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.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;
44 import java.util.ArrayList;
45 import java.util.Arrays;
46 import java.util.Comparator;
47 import java.util.List;
52 private static final String STOP_ASTERIX = "*";
54 private static final Comparator<AlignedCodon> comparator = new CodonComparator();
57 * 'final' variables describe the inputs to the translation, which should not
60 final private List<SequenceI> selection;
62 final private String[] seqstring;
64 final private int[] contigs;
66 final private char gapChar;
68 final private AlignmentAnnotation[] annotations;
70 final private int dnaWidth;
72 final private Alignment dataset;
75 * Working variables for the translation.
77 * The width of the translation-in-progress protein alignment.
79 private int aaWidth = 0;
82 * This array will be built up so that position i holds the codon positions
83 * e.g. [7, 9, 10] that match column i (base 0) in the aligned translation.
84 * Note this implies a contract that if two codons do not align exactly, their
85 * translated products must occupy different column positions.
87 private AlignedCodon[] alignedCodons;
90 * Constructor given a viewport and the visible contigs.
93 * @param visibleContigs
95 public Dna(AlignViewportI viewport, int[] visibleContigs)
97 this.selection = Arrays.asList(viewport.getSequenceSelection());
98 this.seqstring = viewport.getViewAsString(true);
99 this.contigs = visibleContigs;
100 this.gapChar = viewport.getGapCharacter();
101 this.annotations = viewport.getAlignment().getAlignmentAnnotation();
102 this.dnaWidth = viewport.getAlignment().getWidth();
103 this.dataset = viewport.getAlignment().getDataset();
107 * Test whether codon positions cdp1 should align before, with, or after cdp2.
108 * Returns zero if all positions match (or either argument is null). Returns
109 * -1 if any position in the first codon precedes the corresponding position
110 * in the second codon. Else returns +1 (some position in the second codon
111 * precedes the corresponding position in the first).
113 * Note this is not necessarily symmetric, for example:
115 * <li>compareCodonPos([2,5,6], [3,4,5]) returns -1</li>
116 * <li>compareCodonPos([3,4,5], [2,5,6]) also returns -1</li>
123 public static final int compareCodonPos(AlignedCodon ac1, AlignedCodon ac2)
125 return comparator.compare(ac1, ac2);
126 // return jalview_2_8_2compare(ac1, ac2);
130 * Codon comparison up to Jalview 2.8.2. This rule is sequence order dependent
131 * - see http://issues.jalview.org/browse/JAL-1635
137 private static int jalview_2_8_2compare(AlignedCodon ac1, AlignedCodon ac2)
139 if (ac1 == null || ac2 == null || (ac1.equals(ac2)))
143 if (ac1.pos1 < ac2.pos1 || ac1.pos2 < ac2.pos2 || ac1.pos3 < ac2.pos3)
145 // one base in cdp1 precedes the corresponding base in the other codon
148 // one base in cdp1 appears after the corresponding base in the other codon.
156 public AlignmentI translateCdna()
158 AlignedCodonFrame acf = new AlignedCodonFrame();
160 alignedCodons = new AlignedCodon[dnaWidth];
163 int sSize = selection.size();
164 List<SequenceI> pepseqs = new ArrayList<SequenceI>();
165 for (s = 0; s < sSize; s++)
167 SequenceI newseq = translateCodingRegion(selection.get(s),
168 seqstring[s], acf, pepseqs);
173 SequenceI ds = newseq;
176 while (ds.getDatasetSequence() != null)
178 ds = ds.getDatasetSequence();
180 dataset.addSequence(ds);
185 SequenceI[] newseqs = pepseqs.toArray(new SequenceI[pepseqs.size()]);
186 AlignmentI al = new Alignment(newseqs);
187 // ensure we look aligned.
