2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.analysis;
23 import jalview.api.AlignViewportI;
24 import jalview.bin.Cache;
25 import jalview.datamodel.AlignedCodon;
26 import jalview.datamodel.AlignedCodonFrame;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.Annotation;
31 import jalview.datamodel.DBRefEntry;
32 import jalview.datamodel.DBRefSource;
33 import jalview.datamodel.FeatureProperties;
34 import jalview.datamodel.GraphLine;
35 import jalview.datamodel.Mapping;
36 import jalview.datamodel.Sequence;
37 import jalview.datamodel.SequenceFeature;
38 import jalview.datamodel.SequenceI;
39 import jalview.schemes.ResidueProperties;
40 import jalview.util.Comparison;
41 import jalview.util.DBRefUtils;
42 import jalview.util.MapList;
43 import jalview.util.ShiftList;
45 import java.util.ArrayList;
46 import java.util.Arrays;
47 import java.util.Comparator;
48 import java.util.List;
53 private static final String STOP_X = "X";
55 private static final Comparator<AlignedCodon> comparator = new CodonComparator();
58 * 'final' variables describe the inputs to the translation, which should not
61 final private List<SequenceI> selection;
63 final private String[] seqstring;
65 final private int[] contigs;
67 final private char gapChar;
69 final private AlignmentAnnotation[] annotations;
71 final private int dnaWidth;
73 final private Alignment dataset;
76 * Working variables for the translation.
78 * The width of the translation-in-progress protein alignment.
80 private int aaWidth = 0;
83 * This array will be built up so that position i holds the codon positions
84 * e.g. [7, 9, 10] that match column i (base 0) in the aligned translation.
85 * Note this implies a contract that if two codons do not align exactly, their
86 * translated products must occupy different column positions.
88 private AlignedCodon[] alignedCodons;
91 * Constructor given a viewport and the visible contigs.
94 * @param visibleContigs
96 public Dna(AlignViewportI viewport, int[] visibleContigs)
98 this.selection = Arrays.asList(viewport.getSequenceSelection());
99 this.seqstring = viewport.getViewAsString(true);
100 this.contigs = visibleContigs;
101 this.gapChar = viewport.getGapCharacter();
102 this.annotations = viewport.getAlignment().getAlignmentAnnotation();
103 this.dnaWidth = viewport.getAlignment().getWidth();
104 this.dataset = viewport.getAlignment().getDataset();
108 * Test whether codon positions cdp1 should align before, with, or after cdp2.
109 * Returns zero if all positions match (or either argument is null). Returns
110 * -1 if any position in the first codon precedes the corresponding position
111 * in the second codon. Else returns +1 (some position in the second codon
112 * precedes the corresponding position in the first).
114 * Note this is not necessarily symmetric, for example:
116 * <li>compareCodonPos([2,5,6], [3,4,5]) returns -1</li>
117 * <li>compareCodonPos([3,4,5], [2,5,6]) also returns -1</li>
124 public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
126 return comparator.compare(ac1, ac2);
127 // return jalview_2_8_2compare(ac1, ac2);
131 * Codon comparison up to Jalview 2.8.2. This rule is sequence order dependent
132 * - see http://issues.jalview.org/browse/JAL-1635
138 private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2)
140 if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
144 if (ac1.pos1 < ac2.pos1 || ac1.pos2 < ac2.pos2 || ac1.pos3 < ac2.pos3)
146 // one base in cdp1 precedes the corresponding base in the other codon
149 // one base in cdp1 appears after the corresponding base in the other codon.
157 public AlignmentI translateCdna()
159 AlignedCodonFrame acf = new AlignedCodonFrame();
161 alignedCodons = new AlignedCodon[dnaWidth];
164 int sSize = selection.size();
165 List<SequenceI> pepseqs = new ArrayList<SequenceI>();
166 for (s = 0; s < sSize; s++)
168 SequenceI newseq = translateCodingRegion(selection.get(s),
169 seqstring[s], acf, pepseqs);
174 SequenceI ds = newseq;
177 while (ds.getDatasetSequence() != null)
179 ds = ds.getDatasetSequence();
181 dataset.addSequence(ds);
186 SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]);
187 AlignmentI al = new Alignment(newseqs);
188 // ensure we look aligned.
