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Coverage Report

  1. Project Clover database Thu Dec 4 2025 14:43:25 GMT
  2. Package jalview.datamodel

File AlignedCodonFrame.java

 

Coverage histogram

../../img/srcFileCovDistChart9.png
13% of files have more coverage

Code metrics

128
238
39
2
936
559
132
0.55
6.1
19.5
3.38

Classes

Class Line # Actions
AlignedCodonFrame 34 172 97
0.9078498590.8%
AlignedCodonFrame.SequenceToSequenceMapping 40 66 35
0.87587.5%
 

Contributing tests

This file is covered by 86 tests. .

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.AbstractList;
24    import java.util.ArrayList;
25    import java.util.List;
26   
27    import jalview.util.MapList;
28    import jalview.util.MappingUtils;
29   
30    /**
31    * Stores mapping between the columns of a protein alignment and a DNA alignment
32    * and a list of individual codon to amino acid mappings between sequences.
33    */
 
34    public class AlignedCodonFrame
35    {
36   
37    /*
38    * Data bean to hold mappings from one sequence to another
39    */
 
40    public class SequenceToSequenceMapping
41    {
42    private SequenceI fromSeq;
43   
44    private Mapping mapping;
45   
 
46  420 toggle SequenceToSequenceMapping(SequenceI from, Mapping map)
47    {
48  420 this.fromSeq = from;
49  420 this.mapping = map;
50    }
51   
52    /**
53    * Readable representation for debugging only, not guaranteed not to change
54    */
 
55  0 toggle @Override
56    public String toString()
57    {
58  0 return String.format("From %s %s", fromSeq.getName(),
59    mapping.toString());
60    }
61   
62    /**
63    * Returns a hashCode derived from the hashcodes of the mappings and fromSeq
64    *
65    * @see SequenceToSequenceMapping#hashCode()
66    */
 
67  0 toggle @Override
68    public int hashCode()
69    {
70  0 return (fromSeq == null ? 0 : fromSeq.hashCode() * 31)
71    + mapping.hashCode();
72    }
73   
74    /**
75    * Answers true if the objects hold the same mapping between the same two
76    * sequences
77    *
78    * @see Mapping#equals
79    */
 
80  2691 toggle @Override
81    public boolean equals(Object obj)
82    {
83  2691 if (!(obj instanceof SequenceToSequenceMapping))
84    {
85  0 return false;
86    }
87  2691 SequenceToSequenceMapping that = (SequenceToSequenceMapping) obj;
88  2691 if (this.mapping == null)
89    {
90  0 return that.mapping == null;
91    }
92    // TODO: can simplify by asserting fromSeq is a dataset sequence
93  2691 return (this.fromSeq == that.fromSeq
94    || (this.fromSeq != null && that.fromSeq != null
95    && this.fromSeq.getDatasetSequence() != null
96    && this.fromSeq.getDatasetSequence() == that.fromSeq
97    .getDatasetSequence()))
98    && this.mapping.equals(that.mapping);
99    }
100   
 
101  65 toggle public SequenceI getFromSeq()
102    {
103  65 return fromSeq;
104    }
105   
 
106  314 toggle public Mapping getMapping()
107    {
108  314 return mapping;
109    }
110   
111    /**
112    * Returns true if the mapping covers the full length of the given sequence.
113    * This allows us to distinguish the CDS that codes for a protein from
114    * another overlapping CDS in the parent dna sequence.
115    *
116    * @param seq
117    * @return
118    */
 
119  280 toggle public boolean covers(SequenceI seq)
120    {
121  280 return covers(seq, false, false);
122    }
123   
124    /**
125    *
126    * @param seq
127    * @param localCover
128    * - when true - compare extent of seq's dataset sequence rather
129    * than the local extent
130    * @param either
131    * - when true coverage is required for either seq or the mapped
132    * sequence
133    * @return true if mapping covers full length of given sequence (or the
134    * other if either==true)
135    */
 