189 // link the protein translation to the DNA dataset
190 al.setDataset(dataset);
191 translateAlignedAnnotations(al, acf);
192 al.addCodonFrame(acf);
197 * fake the collection of DbRefs with associated exon mappings to identify if
198 * a translation would generate distinct product in the currently selected
205 public static boolean canTranslate(SequenceI[] selection,
208 for (int gd = 0; gd < selection.length; gd++)
210 SequenceI dna = selection[gd];
211 DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
212 jalview.datamodel.DBRefSource.DNACODINGDBS);
215 // intersect with pep
216 List<DBRefEntry> mappedrefs = new ArrayList<DBRefEntry>();
217 DBRefEntry[] refs = dna.getDBRef();
218 for (int d = 0; d < refs.length; d++)
220 if (refs[d].getMap() != null && refs[d].getMap().getMap() != null
221 && refs[d].getMap().getMap().getFromRatio() == 3
222 && refs[d].getMap().getMap().getToRatio() == 1)
224 mappedrefs.add(refs[d]); // add translated protein maps
227 dnarefs = mappedrefs.toArray(new DBRefEntry[mappedrefs.size()]);
228 for (int d = 0; d < dnarefs.length; d++)
230 Mapping mp = dnarefs[d].getMap();
233 for (int vc = 0; vc < viscontigs.length; vc += 2)
235 int[] mpr = mp.locateMappedRange(viscontigs[vc],
250 * Translate nucleotide alignment annotations onto translated amino acid
251 * alignment using codon mapping codons
254 * the translated protein alignment
256 protected void translateAlignedAnnotations(AlignmentI al,
257 AlignedCodonFrame acf)
259 // Can only do this for columns with consecutive codons, or where
260 // annotation is sequence associated.
262 if (annotations != null)
264 for (AlignmentAnnotation annotation : annotations)
267 * Skip hidden or autogenerated annotation. Also (for now), RNA
268 * secondary structure annotation. If we want to show this against
269 * protein we need a smarter way to 'translate' without generating
270 * invalid (unbalanced) structure annotation.
272 if (annotation.autoCalculated || !annotation.visible
273 || annotation.isRNA())
279 Annotation[] anots = (annotation.annotations == null) ? null
280 : new Annotation[aSize];
283 for (int a = 0; a < aSize; a++)
285 // process through codon map.
286 if (a < alignedCodons.length && alignedCodons[a] != null
287 && alignedCodons[a].pos1 == (alignedCodons[a].pos3 - 2))
289 anots[a] = getCodonAnnotation(alignedCodons[a],
290 annotation.annotations);
295 AlignmentAnnotation aa = new AlignmentAnnotation(annotation.label,
296 annotation.description, anots);
297 aa.graph = annotation.graph;
298 aa.graphGroup = annotation.graphGroup;
299 aa.graphHeight = annotation.graphHeight;
300 if (annotation.getThreshold() != null)
302 aa.setThreshold(new GraphLine(annotation.getThreshold()));
304 if (annotation.hasScore)
306 aa.setScore(annotation.getScore());
309 final SequenceI seqRef = annotation.sequenceRef;
312 SequenceI aaSeq = acf.getAaForDnaSeq(seqRef);
315 // aa.compactAnnotationArray(); // throw away alignment annotation
317 aa.setSequenceRef(aaSeq);
319 aa.createSequenceMapping(aaSeq, aaSeq.getStart(), true);
320 aa.adjustForAlignment();
321 aaSeq.addAlignmentAnnotation(aa);
324 al.addAnnotation(aa);
329 private static Annotation getCodonAnnotation(AlignedCodon is,
330 Annotation[] annotations)
332 // Have a look at all the codon positions for annotation and put the first
333 // one found into the translated annotation pos.
335 Annotation annot = null;
336 for (int p = 1; p <= 3; p++)
338 int dnaCol = is.getBaseColumn(p);
339 if (annotations[dnaCol] != null)
343 annot = new Annotation(annotations[dnaCol]);
349 Annotation cpy = new Annotation(annotations[dnaCol]);
350 if (annot.colour == null)
352 annot.colour = cpy.colour;
354 if (annot.description == null || annot.description.length() == 0)
356 annot.description = cpy.description;
358 if (annot.displayCharacter == null)
360 annot.displayCharacter = cpy.displayCharacter;
362 if (annot.secondaryStructure == 0)
364 annot.secondaryStructure = cpy.secondaryStructure;
366 annot.value += cpy.value;
373 annot.value /= contrib;
379 * Translate a na sequence
382 * sequence displayed under viscontigs visible columns
384 * ORF read in some global alignment reference frame
386 * Definition of global ORF alignment reference frame
388 * @return sequence ready to be added to alignment.