190 // link the protein translation to the DNA dataset
191 al.setDataset(dataset);
192 translateAlignedAnnotations(al, acf);
193 al.addCodonFrame(acf);
198 * fake the collection of DbRefs with associated exon mappings to identify if
199 * a translation would generate distinct product in the currently selected
206 public static boolean canTranslate(SequenceI[] selection,
209 for (int gd = 0; gd < selection.length; gd++)
211 SequenceI dna = selection[gd];
212 DBRefEntry[] dnarefs = DBRefUtils
213 .selectRefs(dna.getDBRef(),
214 jalview.datamodel.DBRefSource.DNACODINGDBS);
217 // intersect with pep
218 List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
219 DBRefEntry[] refs = dna.getDBRef();
220 for (int d = 0; d < refs.length; d++)
222 if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
223 && refs[d].getMap().getMap().getFromRatio() == 3
224 && refs[d].getMap().getMap().getToRatio() == 1)
226 mappedrefs.add(refs[d]); // add translated protein maps
229 dnarefs = mappedrefs.toArray(new DBRefEntry[mappedrefs.size()]);
230 for (int d = 0; d < dnarefs.length; d++)
232 Mapping mp = dnarefs[d].getMap();
235 for (int vc = 0; vc < viscontigs.length; vc += 2)
237 int[] mpr = mp.locateMappedRange(viscontigs[vc],
252 * Translate nucleotide alignment annotations onto translated amino acid
253 * alignment using codon mapping codons
256 * the translated protein alignment
258 protected void translateAlignedAnnotations(AlignmentI al,
259 AlignedCodonFrame acf)
261 // Can only do this for columns with consecutive codons, or where
262 // annotation is sequence associated.
264 if (annotations != null)
266 for (AlignmentAnnotation annotation : annotations)
269 * Skip hidden or autogenerated annotation. Also (for now), RNA
270 * secondary structure annotation. If we want to show this against
271 * protein we need a smarter way to 'translate' without generating
272 * invalid (unbalanced) structure annotation.
274 if (annotation.autoCalculated || !annotation.visible
275 || annotation.isRNA())
281 Annotation[] anots = (annotation.annotations == null) ? null
282 : new Annotation[aSize];
285 for (int a = 0; a < aSize; a++)
287 // process through codon map.
288 if (a < alignedCodons.length && alignedCodons[a] != null
289 && alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2))
291 anots[a] = getCodonAnnotation(alignedCodons[a],
292 annotation.annotations);
297 AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label,
298 annotation.description, anots);
299 aa.graph = annotation.graph;
300 aa.graphGroup = annotation.graphGroup;
301 aa.graphHeight = annotation.graphHeight;
302 if (annotation.getThreshold() != null)
304 aa.setThreshold(new GraphLine(annotation
307 if (annotation.hasScore)
309 aa.setScore(annotation.getScore());
312 final SequenceI seqRef = annotation.sequenceRef;
315 SequenceI aaSeq = acf.getAaForDnaSeq(seqRef);
318 // aa.compactAnnotationArray(); // throw away alignment annotation
320 aa.setSequenceRef(aaSeq);
322 aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true);
323 aa.adjustForAlignment();
324 aaSeq.addAlignmentAnnotation(aa);
327 al.addAnnotation(aa);
332 private static Annotation getCodonAnnotation(AlignedCodon is,
333 Annotation[] annotations)
335 // Have a look at all the codon positions for annotation and put the first
336 // one found into the translated annotation pos.
338 Annotation annot = null;
339 for (int p = 1; p <= 3; p++)
341 int dnaCol = is.getBaseColumn(p);
342 if (annotations[dnaCol] != null)
346 annot = new Annotation(annotations[dnaCol]);
352 Annotation cpy = new Annotation(annotations[dnaCol]);
353 if (annot.colour == null)
355 annot.colour = cpy.colour;
357 if (annot.description == null || annot.description.length() == 0)
359 annot.description = cpy.description;
361 if (annot.displayCharacter == null)
363 annot.displayCharacter = cpy.displayCharacter;
365 if (annot.secondaryStructure == 0)
367 annot.secondaryStructure = cpy.secondaryStructure;
369 annot.value += cpy.value;
376 annot.value /= contrib;
382 * Translate a na sequence
385 * sequence displayed under viscontigs visible columns
387 * ORF read in some global alignment reference frame
389 * Definition of global ORF alignment reference frame
391 * @return sequence ready to be added to alignment.