136  577 toggle public boolean covers(SequenceI seq, boolean localCover, boolean either)
137    {
138  577 List<int[]> mappedRanges = null, otherRanges = null;
139  577 MapList mapList = mapping.getMap();
140  577 int mstart = seq.getStart(), mend = seq.getEnd(), ostart, oend;
141  577 ;
142  577 if (fromSeq == seq || fromSeq == seq.getDatasetSequence())
143    {
144  151 if (localCover && fromSeq != seq)
145    {
146  70 mstart = fromSeq.getStart();
147  70 mend = fromSeq.getEnd();
148    }
149  151 mappedRanges = mapList.getFromRanges();
150  151 otherRanges = mapList.getToRanges();
151  151 ostart = mapping.to.getStart();
152  151 oend = mapping.to.getEnd();
153    }
154  426 else if (mapping.to == seq || mapping.to == seq.getDatasetSequence())
155    {
156  124 if (localCover && mapping.to != seq)
157    {
158  65 mstart = mapping.to.getStart();
159  65 mend = mapping.to.getEnd();
160    }
161  124 mappedRanges = mapList.getToRanges();
162  124 otherRanges = mapList.getFromRanges();
163  124 ostart = fromSeq.getStart();
164  124 oend = fromSeq.getEnd();
165    }
166    else
167    {
168  302 return false;
169    }
170   
171    /*
172    * check that each mapped range lies within the sequence range
173    * (necessary for circular CDS - example EMBL:J03321:AAA91567)
174    * and mapped length covers (at least) sequence length
175    */
176  275 int length = countRange(mappedRanges, mstart, mend);
177   
178  275 if (length != -1)
179    {
180    // add 3 to mapped length to allow for a mapped stop codon
181  261 if (length + 3 >= (mend - mstart + 1))
182    {
183  228 return true;
184    }
185    }
186  47 if (either)
187    {
188    // also check coverage of the other range
189  25 length = countRange(otherRanges, ostart, oend);
190  25 if (length != -1)
191    {
192  25 if (length + 1 >= (oend - ostart + 1))
193    {
194  25 return true;
195    }
196    }
197    }
198  22 return false;
199    }
200   
 
201  300 toggle private int countRange(List<int[]> mappedRanges, int mstart, int mend)
202    {
203  300 int length = 0;
204  300 for (int[] range : mappedRanges)
205    {
206  386 int from = Math.min(range[0], range[1]);
207  386 int to = Math.max(range[0], range[1]);
208  386 if (from < mstart || to > mend)
209    {
210  14 return -1;
211    }
212  372 length += (to - from + 1);
213    }
214  286 return length;
215    }
216   
217    /**
218    * Adds any regions mapped to or from position {@code pos} in sequence
219    * {@code seq} to the given search results Note: recommend first using the
220    * .covers(,true,true) to ensure mapping covers both sequences
221    *
222    * @param seq
223    * @param pos
224    * @param sr
225    */
 
226  140 toggle public void markMappedRegion(SequenceI seq, int pos, SearchResultsI sr)
227    {
228  140 int[] codon = null;
229  140 SequenceI mappedSeq = null;
230  140 SequenceI ds = seq.getDatasetSequence();
231  140 if (ds == null)
232    {
233  140 ds = seq;
234    }
235   
236  140 if (this.fromSeq == seq || this.fromSeq == ds)
237    {
238  72 codon = this.mapping.map.locateInTo(pos, pos);
239  72 mappedSeq = this.mapping.to;
240    }
241  68 else if (this.mapping.to == seq || this.mapping.to == ds)
242    {
243  68 codon = this.mapping.map.locateInFrom(pos, pos);
244  68 mappedSeq = this.fromSeq;
245    }
246   
247  140 if (codon != null)
248    {
249  263 for (int i = 0; i < codon.length; i += 2)
250    {
251  140 sr.addResult(mappedSeq, codon[i], codon[i + 1]);
252    }
253    }
254    }
255    }
256   
257    private List<SequenceToSequenceMapping> mappings;
258   
259    /**
260    * Constructor
261    */
 
262  201 toggle public AlignedCodonFrame()
263    {
264  201 mappings = new ArrayList<>();
265    }
266   
267    /**
268    * Adds a mapping between the dataset sequences for the associated dna and
269    * protein sequence objects
270    *
271    * @param dnaseq
272    * @param aaseq
273    * @param map
274    */
 
275  415 toggle public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map)
276    {
277  415 addMap(dnaseq, aaseq, map, null);
278    }
279   
280    /**
281    * Adds a mapping between the dataset sequences for the associated dna and
282    * protein sequence objects
283    *
284    * @param dnaseq
285    * @param aaseq
286    * @param map
287    * @param mapFromId
288    */
 
