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Coverage Report

  1. Project Clover database Fri Dec 6 2024 13:47:14 GMT
  2. Package jalview.analysis

File Dna.java

 

Coverage histogram

../../img/srcFileCovDistChart7.png
29% of files have more coverage

Code metrics

150
371
16
1
1,005
674
138
0.37
23.19
16
8.62

Classes

Class Line # Actions
Dna 50 371 138
0.649906965%
 

Contributing tests

This file is covered by 16 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.analysis;
22   
23    import jalview.api.AlignViewportI;
24    import jalview.datamodel.AlignedCodon;
25    import jalview.datamodel.AlignedCodonFrame;
26    import jalview.datamodel.Alignment;
27    import jalview.datamodel.AlignmentAnnotation;
28    import jalview.datamodel.AlignmentI;
29    import jalview.datamodel.Annotation;
30    import jalview.datamodel.DBRefEntry;
31    import jalview.datamodel.DBRefSource;
32    import jalview.datamodel.FeatureProperties;
33    import jalview.datamodel.GraphLine;
34    import jalview.datamodel.Mapping;
35    import jalview.datamodel.Sequence;
36    import jalview.datamodel.SequenceFeature;
37    import jalview.datamodel.SequenceI;
38    import jalview.schemes.ResidueProperties;
39    import jalview.util.Comparison;
40    import jalview.util.DBRefUtils;
41    import jalview.util.MapList;
42    import jalview.util.ShiftList;
43   
44    import java.util.ArrayList;
45    import java.util.Arrays;
46    import java.util.Comparator;
47    import java.util.Iterator;
48    import java.util.List;
49   
 
50    public class Dna
51    {
52    private static final String STOP_ASTERIX = "*";
53   
54    private static final Comparator<AlignedCodon> comparator = new CodonComparator();
55   
56    /*
57    * 'final' variables describe the inputs to the translation, which should not
58    * be modified.
59    */
60    private final List<SequenceI> selection;
61   
62    private final String[] seqstring;
63   
64    private final Iterator<int[]> contigs;
65   
66    private final char gapChar;
67   
68    private final AlignmentAnnotation[] annotations;
69   
70    private final int dnaWidth;
71   
72    private final AlignmentI dataset;
73   
74    private ShiftList vismapping;
75   
76    private int[] startcontigs;
77   
78    /*
79    * Working variables for the translation.
80    *
81    * The width of the translation-in-progress protein alignment.
82    */
83    private int aaWidth = 0;
84   
85    /*
86    * This array will be built up so that position i holds the codon positions
87    * e.g. [7, 9, 10] that match column i (base 0) in the aligned translation.
88    * Note this implies a contract that if two codons do not align exactly, their
89    * translated products must occupy different column positions.
90    */
91    private AlignedCodon[] alignedCodons;
92   
93    /**
94    * Constructor given a viewport and the visible contigs.
95    *
96    * @param viewport
97    * @param visibleContigs
98    */
 
99  24 toggle public Dna(AlignViewportI viewport, Iterator<int[]> visibleContigs)
100    {
101  24 this.selection = Arrays.asList(viewport.getSequenceSelection());
102  24 this.seqstring = viewport.getViewAsString(true);
103  24 this.contigs = visibleContigs;
104  24 this.gapChar = viewport.getGapCharacter();
105  24 this.annotations = viewport.getAlignment().getAlignmentAnnotation();
106  24 this.dnaWidth = viewport.getAlignment().getWidth();
107  24 this.dataset = viewport.getAlignment().getDataset();
108  24 initContigs();
109    }
110   
111    /**
112    * Initialise contigs used as starting point for translateCodingRegion
113    */
 