390 protected SequenceI translateCodingRegion(SequenceI selection,
391 String seqstring, AlignedCodonFrame acf,
392 List<SequenceI> proteinSeqs)
394 List<int[]> skip = new ArrayList<int[]>();
395 int skipint[] = null;
396 ShiftList vismapping = new ShiftList(); // map from viscontigs to seqstring
399 int[] scontigs = new int[contigs.length];
401 for (vc = 0; vc < contigs.length; vc += 2)
405 vismapping.addShift(npos, contigs[vc]);
410 vismapping.addShift(npos, contigs[vc] - contigs[vc - 1] + 1);
412 scontigs[vc] = contigs[vc];
413 scontigs[vc + 1] = contigs[vc + 1];
416 // allocate a roughly sized buffer for the protein sequence
417 StringBuilder protein = new StringBuilder(seqstring.length() / 2);
418 String seq = seqstring.replace('U', 'T').replace('u', 'T');
419 char codon[] = new char[3];
420 int cdp[] = new int[3];
426 for (npos = 0, nend = seq.length(); npos < nend; npos++)
428 if (!Comparison.isGap(seq.charAt(npos)))
430 cdp[rf] = npos; // store position
431 codon[rf++] = seq.charAt(npos); // store base
436 * Filled up a reading frame...
438 AlignedCodon alignedCodon = new AlignedCodon(cdp[0], cdp[1], cdp[2]);
439 String aa = ResidueProperties.codonTranslate(new String(codon));
441 final String gapString = String.valueOf(gapChar);
447 skipint = new int[] { alignedCodon.pos1, alignedCodon.pos3 /*
452 skipint[1] = alignedCodon.pos3; // cdp[2];
459 skipint[0] = vismapping.shift(skipint[0]);
460 skipint[1] = vismapping.shift(skipint[1]);
461 for (vc = 0; vc < scontigs.length;)
463 if (scontigs[vc + 1] < skipint[0])
465 // before skipint starts
469 if (scontigs[vc] > skipint[1])
471 // finished editing so
474 // Edit the contig list to include the skipped region which did
477 // from : s1 e1 s2 e2 s3 e3
478 // to s: s1 e1 s2 k0 k1 e2 s3 e3
479 // list increases by one unless one boundary (s2==k0 or e2==k1)
480 // matches, and decreases by one if skipint intersects whole
482 if (scontigs[vc] <= skipint[0])
484 if (skipint[0] == scontigs[vc])
486 // skipint at start of contig
487 // shift the start of this contig
488 if (scontigs[vc + 1] > skipint[1])
490 scontigs[vc] = skipint[1];
495 if (scontigs[vc + 1] == skipint[1])
498 t = new int[scontigs.length - 2];
501 System.arraycopy(scontigs, 0, t, 0, vc - 1);
503 if (vc + 2 < t.length)
505 System.arraycopy(scontigs, vc + 2, t, vc, t.length
512 // truncate contig to before the skipint region
513 scontigs[vc + 1] = skipint[0] - 1;
520 // scontig starts before start of skipint
521 if (scontigs[vc + 1] < skipint[1])
523 // skipint truncates end of scontig
524 scontigs[vc + 1] = skipint[0] - 1;
529 // divide region to new contigs
530 t = new int[scontigs.length + 2];
531 System.arraycopy(scontigs, 0, t, 0, vc + 1);
532 t[vc + 1] = skipint[0];
533 t[vc + 2] = skipint[1];
534 System.arraycopy(scontigs, vc + 1, t, vc + 3,
535 scontigs.length - (vc + 1));
545 if (aa.equals("STOP"))
551 boolean findpos = true;
555 * Compare this codon's base positions with those currently aligned to
556 * this column in the translation.
558 final int compareCodonPos = compareCodonPos(alignedCodon,
559 alignedCodons[aspos]);
560 switch (compareCodonPos)
565 * This codon should precede the mapped positions - need to insert a
566 * gap in all prior sequences.
568 insertAAGap(aspos, proteinSeqs);
575 * This codon belongs after the aligned codons at aspos. Prefix it
576 * with a gap and try the next position.
585 * Exact match - codon 'belongs' at this translated position.