289  428 toggle public void addMap(SequenceI dnaseq, SequenceI aaseq, MapList map,
290    String mapFromId)
291    {
292    // JBPNote DEBUG! THIS !
293    // dnaseq.transferAnnotation(aaseq, mp);
294    // aaseq.transferAnnotation(dnaseq, new Mapping(map.getInverse()));
295   
296  428 SequenceI fromSeq = (dnaseq.getDatasetSequence() == null) ? dnaseq
297    : dnaseq.getDatasetSequence();
298  428 SequenceI toSeq = (aaseq.getDatasetSequence() == null) ? aaseq
299    : aaseq.getDatasetSequence();
300   
301    /*
302    * if we already hold a mapping between these sequences, just add to it
303    * note that 'adding' a duplicate map does nothing; this protects against
304    * creating duplicate mappings in AlignedCodonFrame
305    */
306  428 for (SequenceToSequenceMapping ssm : mappings)
307    {
308  1157 if (ssm.fromSeq == fromSeq && ssm.mapping.to == toSeq)
309    {
310  8 ssm.mapping.map.addMapList(map);
311  8 return;
312    }
313    }
314   
315    /*
316    * otherwise, add a new sequence mapping
317    */
318  420 Mapping mp = new Mapping(toSeq, map);
319  420 mp.setMappedFromId(mapFromId);
320  420 mappings.add(new SequenceToSequenceMapping(fromSeq, mp));
321    }
322   
 
323  44 toggle public SequenceI[] getdnaSeqs()
324    {
325    // TODO return a list instead?
326    // return dnaSeqs;
327  44 List<SequenceI> seqs = new ArrayList<>();
328  44 for (SequenceToSequenceMapping ssm : mappings)
329    {
330  52 seqs.add(ssm.fromSeq);
331    }
332  44 return seqs.toArray(new SequenceI[seqs.size()]);
333    }
334   
 
335  16 toggle public SequenceI[] getAaSeqs()
336    {
337    // TODO not used - remove?
338  16 List<SequenceI> seqs = new ArrayList<>();
339  16 for (SequenceToSequenceMapping ssm : mappings)
340    {
341  16 seqs.add(ssm.mapping.to);
342    }
343  16 return seqs.toArray(new SequenceI[seqs.size()]);
344    }
345   
 
346  51 toggle public MapList[] getdnaToProt()
347    {
348  51 List<MapList> maps = new ArrayList<>();
349  51 for (SequenceToSequenceMapping ssm : mappings)
350    {
351  91 maps.add(ssm.mapping.map);
352    }
353  51 return maps.toArray(new MapList[maps.size()]);
354    }
355   
 
356  8 toggle public Mapping[] getProtMappings()
357    {
358  8 List<Mapping> maps = new ArrayList<>();
359  8 for (SequenceToSequenceMapping ssm : mappings)
360    {
361  9 maps.add(ssm.mapping);
362    }
363  8 return maps.toArray(new Mapping[maps.size()]);
364    }
365   
366    /**
367    * Returns the first mapping found which is to or from the given sequence, or
368    * null if none is found
369    *
370    * @param seq
371    * @return
372    */
 
373  32 toggle public Mapping getMappingForSequence(SequenceI seq)
374    {
375  32 SequenceI seqDs = seq.getDatasetSequence();
376  32 seqDs = seqDs != null ? seqDs : seq;
377   
378  32 for (SequenceToSequenceMapping ssm : mappings)
379    {
380  40 if (ssm.fromSeq == seqDs || ssm.mapping.to == seqDs)
381    {
382  32 return ssm.mapping;
383    }
384    }
385  0 return null;
386    }
387   
388    /**
389    * Return the corresponding aligned or dataset aa sequence for given dna
390    * sequence, null if not found.
391    *
392    * @param sequenceRef
393    * @return
394    */
 
