annotation from entry under a sequence
501		* mapping. <br/>
502		* <strong>Note: DOES NOT transfer sequence associated alignment annotation
503		* </strong><br/>
504		*
505		* @param entry
506		* @param mp
507		* null or mapping from entry's numbering to local start/end
508		*/
509		public void transferAnnotation(SequenceI entry, Mapping mp);
510
511		/**
512		* @return The RNA of the sequence in the alignment
513		*/
514
515		public RNA getRNA();
516
517		/**
518		* @param rna
519		* The RNA.
520		*/
521		public void setRNA(RNA rna);
522
523		/**
524		*
525		* @return list of insertions (gap characters) in sequence
526		*/
527		public List<int[]> getInsertions();
528
529		/**
530		* Given a pdbId String, return the equivalent PDBEntry if available in the
531		* given sequence
532		*
533		* @param pdbId
534		* @return
535		*/
536		public PDBEntry getPDBEntry(String pdbId);
537
538		/**
539		* Get all primary database/accessions for this sequence's data. These
540		* DBRefEntry are expected to resolve to a valid record in the associated
541		* external database, either directly or via a provided 1:1 Mapping.
542		*
543		* @return just the primary references (if any) for this sequence, or an empty
544		* list
545		*/
546		public List<DBRefEntry> getPrimaryDBRefs();
547		/**
548		* Answers true if the sequence has annotation for Hidden Markov Model
549		* information content, else false
550		*/
551		boolean hasHMMAnnotation();
552
553		/**
554		* Returns a (possibly empty) list of sequence features that overlap the given
555		* alignment column range, optionally restricted to one or more specified
556		* feature types. If the range is all gaps, then features which enclose it are
557		* included (but not contact features).
558		*
559		* @param fromCol
560		* start column of range inclusive (1..)
561		* @param toCol
562		* end column of range inclusive (1..)
563		* @param types
564		* optional feature types to restrict results to
565		* @return
566		*/
567		List<SequenceFeature> findFeatures(int fromCol, int toCol, String... types);
568
569		/**
570		* Method to call to indicate that the sequence (characters or alignment/gaps)
571		* has been modified. Provided to allow any cursors on residue/column
572		* positions to be invalidated.
573		*/
574		void sequenceChanged();
575
576		/**
577		*
578		* @return BitSet corresponding to index [0,length) where Comparison.isGap()
579		* returns true.
580		*/
581		BitSet getInsertionsAsBits();
582
583		/**
584		* Replaces every occurrence of c1 in the sequence with c2 and returns the
585		* number of characters changed
586		*
587		* @param c1
588		* @param c2
589		*/
590		public int replace(char c1, char c2);
591
592		/**
593		* Answers the GeneLociI, or null if not known
594		*
595		* @return
596		*/
597		GeneLociI getGeneLoci();
598
599		/**
600		* Sets the mapping to gene loci for the sequence
601		*
602		* @param speciesId
603		* @param assemblyId
604		* @param chromosomeId
605		* @param map
606		*/
607		void setGeneLoci(String speciesId, String assemblyId,
608		String chromosomeId, MapList map);
609
610
611		/**
612		* Returns the sequence string constructed from the substrings of a sequence
613		* defined by the int[] ranges provided by an iterator. E.g. the iterator
614		* could iterate over all visible regions of the alignment
615		*
616		* @param it
617		* the iterator to use
618		* @return a String corresponding to the sequence
619		*/
620		public String getSequenceStringFromIterator(Iterator<int[]> it);
621
622		/**
623		* Locate the first position in this sequence which is not contained in an
624		* iterator region. If no such position exists, return 0
625		*
626		* @param it
627		* iterator over regions
628		* @return first residue not contained in regions
629		*/
630		public int firstResidueOutsideIterator(Iterator<int[]> it);
631
632		public void addContactListFor(AlignmentAnnotation annotation,
633		ContactMatrixI cm);
634
635		/**
636		* efficiently insert a char at several different places
637		* @param c
638		* @param inserts
639		*/
640		void insertInserts(char c, int[]... inserts);
641
642		/**
643		* make a single insert in this sequence, but do not call sequenceChanged()
644		* WARNING - CALLERS RESPONSIBILITY TO CALL sequenceChanged() AFTER THIS!
645		* @param i
646		* @param length
647		* @param c
648		*/
649		void doInsert(int i, int length, char c);
650
651		/**
652		* Answers true if this sequence has an associated Hidden Markov Model
653		*
654		* @return
655		*/
656		boolean hasHMMProfile();
657		}
658