114  24 toggle private void initContigs()
115    {
116  24 vismapping = new ShiftList(); // map from viscontigs to seqstring
117    // intervals
118   
119  24 int npos = 0;
120  24 int[] lastregion = null;
121  24 ArrayList<Integer> tempcontigs = new ArrayList<>();
122  50 while (contigs.hasNext())
123    {
124  26 int[] region = contigs.next();
125  26 if (lastregion == null)
126    {
127  24 vismapping.addShift(npos, region[0]);
128    }
129    else
130    {
131    // hidden region
132  2 vismapping.addShift(npos, region[0] - lastregion[1] + 1);
133    }
134  26 lastregion = region;
135  26 tempcontigs.add(region[0]);
136  26 tempcontigs.add(region[1]);
137    }
138   
139  24 startcontigs = new int[tempcontigs.size()];
140  24 int i = 0;
141  24 for (Integer val : tempcontigs)
142    {
143  52 startcontigs[i] = val;
144  52 i++;
145    }
146  24 tempcontigs = null;
147    }
148   
149    /**
150    * Test whether codon positions cdp1 should align before, with, or after cdp2.
151    * Returns zero if all positions match (or either argument is null). Returns
152    * -1 if any position in the first codon precedes the corresponding position
153    * in the second codon. Else returns +1 (some position in the second codon
154    * precedes the corresponding position in the first).
155    *
156    * Note this is not necessarily symmetric, for example:
157    * <ul>
158    * <li>compareCodonPos([2,5,6], [3,4,5]) returns -1</li>
159    * <li>compareCodonPos([3,4,5], [2,5,6]) also returns -1</li>
160    * </ul>
161    *
162    * @param ac1
163    * @param ac2
164    * @return
165    */
 
166  3347 toggle public static final int compareCodonPos(AlignedCodon ac1,
167    AlignedCodon ac2)
168    {
169  3347 return comparator.compare(ac1, ac2);
170    // return jalview_2_8_2compare(ac1, ac2);
171    }
172   
173    /**
174    * Codon comparison up to Jalview 2.8.2. This rule is sequence order dependent
175    * - see http://issues.jalview.org/browse/JAL-1635
176    *
177    * @param ac1
178    * @param ac2
179    * @return
180    */
 
181  0 toggle private static int jalview_2_8_2compare(AlignedCodon ac1,
182    AlignedCodon ac2)
183    {
184  0 if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
185    {
186  0 return 0;
187    }
188  0 if (ac1.pos1 < ac2.pos1 || ac1.pos2 < ac2.pos2 || ac1.pos3 < ac2.pos3)
189    {
190    // one base in cdp1 precedes the corresponding base in the other codon
191  0 return -1;
192    }
193    // one base in cdp1 appears after the corresponding base in the other codon.
194  0 return 1;
195    }
196   
197    /**
198    * Translates cDNA using the specified code table
199    *
200    * @return
201    */
 
202  23 toggle public AlignmentI translateCdna(GeneticCodeI codeTable)
203    {
204  23 AlignedCodonFrame acf = new AlignedCodonFrame();
205   
206  23 alignedCodons = new AlignedCodon[dnaWidth];
207   
208  23 int s;
209  23 int sSize = selection.size();
210  23 List<SequenceI> pepseqs = new ArrayList<>();
211  240 for (s = 0; s < sSize; s++)
212    {
213  217 SequenceI newseq = translateCodingRegion(selection.get(s),
214    seqstring[s], acf, pepseqs, codeTable);
215   
216  217 if (newseq != null)
217    {
218  217 pepseqs.add(newseq);
219  217 SequenceI ds = newseq;
220  217 if (dataset != null)
221    {
222  2 while (ds.getDatasetSequence() != null)
223    {
224  1 ds = ds.getDatasetSequence();
225    }
226  1 dataset.addSequence(ds);
227    }
228    }
229    }
230   
231  23 SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]);
232  23 AlignmentI al = new Alignment(newseqs);
233    // ensure we look aligned.
234  23 al.padGaps();
235    // link the protein translation to the DNA dataset
236  23 al.setDataset(dataset);
237  23 translateAlignedAnnotations(al, acf);
238  23 al.addCodonFrame(acf);
239  23 return al;
240    }
241   
242    /**
243    * fake the collection of DbRefs with associated exon mappings to identify if
244    * a translation would generate distinct product in the currently selected
245    * region.
246    *
247    * @param selection
248    * @param viscontigs
249    * @return
250    */
 