395  124138 toggle public SequenceI getAaForDnaSeq(SequenceI dnaSeqRef)
396    {
397  124138 SequenceI dnads = dnaSeqRef.getDatasetSequence();
398  124138 for (SequenceToSequenceMapping ssm : mappings)
399    {
400  178170 if (ssm.fromSeq == dnaSeqRef || ssm.fromSeq == dnads)
401    {
402  124 return ssm.mapping.to;
403    }
404    }
405  124014 return null;
406    }
407   
408    /**
409    * Return the corresponding aligned or dataset dna sequence for given amino
410    * acid sequence, or null if not found. returns the sequence from the first
411    * mapping found that involves the protein sequence.
412    *
413    * @param aaSeqRef
414    * @return
415    */
 
416  124030 toggle public SequenceI getDnaForAaSeq(SequenceI aaSeqRef)
417    {
418  124030 SequenceI aads = aaSeqRef.getDatasetSequence();
419  124030 for (SequenceToSequenceMapping ssm : mappings)
420    {
421  148802 if (ssm.mapping.to == aaSeqRef || ssm.mapping.to == aads)
422    {
423  10803 return ssm.fromSeq;
424    }
425    }
426  113227 return null;
427    }
428   
429    /**
430    * test to see if codon frame involves seq in any way
431    *
432    * @param seq
433    * a nucleotide or protein sequence
434    * @return true if a mapping exists to or from this sequence to any translated
435    * sequence
436    */
 
437  124125 toggle public boolean involvesSequence(SequenceI seq)
438    {
439  124125 return getAaForDnaSeq(seq) != null || getDnaForAaSeq(seq) != null;
440    }
441   
442    /**
443    * Add search results for regions in other sequences that translate or are
444    * translated from a particular position in seq (which may be an aligned or
445    * dataset sequence)
446    *
447    * @param seq
448    * @param index
449    * position in seq
450    * @param results
451    * where highlighted regions go
452    */
 
453  131 toggle public void markMappedRegion(SequenceI seq, int index,
454    SearchResultsI results)
455    {
456  131 SequenceI ds = seq.getDatasetSequence();
457  131 if (ds == null)
458    {
459  3 ds = seq;
460    }
461  131 for (SequenceToSequenceMapping ssm : mappings)
462    {
463  297 if (ssm.covers(seq, true, true))
464    {
465  138 ssm.markMappedRegion(ds, index, results);
466    }
467    }
468    }
469   
470    /**
471    * Convenience method to return the first aligned sequence in the given
472    * alignment whose dataset has a mapping with the given (aligned or dataset)
473    * sequence.
474    *
475    * @param seq
476    *
477    * @param al
478    * @return
479    */
 
480  1043 toggle public SequenceI findAlignedSequence(SequenceI seq, AlignmentI al)
481    {
482    /*
483    * Search mapped protein ('to') sequences first.
484    */
485  1043 for (SequenceToSequenceMapping ssm : mappings)
486    {
487  1495 if (ssm.fromSeq == seq || ssm.fromSeq == seq.getDatasetSequence())
488    {
489  65 for (SequenceI sourceAligned : al.getSequences())
490    {
491  644 if (ssm.mapping.to == sourceAligned.getDatasetSequence()
492    || ssm.mapping.to == sourceAligned)
493    {
494  39 return sourceAligned;
495    }
496    }
497    }
498    }
499   
500    /*
501    * Then try mapped dna sequences.
502    */
503  1004 for (SequenceToSequenceMapping ssm : mappings)
504    {
505  1445 if (ssm.mapping.to == seq
506    || ssm.mapping.to == seq.getDatasetSequence())
507    {
508  53 for (SequenceI sourceAligned : al.getSequences())
509    {
510  497 if (ssm.fromSeq == sourceAligned.getDatasetSequence())
511    {
512  31 return sourceAligned;
513    }
514    }
515    }
516    }
517   
518  973 return null;
519    }
520   
521    /**
522    * Returns the region in the target sequence's dataset that is mapped to the
523    * given position (base 1) in the query sequence's dataset. The region is a
524    * set of start/end position pairs.
525    *
526    * @param target
527    * @param query
528    * @param queryPos
529    * @return
530    */
 