393 protected SequenceI translateCodingRegion(SequenceI selection,
394 String seqstring, AlignedCodonFrame acf,
395 List<SequenceI> proteinSeqs)
397 List<int[]> skip = new ArrayList<int[]>();
398 int skipint[] = null;
399 ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
402 int[] scontigs = new int[contigs.length];
404 for (vc = 0; vc < contigs.length; vc += 2)
408 vismapping.addShift(npos, contigs[vc]);
413 vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1);
415 scontigs[vc] = contigs[vc];
416 scontigs[vc + 1] = contigs[vc + 1];
419 // allocate a roughly sized buffer for the protein sequence
420 StringBuilder protein = new StringBuilder(seqstring.length() / 2);
421 String seq = seqstring.replace('U', 'T').replace('u', 'T');
422 char codon[] = new char[3];
423 int cdp[] = new int[3];
429 for (npos = 0, nend = seq.length(); npos < nend; npos++)
431 if (!Comparison.isGap(seq.charAt(npos)))
433 cdp[rf] = npos; // store position
434 codon[rf++] = seq.charAt(npos); // store base
439 * Filled up a reading frame...
441 AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
442 String aa = ResidueProperties.codonTranslate(new String(codon));
444 final String gapString = String.valueOf(gapChar);
451 { alignedCodon.pos1, alignedCodon.pos3 /* cdp[0], cdp[2] */};
453 skipint[1] = alignedCodon.pos3; // cdp[2];
460 skipint[0] = vismapping.shift(skipint[0]);
461 skipint[1] = vismapping.shift(skipint[1]);
462 for (vc = 0; vc < scontigs.length;)
464 if (scontigs[vc + 1] < skipint[0])
466 // before skipint starts
470 if (scontigs[vc] > skipint[1])
472 // finished editing so
475 // Edit the contig list to include the skipped region which did
478 // from : s1 e1 s2 e2 s3 e3
479 // to s: s1 e1 s2 k0 k1 e2 s3 e3
480 // list increases by one unless one boundary (s2==k0 or e2==k1)
481 // matches, and decreases by one if skipint intersects whole
483 if (scontigs[vc] <= skipint[0])
485 if (skipint[0] == scontigs[vc])
487 // skipint at start of contig
488 // shift the start of this contig
489 if (scontigs[vc + 1] > skipint[1])
491 scontigs[vc] = skipint[1];
496 if (scontigs[vc + 1] == skipint[1])
499 t = new int[scontigs.length - 2];
502 System.arraycopy(scontigs, 0, t, 0, vc - 1);
504 if (vc + 2 < t.length)
506 System.arraycopy(scontigs, vc + 2, t, vc, t.length
513 // truncate contig to before the skipint region
514 scontigs[vc + 1] = skipint[0] - 1;
521 // scontig starts before start of skipint
522 if (scontigs[vc + 1] < skipint[1])
524 // skipint truncates end of scontig
525 scontigs[vc + 1] = skipint[0] - 1;
530 // divide region to new contigs
531 t = new int[scontigs.length + 2];
532 System.arraycopy(scontigs, 0, t, 0, vc + 1);
533 t[vc + 1] = skipint[0];
534 t[vc + 2] = skipint[1];
535 System.arraycopy(scontigs, vc + 1, t, vc + 3,
536 scontigs.length - (vc + 1));
546 if (aa.equals("STOP"))
552 boolean findpos = true;
556 * Compare this codon's base positions with those currently aligned to
557 * this column in the translation.
559 final int compareCodonPos = compareCodonPos(alignedCodon,
560 alignedCodons[aspos]);
561 switch (compareCodonPos)
566 * This codon should precede the mapped positions - need to insert a
567 * gap in all prior sequences.
569 insertAAGap(aspos, proteinSeqs);
576 * This codon belongs after the aligned codons at aspos. Prefix it
577 * with a gap and try the next position.
586 * Exact match - codon 'belongs' at this translated position.