251  0 toggle public static boolean canTranslate(SequenceI[] selection,
252    int viscontigs[])
253    {
254  0 for (int gd = 0; gd < selection.length; gd++)
255    {
256  0 SequenceI dna = selection[gd];
257  0 List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
258    jalview.datamodel.DBRefSource.DNACODINGDBS);
259  0 if (dnarefs != null)
260    {
261    // intersect with pep
262  0 List<DBRefEntry> mappedrefs = new ArrayList<>();
263  0 List<DBRefEntry> refs = dna.getDBRefs();
264  0 for (int d = 0, nd = refs.size(); d < nd; d++)
265    {
266  0 DBRefEntry ref = refs.get(d);
267  0 if (ref.getMap() != null && ref.getMap().getMap() != null
268    && ref.getMap().getMap().getFromRatio() == 3
269    && ref.getMap().getMap().getToRatio() == 1)
270    {
271  0 mappedrefs.add(ref); // add translated protein maps
272    }
273    }
274  0 dnarefs = mappedrefs;// .toArray(new DBRefEntry[mappedrefs.size()]);
275  0 for (int d = 0, nd = dnarefs.size(); d < nd; d++)
276    {
277  0 Mapping mp = dnarefs.get(d).getMap();
278  0 if (mp != null)
279    {
280  0 for (int vc = 0, nv = viscontigs.length; vc < nv; vc += 2)
281    {
282  0 int[] mpr = mp.locateMappedRange(viscontigs[vc],
283    viscontigs[vc + 1]);
284  0 if (mpr != null)
285    {
286  0 return true;
287    }
288    }
289    }
290    }
291    }
292    }
293  0 return false;
294    }
295   
296    /**
297    * Translate nucleotide alignment annotations onto translated amino acid
298    * alignment using codon mapping codons
299    *
300    * @param al
301    * the translated protein alignment
302    */
 
303  23 toggle protected void translateAlignedAnnotations(AlignmentI al,
304    AlignedCodonFrame acf)
305    {
306    // Can only do this for columns with consecutive codons, or where
307    // annotation is sequence associated.
308   
309  23 if (annotations != null)
310    {
311  23 for (AlignmentAnnotation annotation : annotations)
312    {
313    /*
314    * Skip hidden or autogenerated annotation. Also (for now), RNA
315    * secondary structure annotation. If we want to show this against
316    * protein we need a smarter way to 'translate' without generating
317    * invalid (unbalanced) structure annotation.
318    */
319  318 if (annotation.autoCalculated || !annotation.visible
320    || annotation.isRNA())
321    {
322  318 continue;
323    }
324   
325  0 int aSize = aaWidth;
326  0 Annotation[] anots = (annotation.annotations == null) ? null
327    : new Annotation[aSize];
328  0 if (anots != null)
329    {
330  0 for (int a = 0; a < aSize; a++)
331    {
332    // process through codon map.
333  0 if (a < alignedCodons.length && alignedCodons[a] != null
334    && alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2))
335    {
336  0 anots[a] = getCodonAnnotation(alignedCodons[a],
337    annotation.annotations);
338    }
339    }
340    }
341   
342  0 AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label,
343    annotation.description, anots);
344  0 aa.graph = annotation.graph;
345  0 aa.graphGroup = annotation.graphGroup;
346  0 aa.graphHeight = annotation.graphHeight;
347  0 if (annotation.getThreshold() != null)
348    {
349  0 aa.setThreshold(new GraphLine(annotation.getThreshold()));
350    }
351  0 if (annotation.hasScore)
352    {
353  0 aa.setScore(annotation.getScore());
354    }
355   
356  0 final SequenceI seqRef = annotation.sequenceRef;
357  0 if (seqRef != null)
358    {
359  0 SequenceI aaSeq = acf.getAaForDnaSeq(seqRef);
360  0 if (aaSeq != null)
361    {
362    // aa.compactAnnotationArray(); // throw away alignment annotation
363    // positioning
364  0 aa.setSequenceRef(aaSeq);
365    // rebuild mapping
366  0 aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true);
367  0 aa.adjustForAlignment();
368  0 aaSeq.addAlignmentAnnotation(aa);
369    }
370    }
371  0 al.addAnnotation(aa);
372    }
373    }
374    }
375   
 