531  161 toggle public int[] getMappedRegion(SequenceI target, SequenceI query,
532    int queryPos)
533    {
534  161 SequenceI targetDs = target.getDatasetSequence() == null ? target
535    : target.getDatasetSequence();
536  161 SequenceI queryDs = query.getDatasetSequence() == null ? query
537    : query.getDatasetSequence();
538  161 if (targetDs == null || queryDs == null /*|| dnaToProt == null*/)
539    {
540  0 return null;
541    }
542  161 for (SequenceToSequenceMapping ssm : mappings)
543    {
544    /*
545    * try mapping from target to query
546    */
547  172 if (ssm.fromSeq == targetDs && ssm.mapping.to == queryDs)
548    {
549  40 int[] codon = ssm.mapping.map.locateInFrom(queryPos, queryPos);
550  40 if (codon != null)
551    {
552  36 return codon;
553    }
554    }
555    /*
556    * else try mapping from query to target
557    */
558  132 else if (ssm.fromSeq == queryDs && ssm.mapping.to == targetDs)
559    {
560  119 int[] codon = ssm.mapping.map.locateInTo(queryPos, queryPos);
561  119 if (codon != null)
562    {
563  26 return codon;
564    }
565    }
566    }
567  99 return null;
568    }
569   
570    /**
571    * Returns the mapped DNA codons for the given position in a protein sequence,
572    * or null if no mapping is found. Returns a list of (e.g.) ['g', 'c', 't']
573    * codons. There may be more than one codon mapped to the protein if (for
574    * example), there are mappings to cDNA variants.
575    *
576    * @param protein
577    * the peptide dataset sequence
578    * @param aaPos
579    * residue position (base 1) in the peptide sequence
580    * @return
581    */
 
582  10713 toggle public List<char[]> getMappedCodons(SequenceI protein, int aaPos)
583    {
584  10713 MapList ml = null;
585  10713 SequenceI dnaSeq = null;
586  10713 List<char[]> result = new ArrayList<>();
587   
588  10713 for (SequenceToSequenceMapping ssm : mappings)
589    {
590  63979 if (ssm.mapping.to == protein
591    && ssm.mapping.getMap().getFromRatio() == 3)
592    {
593  10689 ml = ssm.mapping.map;
594  10689 dnaSeq = ssm.fromSeq;
595   
596  10689 int[] codonPos = ml.locateInFrom(aaPos, aaPos);
597  10689 if (codonPos == null)
598    {
599  21 return null;
600    }
601   
602    /*
603    * Read off the mapped nucleotides (converting to position base 0)
604    */
605  10668 codonPos = MappingUtils.flattenRanges(codonPos);
606  10668 int start = dnaSeq.getStart();
607  10668 char c1 = dnaSeq.getCharAt(codonPos[0] - start);
608  10668 char c2 = dnaSeq.getCharAt(codonPos[1] - start);
609  10668 char c3 = dnaSeq.getCharAt(codonPos[2] - start);
610  10668 result.add(new char[] { c1, c2, c3 });
611    }
612    }
613  10692 return result.isEmpty() ? null : result;
614    }
615   
616    /**
617    * Returns any mappings found which are from the given sequence, and to
618    * distinct sequences.
619    *
620    * @param seq
621    * @return
622    */
 
623  46 toggle public List<Mapping> getMappingsFromSequence(SequenceI seq)
624    {
625  46 List<Mapping> result = new ArrayList<>();
626  46 List<SequenceI> related = new ArrayList<>();
627  46 SequenceI seqDs = seq.getDatasetSequence();
628  46 seqDs = seqDs != null ? seqDs : seq;
629   
630  46 for (SequenceToSequenceMapping ssm : mappings)
631    {
632  268 final Mapping mapping = ssm.mapping;
633  268 if (ssm.fromSeq == seqDs)
634    {
635  48 if (!related.contains(mapping.to))
636    {
637  48 result.add(mapping);
638  48 related.add(mapping.to);
639    }
640    }
641    }
642  46 return result;
643    }
644   
645    /**
646    * Test whether the given sequence is substitutable for one or more dummy
647    * sequences in this mapping
648    *
649    * @param map
650    * @param seq
651    * @return
652    */
 
653  7 toggle public boolean isRealisableWith(SequenceI seq)
654    {
655  7 return realiseWith(seq, false) > 0;
656    }
657   
658    /**
659    * Replace any matchable mapped dummy sequences with the given real one.
660    * Returns the count of sequence mappings instantiated.
661    *
662    * @param seq
663    * @return
664    */
 
