Classes

Class	Line #	Total Statements	Complexity	TOTAL Coverage	Actions
AlignmentI	31	0	0	-1.0 -	Show methods

Class AlignmentI

Class AlignmentI	Line # 31	Total Statements 0	Complexity 0	TOTAL Coverage -1.0 -

 

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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.Hashtable;
24		import java.util.List;
25		import java.util.Map;
26		import java.util.Set;
27
28		/**
29		* Data structure to hold and manipulate a multiple sequence alignment
30		*/
		- Uncovered Elements: 0 (0) Complexity: 0 Complexity Density: -
31		public interface AlignmentI extends AnnotatedCollectionI
32		{
33		/**
34		* Calculates the number of sequences in an alignment, excluding hidden
35		* sequences
36		*
37		* @return Number of sequences in alignment
38		*/
39		int getHeight();
40
41		/**
42		* Calculates the number of sequences in an alignment, including hidden
43		* sequences
44		*
45		* @return Number of sequences in alignment
46		*/
47		int getAbsoluteHeight();
48
49		/**
50		*
51		* Answers the width of the alignment, including gaps, that is, the length of
52		* the longest sequence, or -1 if there are no sequences. Avoid calling this
53		* method repeatedly where possible, as it has to perform a calculation. Note
54		* that this width includes any hidden columns.
55		*
56		* @return
57		* @see AlignmentI#getVisibleWidth()
58		*/
59		@Override
60		int getWidth();
61
62		/**
63		*
64		* Answers the visible width of the alignment, including gaps, that is, the
65		* length of the longest sequence, excluding any hidden columns. Answers -1 if
66		* there are no sequences. Avoid calling this method repeatedly where
67		* possible, as it has to perform a calculation.
68		*
69		* @return
70		*/
71		int getVisibleWidth();
72
73		/**
74		* Calculates if this set of sequences (visible and invisible) are all the
75		* same length
76		*
77		* @return true if all sequences in alignment are the same length
78		*/
79		boolean isAligned();
80
81		/**
82		* Calculates if this set of sequences is all the same length
83		*
84		* @param includeHidden
85		* optionally exclude hidden sequences from test
86		* @return true if all (or just visible) sequences are the same length
87		*/
88		boolean isAligned(boolean includeHidden);
89
90		/**
91		* Answers if the sequence at alignmentIndex is hidden
92		*
93		* @param alignmentIndex
94		* the index to check
95		* @return true if the sequence is hidden
96		*/
97		boolean isHidden(int alignmentIndex);
98
99		/**
100		* Gets sequences as a Synchronized collection
101		*
102		* @return All sequences in alignment.
103		*/
104		@Override
105		List<SequenceI> getSequences();
106
107		/**
108		* Gets sequences as a SequenceI[]
109		*
110		* @return All sequences in alignment.
111		*/
112		SequenceI[] getSequencesArray();
113
114		/**
115		* Find a specific sequence in this alignment.
116		*
117		* @param i
118		* Index of required sequence.
119		*
120		* @return SequenceI at given index.
121		*/
122		SequenceI getSequenceAt(int i);
123
124		/**
125		* Find a specific sequence in this alignment.
126		*
127		* @param i
128		* Index of required sequence in full alignment, i.e. if all columns
129		* were visible
130		*
131		* @return SequenceI at given index.
132		*/
133		SequenceI getSequenceAtAbsoluteIndex(int i);
134
135		/**
136		* Returns a map of lists of sequences keyed by sequence name.
137		*
138		* @return
139		*/
140		Map<String, List<SequenceI>> getSequencesByName();
141
142		/**
143		* Add a new sequence to this alignment.
144		*
145		* @param seq
146		* New sequence will be added at end of alignment.
147		*/
148		void addSequence(SequenceI seq);
149
150		/**
151		* Used to set a particular index of the alignment with the given sequence.
152		*
153		* @param i
154		* Index of sequence to be updated. if i>length, sequence will be
155		* added to end, with no intervening positions.
156		* @param seq
157		* New sequence to be inserted. The existing sequence at position i
158		* will be replaced.
159		* @return existing sequence (or null if i>current length)
160		*/
161		SequenceI replaceSequenceAt(int i, SequenceI seq);
162
163		/**
164		* Deletes a sequence from the alignment. Updates hidden sequences to account
165		* for the removed sequence. Do NOT use this method to delete sequences which
166		* are just hidden.