376  0 toggle private static Annotation getCodonAnnotation(AlignedCodon is,
377    Annotation[] annotations)
378    {
379    // Have a look at all the codon positions for annotation and put the first
380    // one found into the translated annotation pos.
381  0 int contrib = 0;
382  0 Annotation annot = null;
383  0 for (int p = 1; p <= 3; p++)
384    {
385  0 int dnaCol = is.getBaseColumn(p);
386  0 if (annotations[dnaCol] != null)
387    {
388  0 if (annot == null)
389    {
390  0 annot = new Annotation(annotations[dnaCol]);
391  0 contrib = 1;
392    }
393    else
394    {
395    // merge with last
396  0 Annotation cpy = new Annotation(annotations[dnaCol]);
397  0 if (annot.colour == null)
398    {
399  0 annot.colour = cpy.colour;
400    }
401  0 if (annot.description == null || annot.description.length() == 0)
402    {
403  0 annot.description = cpy.description;
404    }
405  0 if (annot.displayCharacter == null)
406    {
407  0 annot.displayCharacter = cpy.displayCharacter;
408    }
409  0 if (annot.secondaryStructure == 0)
410    {
411  0 annot.secondaryStructure = cpy.secondaryStructure;
412    }
413  0 annot.value += cpy.value;
414  0 contrib++;
415    }
416    }
417    }
418  0 if (contrib > 1)
419    {
420  0 annot.value /= contrib;
421    }
422  0 return annot;
423    }
424   
425    /**
426    * Translate a na sequence
427    *
428    * @param selection
429    * sequence displayed under viscontigs visible columns
430    * @param seqstring
431    * ORF read in some global alignment reference frame
432    * @param acf
433    * Definition of global ORF alignment reference frame
434    * @param proteinSeqs
435    * @param codeTable
436    * @return sequence ready to be added to alignment.
437    */
 