665  2 toggle public int realiseWith(SequenceI seq)
666    {
667  2 return realiseWith(seq, true);
668    }
669   
670    /**
671    * Returns the number of mapped dummy sequences that could be replaced with
672    * the given real sequence.
673    *
674    * @param seq
675    * a dataset sequence
676    * @param doUpdate
677    * if true, performs replacements, else only counts
678    * @return
679    */
 
680  9 toggle protected int realiseWith(SequenceI seq, boolean doUpdate)
681    {
682  9 SequenceI ds = seq.getDatasetSequence() != null
683    ? seq.getDatasetSequence()
684    : seq;
685  9 int count = 0;
686   
687    /*
688    * check for replaceable DNA ('map from') sequences
689    */
690  9 for (SequenceToSequenceMapping ssm : mappings)
691    {
692  10 SequenceI dna = ssm.fromSeq;
693  10 if (dna instanceof SequenceDummy
694    && dna.getName().equals(ds.getName()))
695    {
696  8 Mapping mapping = ssm.mapping;
697  8 int mapStart = mapping.getMap().getFromLowest();
698  8 int mapEnd = mapping.getMap().getFromHighest();
699  8 boolean mappable = couldRealiseSequence(dna, ds, mapStart, mapEnd);
700  8 if (mappable)
701    {
702  6 count++;
703  6 if (doUpdate)
704    {
705    // TODO: new method ? ds.realise(dna);
706    // might want to copy database refs as well
707  3 ds.setSequenceFeatures(dna.getSequenceFeatures());
708    // dnaSeqs[i] = ds;
709  3 ssm.fromSeq = ds;
710  3 jalview.bin.Console
711    .outPrintln("Realised mapped sequence " + ds.getName());
712    }
713    }
714    }
715   
716    /*
717    * check for replaceable protein ('map to') sequences
718    */
719  10 Mapping mapping = ssm.mapping;
720  10 SequenceI prot = mapping.getTo();
721  10 int mapStart = mapping.getMap().getToLowest();
722  10 int mapEnd = mapping.getMap().getToHighest();
723  10 boolean mappable = couldRealiseSequence(prot, ds, mapStart, mapEnd);
724  10 if (mappable)
725    {
726  0 count++;
727  0 if (doUpdate)
728    {
729    // TODO: new method ? ds.realise(dna);
730    // might want to copy database refs as well
731  0 ds.setSequenceFeatures(dna.getSequenceFeatures());
732  0 ssm.mapping.setTo(ds);
733    }
734    }
735    }
736  9 return count;
737    }
738   
739    /**
740    * Helper method to test whether a 'real' sequence could replace a 'dummy'
741    * sequence in the map. The criteria are that they have the same name, and
742    * that the mapped region overlaps the candidate sequence.
743    *
744    * @param existing
745    * @param replacement
746    * @param mapStart
747    * @param mapEnd
748    * @return
749    */
 
750  28 toggle protected static boolean couldRealiseSequence(SequenceI existing,
751    SequenceI replacement, int mapStart, int mapEnd)
752    {
753  28 if (existing instanceof SequenceDummy
754    && !(replacement instanceof SequenceDummy)
755    && existing.getName().equals(replacement.getName()))
756    {
757  13 int start = replacement.getStart();
758  13 int end = replacement.getEnd();
759  13 boolean mappingOverlapsSequence = (mapStart >= start
760    && mapStart <= end) || (mapEnd >= start && mapEnd <= end);
761  13 if (mappingOverlapsSequence)
762    {
763  9 return true;
764    }
765    }
766  19 return false;
767    }
768   
769    /**
770    * Change any mapping to the given sequence to be to its dataset sequence
771    * instead. For use when mappings are created before their referenced
772    * sequences are instantiated, for example when parsing GFF data.
773    *
774    * @param seq
775    */
 
776  8 toggle public void updateToDataset(SequenceI seq)
777    {
778  8 if (seq == null || seq.getDatasetSequence() == null)
779    {
780  0 return;
781    }
782  8 SequenceI ds = seq.getDatasetSequence();
783   
784  8 for (SequenceToSequenceMapping ssm : mappings)
785    /*
786    * 'from' sequences
787    */
788    {
789  8 if (ssm.fromSeq == seq)
790    {
791  4 ssm.fromSeq = ds;
792    }
793   
794    /*
795    * 'to' sequences
796    */
797  8 if (ssm.mapping.to == seq)
798    {
799  4 ssm.mapping.to = ds;
800    }
801    }
802    }
803   
804    /**
805    * Answers true if this object contains no mappings
806    *
807    * @return
808    */
 
