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  2. Package jalview.datamodel

File AlignmentI.java

 

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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    */
 
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    }