438  217 toggle protected SequenceI translateCodingRegion(SequenceI selection,
439    String seqstring, AlignedCodonFrame acf,
440    List<SequenceI> proteinSeqs, GeneticCodeI codeTable)
441    {
442  217 List<int[]> skip = new ArrayList<>();
443  217 int[] skipint = null;
444   
445  217 int npos = 0;
446  217 int vc = 0;
447   
448  217 int[] scontigs = new int[startcontigs.length];
449  217 System.arraycopy(startcontigs, 0, scontigs, 0, startcontigs.length);
450   
451    // allocate a roughly sized buffer for the protein sequence
452  217 StringBuilder protein = new StringBuilder(seqstring.length() / 2);
453  217 String seq = seqstring.replace('U', 'T').replace('u', 'T');
454  217 char codon[] = new char[3];
455  217 int cdp[] = new int[3];
456  217 int rf = 0;
457  217 int lastnpos = 0;
458  217 int nend;
459  217 int aspos = 0;
460  217 int resSize = 0;
461  6275 for (npos = 0, nend = seq.length(); npos < nend; npos++)
462    {
463  6058 if (!Comparison.isGap(seq.charAt(npos)))
464    {
465  6028 cdp[rf] = npos; // store position
466  6028 codon[rf++] = seq.charAt(npos); // store base
467    }
468  6058 if (rf == 3)
469    {
470    /*
471    * Filled up a reading frame...
472    */
473  1888 AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1],
474    cdp[2]);
475  1888 String aa = codeTable.translate(new String(codon));
476  1888 rf = 0;
477  1888 final String gapString = String.valueOf(gapChar);
478  1888 if (aa == null)
479    {
480  1 aa = gapString;
481  1 if (skipint == null)
482    {
483  1 skipint = new int[] { alignedCodon.pos1,
484    alignedCodon.pos3 /*
485    * cdp[0],
486    * cdp[2]
487    */ };
488    }
489  1 skipint[1] = alignedCodon.pos3; // cdp[2];
490    }
491    else
492    {
493  1887 if (skipint != null)
494    {
495    // edit scontigs
496  1 skipint[0] = vismapping.shift(skipint[0]);
497  1 skipint[1] = vismapping.shift(skipint[1]);
498  2 for (vc = 0; vc < scontigs.length;)
499    {
500  1 if (scontigs[vc + 1] < skipint[0])
501    {
502    // before skipint starts
503  0 vc += 2;
504  0 continue;
505    }
506  1 if (scontigs[vc] > skipint[1])
507    {
508    // finished editing so
509  0 break;
510    }
511    // Edit the contig list to include the skipped region which did
512    // not translate
513  1 int[] t;
514    // from : s1 e1 s2 e2 s3 e3
515    // to s: s1 e1 s2 k0 k1 e2 s3 e3
516    // list increases by one unless one boundary (s2==k0 or e2==k1)
517    // matches, and decreases by one if skipint intersects whole
518    // visible contig
519  1 if (scontigs[vc] <= skipint[0])
520    {
521  1 if (skipint[0] == scontigs[vc])
522    {
523    // skipint at start of contig
524    // shift the start of this contig
525  0 if (scontigs[vc + 1] > skipint[1])
526    {
527  0 scontigs[vc] = skipint[1];
528  0 vc += 2;
529    }
530    else
531    {
532  0 if (scontigs[vc + 1] == skipint[1])
533    {
534    // remove the contig
535  0 t = new int[scontigs.length - 2];
536  0 if (vc > 0)
537    {
538  0 System.arraycopy(scontigs, 0, t, 0, vc - 1);
539    }
540  0 if (vc + 2 < t.length)
541    {
542  0 System.arraycopy(scontigs, vc + 2, t, vc,
543    t.length - vc + 2);
544    }
545  0 scontigs = t;
546    }
547    else
548    {
549    // truncate contig to before the skipint region
550  0 scontigs[vc + 1] = skipint[0] - 1;
551  0 vc += 2;
552    }
553    }
554    }
555    else
556    {
557    // scontig starts before start of skipint
558  1 if (scontigs[vc + 1] < skipint[1])
559    {
560    // skipint truncates end of scontig
561  0 scontigs[vc + 1] = skipint[0] - 1;
562  0 vc += 2;
563    }
564    else
565    {
566    // divide region to new contigs
567  1 t = new int[scontigs.length + 2];
568  1 System.arraycopy(scontigs, 0, t, 0, vc + 1);
569  1 t[vc + 1] = skipint[0];
570  1 t[vc + 2] = skipint[1];
571  1 System.arraycopy(scontigs, vc + 1, t, vc + 3,
572    scontigs.length - (vc + 1));
573  1 scontigs = t;
574  1 vc += 4;
575    }
576    }
577    }
578    }
579  1 skip.add(skipint);
580  1 skipint = null;
581    }
582  1887 if (aa.equals(ResidueProperties.STOP))
583    {
584  0 aa = STOP_ASTERIX;
585    }
586  1887 resSize++;
587    }
588  1888 boolean findpos = true;
589  5150 while (findpos)
590    {
591    /*
592    * Compare this codon's base positions with those currently aligned to
593    * this column in the translation.
594    */
595  3262 final int compareCodonPos = compareCodonPos(alignedCodon,
596    alignedCodons[aspos]);
597  3262 switch (compareCodonPos)
598    {
599  178 case -1:
600   
601    /*
602    * This codon should precede the mapped positions - need to insert a
603    * gap in all prior sequences.