809  7 toggle public boolean isEmpty()
810    {
811  7 return mappings.isEmpty();
812    }
813   
814    /**
815    * Method for debug / inspection purposes only, may change in future
816    */
 
817  0 toggle @Override
818    public String toString()
819    {
820  0 return mappings == null ? "null" : mappings.toString();
821    }
822   
823    /**
824    * Returns the first mapping found that is between 'fromSeq' and 'toSeq', or
825    * null if none found
826    *
827    * @param fromSeq
828    * aligned or dataset sequence
829    * @param toSeq
830    * aligned or dataset sequence
831    * @return
832    */
 
833  42 toggle public Mapping getMappingBetween(SequenceI fromSeq, SequenceI toSeq)
834    {
835  42 SequenceI dssFrom = fromSeq.getDatasetSequence() == null ? fromSeq
836    : fromSeq.getDatasetSequence();
837  42 SequenceI dssTo = toSeq.getDatasetSequence() == null ? toSeq
838    : toSeq.getDatasetSequence();
839   
840  42 for (SequenceToSequenceMapping mapping : mappings)
841    {
842  89 SequenceI from = mapping.fromSeq;
843  89 SequenceI to = mapping.mapping.to;
844  89 if ((from == dssFrom && to == dssTo)
845    || (from == dssTo && to == dssFrom))
846    {
847  31 return mapping.mapping;
848    }
849    }
850  11 return null;
851    }
852   
853    /**
854    * Returns a hashcode derived from the list of sequence mappings
855    *
856    * @see SequenceToSequenceMapping#hashCode()
857    * @see AbstractList#hashCode()
858    */
 
859  0 toggle @Override
860    public int hashCode()
861    {
862  0 return this.mappings.hashCode();
863    }
864   
865    /**
866    * Two AlignedCodonFrame objects are equal if they hold the same ordered list
867    * of mappings
868    *
869    * @see SequenceToSequenceMapping#equals
870    */
 
871  3227 toggle @Override
872    public boolean equals(Object obj)
873    {
874  3227 if (!(obj instanceof AlignedCodonFrame))
875    {
876  0 return false;
877    }
878  3227 return this.mappings.equals(((AlignedCodonFrame) obj).mappings);
879    }
880   
 
881  140 toggle public List<SequenceToSequenceMapping> getMappings()
882    {
883  140 return mappings;
884    }
885   
886    /**
887    * Returns the first mapping found which is between the two given sequences,
888    * and covers the full extent of both.
889    *
890    * @param seq1
891    * @param seq2
892    * @return
893    */
 
894  11 toggle public SequenceToSequenceMapping getCoveringMapping(SequenceI seq1,
895    SequenceI seq2)
896    {
897  11 for (SequenceToSequenceMapping mapping : mappings)
898    {
899  7 if (mapping.covers(seq2) && mapping.covers(seq1))
900    {
901  2 return mapping;
902    }
903    }
904  9 return null;
905    }
906   
907    /**
908    * Returns the first mapping found which is between the given dataset sequence
909    * and another, is a triplet mapping (3:1 or 1:3), and covers the full extent
910    * of both sequences involved
911    *
912    * @param seq
913    * @return
914    */
 
915  14 toggle public SequenceToSequenceMapping getCoveringCodonMapping(SequenceI seq)
916    {
917  14 for (SequenceToSequenceMapping mapping : mappings)
918    {
919  11 if (mapping.getMapping().getMap().isTripletMap()
920    && mapping.covers(seq))
921    {
922  8 if (mapping.fromSeq == seq
923    && mapping.covers(mapping.getMapping().getTo()))
924    {
925  2 return mapping;
926    }
927  6 else if (mapping.getMapping().getTo() == seq
928    && mapping.covers(mapping.fromSeq))
929    {
930  4 return mapping;
931    }
932    }
933    }
934  8 return null;
935    }
936    }
  • Report generated by OpenClover v 4.4.1 on Thu Dec 4 2025 14:53:28 GMT using coverage data from Thu Dec 4 2025 14:53:14 GMT.
  • OpenClover is free and open-source software.