593 if (alignedCodons[aspos] == null)
595 // mark this column as aligning to this aligned reading frame
596 alignedCodons[aspos] = alignedCodon;
598 else if (!alignedCodons[aspos].equals(alignedCodon))
600 throw new IllegalStateException("Tried to coalign "
601 + alignedCodons[aspos].toString() + " with "
602 + alignedCodon.toString());
604 if (aspos >= aaWidth)
606 // update maximum alignment width
609 // ready for next translated reading frame alignment position (if any)
615 SequenceI newseq = new Sequence(selection.getName(),
619 final String errMsg = "trimming contigs for incomplete terminal codon.";
620 if (Cache.log != null)
622 Cache.log.debug(errMsg);
626 System.err.println(errMsg);
628 // map and trim contigs to ORF region
629 vc = scontigs.length - 1;
630 lastnpos = vismapping.shift(lastnpos); // place npos in context of
631 // whole dna alignment (rather
632 // than visible contigs)
633 // incomplete ORF could be broken over one or two visible contig
635 while (vc >= 0 && scontigs[vc] > lastnpos)
637 if (vc > 0 && scontigs[vc - 1] > lastnpos)
643 // correct last interval in list.
644 scontigs[vc] = lastnpos;
648 if (vc > 0 && (vc + 1) < scontigs.length)
650 // truncate map list to just vc elements
651 int t[] = new int[vc + 1];
652 System.arraycopy(scontigs, 0, t, 0, vc + 1);
660 if (scontigs != null)
663 // map scontigs to actual sequence positions on selection
664 for (vc = 0; vc < scontigs.length; vc += 2)
666 scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
667 scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
668 if (scontigs[vc + 1] == selection.getEnd())
673 // trim trailing empty intervals.
674 if ((vc + 2) < scontigs.length)
676 int t[] = new int[vc + 2];
677 System.arraycopy(scontigs, 0, t, 0, vc + 2);
681 * delete intervals in scontigs which are not translated. 1. map skip
682 * into sequence position intervals 2. truncate existing ranges and add
683 * new ranges to exclude untranslated regions. if (skip.size()>0) {
684 * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {
685 * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
686 * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);
687 * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&
688 * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of
689 * range } else { // truncate range and create new one if necessary iv =
690 * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate
691 * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
692 * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
694 MapList map = new MapList(scontigs, new int[]
695 { 1, resSize }, 3, 1);
697 transferCodedFeatures(selection, newseq, map, null, null);
700 * Construct a dataset sequence for our new peptide.
702 SequenceI rseq = newseq.deriveSequence();
705 * Store a mapping (between the dataset sequences for the two
708 // SIDE-EFFECT: acf stores the aligned sequence reseq; to remove!
709 acf.addMap(selection, rseq, map);
713 // register the mapping somehow
719 * Insert a gap into the aligned proteins and the codon mapping array.
725 protected void insertAAGap(int pos,
726 List<SequenceI> proteinSeqs)
729 for (SequenceI seq : proteinSeqs)
731 seq.insertCharAt(pos, gapChar);
734 checkCodonFrameWidth();
740 * Shift from [pos] to the end one to the right, and null out [pos]
742 System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1,
743 alignedCodons.length - pos - 1);
744 alignedCodons[pos] = null;
749 * Check the codons array can accommodate a single insertion, if not resize
752 protected void checkCodonFrameWidth()
754 if (alignedCodons[alignedCodons.length - 1] != null)
757 * arraycopy insertion would bump a filled slot off the end, so expand.
759 AlignedCodon[] c = new AlignedCodon[alignedCodons.length + 10];
760 System.arraycopy(alignedCodons, 0, c, 0, alignedCodons.length);
766 * Given a peptide newly translated from a dna sequence, copy over and set any
767 * features on the peptide from the DNA. If featureTypes is null, all features
768 * on the dna sequence are searched (rather than just the displayed ones), and
769 * similarly for featureGroups.
774 * @param featureTypes
775 * hash whose keys are the displayed feature type strings
776 * @param featureGroups
777 * hash where keys are feature groups and values are Boolean objects
778 * indicating if they are displayed.
780 private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
781 MapList map, Map<String, Object> featureTypes,
782 Map<String, Boolean> featureGroups)
784 SequenceFeature[] sfs = dna.getSequenceFeatures();
786 DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
787 DBRefSource.DNACODINGDBS);
790 // intersect with pep
791 for (int d = 0; d < dnarefs.length; d++)
793 Mapping mp = dnarefs[d].getMap();
801 for (SequenceFeature sf : sfs)
803 fgstate = (featureGroups == null) ? null : featureGroups
804 .get(sf.featureGroup);
805 if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
806 && (fgstate == null || fgstate.booleanValue()))
808 if (FeatureProperties.isCodingFeature(null, sf.getType()))
810 // if (map.intersectsFrom(sf[f].begin, sf[f].end))