604    */
605  178 insertAAGap(aspos, proteinSeqs);
606  178 findpos = false;
607  178 break;
608   
609  1374 case +1:
610   
611    /*
612    * This codon belongs after the aligned codons at aspos. Prefix it
613    * with a gap and try the next position.
614    */
615  1374 aa = gapString + aa;
616  1374 aspos++;
617  1374 break;
618   
619  1710 case 0:
620   
621    /*
622    * Exact match - codon 'belongs' at this translated position.
623    */
624  1710 findpos = false;
625    }
626    }
627  1888 protein.append(aa);
628  1888 lastnpos = npos;
629  1888 if (alignedCodons[aspos] == null)
630    {
631    // mark this column as aligning to this aligned reading frame
632  466 alignedCodons[aspos] = alignedCodon;
633    }
634  1422 else if (!alignedCodons[aspos].equals(alignedCodon))
635    {
636  0 throw new IllegalStateException(
637    "Tried to coalign " + alignedCodons[aspos].toString()
638    + " with " + alignedCodon.toString());
639    }
640  1888 if (aspos >= aaWidth)
641    {
642    // update maximum alignment width
643  449 aaWidth = aspos;
644    }
645    // ready for next translated reading frame alignment position (if any)
646  1888 aspos++;
647    }
648    }
649  217 if (resSize > 0)
650    {
651  217 SequenceI newseq = new Sequence(selection.getName(),
652    protein.toString());
653  217 if (rf != 0)
654    {
655  188 final String errMsg = "trimming contigs for incomplete terminal codon.";
656  188 jalview.bin.Console.errPrintln(errMsg);
657    // map and trim contigs to ORF region
658  188 vc = scontigs.length - 1;
659  188 lastnpos = vismapping.shift(lastnpos); // place npos in context of
660    // whole dna alignment (rather
661    // than visible contigs)
662    // incomplete ORF could be broken over one or two visible contig
663    // intervals.
664  376 while (vc >= 0 && scontigs[vc] > lastnpos)
665    {
666  188 if (vc > 0 && scontigs[vc - 1] > lastnpos)
667    {
668  0 vc -= 2;
669    }
670    else
671    {
672    // correct last interval in list.
673  188 scontigs[vc] = lastnpos;
674    }
675    }
676   
677  188 if (vc > 0 && (vc + 1) < scontigs.length)
678    {
679    // truncate map list to just vc elements
680  0 int t[] = new int[vc + 1];
681  0 System.arraycopy(scontigs, 0, t, 0, vc + 1);
682  0 scontigs = t;
683    }
684  188 if (vc <= 0)
685    {
686  0 scontigs = null;
687    }
688    }
689  217 if (scontigs != null)
690    {
691  217 npos = 0;
692    // map scontigs to actual sequence positions on selection
693  412 for (vc = 0; vc < scontigs.length; vc += 2)
694    {
695  220 scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
696  220 scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
697  220 if (scontigs[vc + 1] == selection.getEnd())
698    {
699  25 break;
700    }
701    }
702    // trim trailing empty intervals.
703  217 if ((vc + 2) < scontigs.length)
704    {
705  0 int t[] = new int[vc + 2];
706  0 System.arraycopy(scontigs, 0, t, 0, vc + 2);
707  0 scontigs = t;
708    }
709    /*
710    * delete intervals in scontigs which are not translated. 1. map skip
711    * into sequence position intervals 2. truncate existing ranges and add
712    * new ranges to exclude untranslated regions. if (skip.size()>0) {
713    * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {
714    * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
715    * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);
716    * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&
717    * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of
718    * range } else { // truncate range and create new one if necessary iv =
719    * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate
720    * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
721    * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
722    */
723  217 MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
724   
725  217 transferCodedFeatures(selection, newseq, map);
726   
727    /*
728    * Construct a dataset sequence for our new peptide.
729    */
730  217 SequenceI rseq = newseq.deriveSequence();
731   
732    /*
733    * Store a mapping (between the dataset sequences for the two
734    * sequences).
735    */
736    // SIDE-EFFECT: acf stores the aligned sequence reseq; to remove!
737  217 acf.addMap(selection, rseq, map);
738  217 return rseq;
739    }
740    }
741    // register the mapping somehow
742    //
743  0 return null;
744    }
745   
746    /**
747    * Insert a gap into the aligned proteins and the codon mapping array.
748    *
749    * @param pos
750    * @param proteinSeqs
751    * @return
752    */
 