167		*
168		* @param s
169		* Sequence to be deleted.
170		*/
171		void deleteSequence(SequenceI s);
172
173		/**
174		* Deletes a sequence from the alignment. Updates hidden sequences to account
175		* for the removed sequence. Do NOT use this method to delete sequences which
176		* are just hidden.
177		*
178		* @param i
179		* Index of sequence to be deleted.
180		*/
181		void deleteSequence(int i);
182
183		/**
184		* Deletes a sequence in the alignment which has been hidden.
185		*
186		* @param i
187		* Index of sequence to be deleted
188		*/
189		void deleteHiddenSequence(int i);
190
191		/**
192		* Finds sequence in alignment using sequence name as query.
193		*
194		* @param name
195		* Id of sequence to search for.
196		*
197		* @return Sequence matching query, if found. If not found returns null.
198		*/
199		SequenceI findName(String name);
200
201		SequenceI[] findSequenceMatch(String name);
202
203		/**
204		* Finds index of a given sequence in the alignment.
205		*
206		* @param s
207		* Sequence to look for.
208		*
209		* @return Index of sequence within the alignment or -1 if not found
210		*/
211		int findIndex(SequenceI s);
212
213		/**
214		* Returns the first group (in the order in which groups were added) that
215		* includes the given sequence instance and aligned position (base 0), or null
216		* if none found
217		*
218		* @param seq
219		* - must be contained in the alignment (not a dataset sequence)
220		* @param position
221		*
222		* @return
223		*/
224		SequenceGroup findGroup(SequenceI seq, int position);
225
226		/**
227		* Finds all groups that a given sequence is part of.
228		*
229		* @param s
230		* Sequence in alignment.
231		*
232		* @return All groups containing given sequence.
233		*/
234		SequenceGroup[] findAllGroups(SequenceI s);
235
236		/**
237		* Adds a new SequenceGroup to this alignment.
238		*
239		* @param sg
240		* New group to be added.
241		*/
242		void addGroup(SequenceGroup sg);
243
244		/**
245		* Deletes a specific SequenceGroup
246		*
247		* @param g
248		* Group will be deleted from alignment.
249		*/
250		void deleteGroup(SequenceGroup g);
251
252		/**
253		* Get all the groups associated with this alignment.
254		*
255		* @return All groups as a list.
256		*/
257		List<SequenceGroup> getGroups();
258
259		/**
260		* Deletes all groups from this alignment.
261		*/
262		void deleteAllGroups();
263
264		/**
265		* Adds a new AlignmentAnnotation to this alignment
266		*
267		* @note Care should be taken to ensure that annotation is at least as wide as
268		* the longest sequence in the alignment for rendering purposes.
269		*/
270		void addAnnotation(AlignmentAnnotation aa);
271
272		/**
273		* moves annotation to a specified index in alignment annotation display stack
274		*
275		* @param aa
276		* the annotation object to be moved
277		* @param index
278		* the destination position
279		*/
280		void setAnnotationIndex(AlignmentAnnotation aa, int index);
281
282		/**
283		* Delete all annotations, including auto-calculated if the flag is set true.
284		* Returns true if at least one annotation was deleted, else false.
285		*
286		* @param includingAutoCalculated
287		* @return
288		*/
289		boolean deleteAllAnnotations(boolean includingAutoCalculated);
290
291		/**
292		* Deletes a specific AlignmentAnnotation from the alignment, and removes its
293		* reference from any SequenceI or SequenceGroup object's annotation if and
294		* only if aa is contained within the alignment's annotation vector.
295		* Otherwise, it will do nothing.
296		*
297		* @param aa
298		* the annotation to delete
299		* @return true if annotation was deleted from this alignment.
300		*/
301		boolean deleteAnnotation(AlignmentAnnotation aa);
302
303		/**
304		* Deletes a specific AlignmentAnnotation from the alignment, and optionally
305		* removes any reference from any SequenceI or SequenceGroup object's
306		* annotation if and only if aa is contained within the alignment's annotation
307		* vector. Otherwise, it will do nothing.
308		*
309		* @param aa
310		* the annotation to delete
311		* @param unhook
312		* flag indicating if any references should be removed from
313		* annotation - use this if you intend to add the annotation back
314		* into the alignment
315		* @return true if annotation was deleted from this alignment.