753  178 toggle protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)
754    {
755  178 aaWidth++;
756  178 for (SequenceI seq : proteinSeqs)
757    {
758  598 seq.insertCharAt(pos, gapChar);
759    }
760   
761  178 checkCodonFrameWidth();
762  178 if (pos < aaWidth)
763    {
764  178 aaWidth++;
765   
766    /*
767    * Shift from [pos] to the end one to the right, and null out [pos]
768    */
769  178 System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1,
770    alignedCodons.length - pos - 1);
771  178 alignedCodons[pos] = null;
772    }
773    }
774   
775    /**
776    * Check the codons array can accommodate a single insertion, if not resize
777    * it.
778    */
 
779  178 toggle protected void checkCodonFrameWidth()
780    {
781  178 if (alignedCodons[alignedCodons.length - 1] != null)
782    {
783    /*
784    * arraycopy insertion would bump a filled slot off the end, so expand.
785    */
786  0 AlignedCodon[] c = new AlignedCodon[alignedCodons.length + 10];
787  0 System.arraycopy(alignedCodons, 0, c, 0, alignedCodons.length);
788  0 alignedCodons = c;
789    }
790    }
791   
792    /**
793    * Given a peptide newly translated from a dna sequence, copy over and set any
794    * features on the peptide from the DNA.
795    *
796    * @param dna
797    * @param pep
798    * @param map
799    */
 
800  217 toggle private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
801    MapList map)
802    {
803    // BH 2019.01.25 nop?
804    // List<DBRefEntry> dnarefs = DBRefUtils.selectRefs(dna.getDBRefs(),
805    // DBRefSource.DNACODINGDBS);
806    // if (dnarefs != null)
807    // {
808    // // intersect with pep
809    // for (int d = 0, nd = dnarefs.size(); d < nd; d++)
810    // {
811    // Mapping mp = dnarefs.get(d).getMap();
812    // if (mp != null)
813    // {
814    // }
815    // }
816    // }
817  217 for (SequenceFeature sf : dna.getFeatures().getAllFeatures())
818    {
819  0 if (FeatureProperties.isCodingFeature(null, sf.getType()))
820    {
821    // if (map.intersectsFrom(sf[f].begin, sf[f].end))
822    {
823   
824    }
825    }
826    }
827    }
828   
829    /**
830    * Returns an alignment consisting of the reversed (and optionally
831    * complemented) sequences set in this object's constructor
832    *
833    * @param complement
834    * @return
835    */
 
836  1 toggle public AlignmentI reverseCdna(boolean complement)
837    {
838  1 int sSize = selection.size();
839  1 List<SequenceI> reversed = new ArrayList<>();
840  2 for (int s = 0; s < sSize; s++)
841    {
842  1 SequenceI newseq = reverseSequence(selection.get(s).getName(),
843    seqstring[s], complement);
844   
845  1 if (newseq != null)
846    {
847  1 reversed.add(newseq);
848    }
849    }
850   
851  1 SequenceI[] newseqs = reversed.toArray(new SequenceI[reversed.size()]);
852  1 AlignmentI al = new Alignment(newseqs);
853  1 ((Alignment) al).createDatasetAlignment();
854  1 return al;
855    }
856   
857    /**
858    * Returns a reversed, and optionally complemented, sequence. The new
859    * sequence's name is the original name with "|rev" or "|revcomp" appended.
860    * aAcCgGtT and DNA ambiguity codes are complemented, any other characters are
861    * left unchanged.
862    *
863    * @param seq
864    * @param complement
865    * @return
866    */
 
867  3 toggle public static SequenceI reverseSequence(String seqName, String sequence,
868    boolean complement)
869    {
870  3 String newName = seqName + "|rev" + (complement ? "comp" : "");
871  3 char[] originalSequence = sequence.toCharArray();
872  3 int length = originalSequence.length;
873  3 char[] reversedSequence = new char[length];
874  3 int bases = 0;
875  63 for (int i = 0; i < length; i++)
876    {
877  60 char c = complement ? getComplement(originalSequence[i])
878    : originalSequence[i];
879  60 reversedSequence[length - i - 1] = c;
880  60 if (!Comparison.isGap(c))
881    {
882  45 bases++;
883    }
884    }
885  3 SequenceI reversed = new Sequence(newName, reversedSequence, 1, bases);
886  3 return reversed;
887    }
888   
889    /**
890    * Answers the reverse complement of the input string
891    *
892    * @see #getComplement(char)
893    * @param s
894    * @return
895    */
 
896  36 toggle public static String reverseComplement(String s)
897    {
898  36 StringBuilder sb = new StringBuilder(s.length());
899  76 for (int i = s.length() - 1; i >= 0; i--)
900    {
901  40 sb.append(Dna.getComplement(s.charAt(i)));
902    }
903  36 return sb.toString();
904    }
905   
906    /**
907    * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
908    * are treated as on http://reverse-complement.com/. Anything else is left
909    * unchanged.
910    *
911    * @param c
912    * @return
913    */
 
914  106 toggle public static char getComplement(char c)
915    {
916  106 char result = c;
917  106 switch (c)
918    {
919  7 case '-':
920  0 case '.':
921  0 case ' ':
922  7 break;
923  2 case 'a':
924  2 result = 't';
925  2 break;
926  13 case 'A':
927  13 result = 'T';
928  13 break;
929  3 case 'c':
930  3 result = 'g';
931  3 break;
932  22 case 'C':
933  22 result = 'G';
934  22 break;
935  3 case 'g':
936  3 result = 'c';
937  3 break;
938  17 case 'G':
939  17 result = 'C';
940  17 break;
941  3 case 't':
942  3 result = 'a';
943  3 break;
944  6 case 'T':
945  6 result = 'A';
946  6 break;
947  1 case 'u':
948  1 result = 'a';
949  1 break;
950  2 case 'U':
951  2 result = 'A';
952  2 break;
953  2 case 'r':
954  2 result = 'y';
955  2 break;
956  1 case 'R':
957  1 result = 'Y';
958  1 break;
959  1 case 'y':
960  1 result = 'r';
961  1 break;
962  2 case 'Y':
963  2 result = 'R';
964  2 break;
965  2 case 'k':
966  2 result = 'm';
967  2 break;
968  1 case 'K':
969  1 result = 'M';
970  1 break;
971  1 case 'm':
972  1 result = 'k';
973  1 break;
974  2 case 'M':
975  2 result = 'K';
976  2 break;
977  2 case 'b':
978  2 result = 'v';
979  2 break;
980  1 case 'B':
981  1 result = 'V';
982  1 break;
983  1 case 'v':
984  1 result = 'b';
985  1 break;
986  2 case 'V':
987  2 result = 'B';
988  2 break;
989  2 case 'd':
990  2 result = 'h';
991  2 break;
992  1 case 'D':
993  1 result = 'H';
994  1 break;
995  1 case 'h':
996  1 result = 'd';
997  1 break;
998  2 case 'H':
999  2 result = 'D';
1000  2 break;
1001    }
1002   
1003  106 return result;
1004    }
1005    }
  • Report generated by OpenClover v 4.4.1 on Fri Dec 6 2024 13:54:25 GMT using coverage data from Fri Dec 6 2024 13:54:13 GMT.
  • OpenClover is free and open-source software.