316		*/
317		boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook);
318
319		/**
320		* Get the annotation associated with this alignment (this can be null if no
321		* annotation has ever been created on the alignment)
322		*
323		* @return array of AlignmentAnnotation objects
324		*/
325		@Override
326		AlignmentAnnotation[] getAlignmentAnnotation();
327
328		/**
329		* Change the gap character used in this alignment to 'gc'
330		*
331		* @param gc
332		* the new gap character.
333		*/
334		void setGapCharacter(char gc);
335
336		/**
337		* Get the gap character used in this alignment
338		*
339		* @return gap character
340		*/
341		char getGapCharacter();
342
343		/**
344		* Test if alignment contains RNA structure
345		*
346		* @return true if RNA structure AligmnentAnnotation was added to alignment
347		*/
348		boolean hasRNAStructure();
349
350		/**
351		* Get the associated dataset for the alignment.
352		*
353		* @return Alignment containing dataset sequences or null of this is a
354		* dataset.
355		*/
356		AlignmentI getDataset();
357
358		/**
359		* Set the associated dataset for the alignment, or create one.
360		*
361		* @param dataset
362		* The dataset alignment or null to construct one.
363		*/
364		void setDataset(AlignmentI dataset);
365
366		/**
367		* pads sequences with gaps (to ensure the set looks like an alignment)
368		*
369		* @return boolean true if alignment was modified
370		*/
371		boolean padGaps();
372
373		HiddenSequences getHiddenSequences();
374
375		HiddenColumns getHiddenColumns();
376
377		/**
378		* Compact representation of alignment
379		*
380		* @return CigarArray
381		*/
382		CigarArray getCompactAlignment();
383
384		/**
385		* Set an arbitrary key value pair for an alignment. Note: both key and value
386		* objects should return a meaningful, human readable response to .toString()
387		*
388		* @param key
389		* @param value
390		*/
391		void setProperty(Object key, Object value);
392
393		/**
394		* Get a named property from the alignment.
395		*
396		* @param key
397		* @return value of property
398		*/
399		Object getProperty(Object key);
400
401		/**
402		* Get the property hashtable.
403		*
404		* @return hashtable of alignment properties (or null if none are defined)
405		*/
406		Hashtable getProperties();
407
408		/**
409		* add a reference to a frame of aligned codons for this alignment
410		*
411		* @param codons
412		*/
413		void addCodonFrame(AlignedCodonFrame codons);
414
415		/**
416		* remove a particular codon frame reference from this alignment
417		*
418		* @param codons
419		* @return true if codon frame was removed.
420		*/
421		boolean removeCodonFrame(AlignedCodonFrame codons);
422
423		/**
424		* get all codon frames associated with this alignment
425		*
426		* @return
427		*/
428		List<AlignedCodonFrame> getCodonFrames();
429
430		/**
431		* Set the codon frame mappings (replacing any existing list).
432		*/
433		void setCodonFrames(List<AlignedCodonFrame> acfs);
434
435		/**
436		* get codon frames involving sequenceI
437		*/
438		List<AlignedCodonFrame> getCodonFrame(SequenceI seq);
439
440		/**
441		* find sequence with given name in alignment
442		*
443		* @param token
444		* name to find
445		* @param b
446		* true implies that case insensitive matching will <em>also</em> be
447		* tried
448		* @return matched sequence or null
449		*/
450		SequenceI findName(String token, boolean b);
451
452		/**
453		* find next sequence with given name in alignment starting after a given
454		* sequence
455		*
456		* @param startAfter
457		* the sequence after which the search will be started (usually the
458		* result of the last call to findName)
459		* @param token
460		* name to find
461		* @param b
462		* true implies that case insensitive matching will <em>also</em> be
463		* tried
464		* @return matched sequence or null
465		*/
466		SequenceI findName(SequenceI startAfter, String token, boolean b);
467
468		/**
469		* find first sequence in alignment which is involved in the given search
470		* result object
471		*
472		* @param results
473		* @return -1 or index of sequence in alignment
474		*/
475		int findIndex(SearchResultsI results);
476
477		/**
478		* append sequences and annotation from another alignment object to this one.
479		* Note: this is a straight transfer of object references, and may result in
480		* toappend's dependent data being transformed to fit the alignment (changing
481		* gap characters, etc...). If you are uncertain, use the copy Alignment copy
482		* constructor to create a new version which can be appended without side
483		* effect.
484		*
485		* @param toappend
486		* - the alignment to be appended.
487		*/
488		void append(AlignmentI toappend);
489
490		/**
491		* Justify the sequences to the left or right by deleting and inserting gaps
492		* before the initial residue or after the terminal residue
493		*
494		* @param right
495		* true if alignment padded to right, false to justify to left
496		* @return true if alignment was changed TODO: return undo object
497		*/
498		boolean justify(boolean right);
499
500		/**
501		* add given annotation row at given position (0 is start, -1 is end)
502		*
503		* @param consensus
504		* @param i
505		*/
506		void addAnnotation(AlignmentAnnotation consensus, int i);
507
508		/**
509		* search for or create a specific annotation row on the alignment
510		*
511		* @param name
512		* name for annotation (must match)
513		* @param calcId
514		* calcId for the annotation (null or must match)
515		* @param autoCalc
516		* - value of autocalc flag for the annotation
517		* @param seqRef
518		* - null or specific sequence reference
519		* @param groupRef
520		* - null or specific group reference
521		* @param method
522		* - CalcId for the annotation (must match)
523		*
524		* @return existing annotation matching the given attributes
525		*/
526		AlignmentAnnotation findOrCreateAnnotation(String name, String calcId,
527		boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef);
528
529		/**
530		* move the given group up or down in the alignment by the given number of
531		* rows. Implementor assumes given group is already present on alignment - no
532		* recalculations are triggered.
533		*
534		* @param sg
535		* @param map
536		* @param up
537		* @param i
538		*/
539		void moveSelectedSequencesByOne(SequenceGroup sg,
540		Map<SequenceI, SequenceCollectionI> map, boolean up);
541
542		/**
543		* validate annotation after an edit and update any alignment state flags
544		* accordingly
545		*
546		* @param alignmentAnnotation
547		*/
548		void validateAnnotation(AlignmentAnnotation alignmentAnnotation);
549
550		/**
551		* Align this alignment the same as the given one. If both of the same type
552		* (nucleotide/protein) then align both identically. If this is nucleotide and
553		* the other is protein, make 3 gaps for each gap in the protein sequences. If
554		* this is protein and the other is nucleotide, insert a gap for each 3 gaps
555		* (or part thereof) between nucleotide bases. Returns the number of mapped
556		* sequences that were realigned .
557		*
558		* @param al
559		* @return
560		*/
561		int alignAs(AlignmentI al);
562
563		/**
564		* Returns the set of distinct sequence names in the alignment.
565		*
566		* @return
567		*/
568		Set<String> getSequenceNames();
569
570		/**
571		* Checks if the alignment has at least one sequence with one non-gaped
572		* residue
573		*
574		* @return
575		*/
576		public boolean hasValidSequence();
577
578		/**
579		* Update any mappings to 'virtual' sequences to compatible real ones, if
580		* present in the added sequences. Returns a count of mappings updated.
581		*
582		* @param seqs
583		* @return
584		*/
585		int realiseMappings(List<SequenceI> seqs);
586
587		/**
588		* Returns the first AlignedCodonFrame that has a mapping between the given
589		* dataset sequences
590		*
591		* @param mapFrom
592		* @param mapTo
593		* @return
594		*/
595		AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo);
596
597		/**
598		* Set the hidden columns collection on the alignment. Answers true if the
599		* hidden column selection changed, else false.
600		*
601		* @param cols
602		* @return
603		*/
604		public boolean setHiddenColumns(HiddenColumns cols);
605
606		/**
607		* Set the first sequence as representative and hide its insertions. Typically
608		* used when loading JPred files.
609		*/
610		public void setupJPredAlignment();
611
612		/**
613		* Add gaps into the sequences aligned to profileseq under the given
614		* AlignmentView
615		*
616		* @param profileseq
617		* sequence in al which sequences are aligned to
618		* @param input
619		* alignment view where sequence corresponding to profileseq is first
620		* entry
621		* @return new HiddenColumns for new alignment view, with insertions into
622		* profileseq marked as hidden.
623		*/
624		public HiddenColumns propagateInsertions(SequenceI profileseq,
625		AlignmentView input);
626
627		}