592 if (alignedCodons[aspos] == null)
594 // mark this column as aligning to this aligned reading frame
595 alignedCodons[aspos] = alignedCodon;
597 else if (!alignedCodons[aspos].equals(alignedCodon))
599 throw new IllegalStateException("Tried to coalign "
600 + alignedCodons[aspos].toString() + " with "
601 + alignedCodon.toString());
603 if (aspos >= aaWidth)
605 // update maximum alignment width
608 // ready for next translated reading frame alignment position (if any)
614 SequenceI newseq = new Sequence(selection.getName(),
618 final String errMsg = "trimming contigs for incomplete terminal codon.";
619 System.err.println(errMsg);
620 // map and trim contigs to ORF region
621 vc = scontigs.length - 1;
622 lastnpos = vismapping.shift(lastnpos); // place npos in context of
623 // whole dna alignment (rather
624 // than visible contigs)
625 // incomplete ORF could be broken over one or two visible contig
627 while (vc >= 0 && scontigs[vc] > lastnpos)
629 if (vc > 0 && scontigs[vc - 1] > lastnpos)
635 // correct last interval in list.
636 scontigs[vc] = lastnpos;
640 if (vc > 0 && (vc + 1) < scontigs.length)
642 // truncate map list to just vc elements
643 int t[] = new int[vc + 1];
644 System.arraycopy(scontigs, 0, t, 0, vc + 1);
652 if (scontigs != null)
655 // map scontigs to actual sequence positions on selection
656 for (vc = 0; vc < scontigs.length; vc += 2)
658 scontigs[vc] = selection.findPosition(scontigs[vc]); // not from 1!
659 scontigs[vc + 1] = selection.findPosition(scontigs[vc + 1]); // exclusive
660 if (scontigs[vc + 1] == selection.getEnd())
665 // trim trailing empty intervals.
666 if ((vc + 2) < scontigs.length)
668 int t[] = new int[vc + 2];
669 System.arraycopy(scontigs, 0, t, 0, vc + 2);
673 * delete intervals in scontigs which are not translated. 1. map skip
674 * into sequence position intervals 2. truncate existing ranges and add
675 * new ranges to exclude untranslated regions. if (skip.size()>0) {
676 * Vector narange = new Vector(); for (vc=0; vc<scontigs.length; vc++) {
677 * narange.addElement(new int[] {scontigs[vc]}); } int sint=0,iv[]; vc =
678 * 0; while (sint<skip.size()) { skipint = (int[]) skip.elementAt(sint);
679 * do { iv = (int[]) narange.elementAt(vc); if (iv[0]>=skipint[0] &&
680 * iv[0]<=skipint[1]) { if (iv[0]==skipint[0]) { // delete beginning of
681 * range } else { // truncate range and create new one if necessary iv =
682 * (int[]) narange.elementAt(vc+1); if (iv[0]<=skipint[1]) { // truncate
683 * range iv[0] = skipint[1]; } else { } } } else if (iv[0]<skipint[0]) {
684 * iv = (int[]) narange.elementAt(vc+1); } } while (iv[0]) } }
686 MapList map = new MapList(scontigs, new int[] { 1, resSize }, 3, 1);
688 transferCodedFeatures(selection, newseq, map, null, null);
691 * Construct a dataset sequence for our new peptide.
693 SequenceI rseq = newseq.deriveSequence();
696 * Store a mapping (between the dataset sequences for the two
699 // SIDE-EFFECT: acf stores the aligned sequence reseq; to remove!
700 acf.addMap(selection, rseq, map);
704 // register the mapping somehow
710 * Insert a gap into the aligned proteins and the codon mapping array.
716 protected void insertAAGap(int pos, List<SequenceI> proteinSeqs)
719 for (SequenceI seq : proteinSeqs)
721 seq.insertCharAt(pos, gapChar);
724 checkCodonFrameWidth();
730 * Shift from [pos] to the end one to the right, and null out [pos]
732 System.arraycopy(alignedCodons, pos, alignedCodons, pos + 1,
733 alignedCodons.length - pos - 1);
734 alignedCodons[pos] = null;
739 * Check the codons array can accommodate a single insertion, if not resize
742 protected void checkCodonFrameWidth()
744 if (alignedCodons[alignedCodons.length - 1] != null)
747 * arraycopy insertion would bump a filled slot off the end, so expand.
749 AlignedCodon[] c = new AlignedCodon[alignedCodons.length + 10];
750 System.arraycopy(alignedCodons, 0, c, 0, alignedCodons.length);
756 * Given a peptide newly translated from a dna sequence, copy over and set any
757 * features on the peptide from the DNA. If featureTypes is null, all features
758 * on the dna sequence are searched (rather than just the displayed ones), and
759 * similarly for featureGroups.
764 * @param featureTypes
765 * hash whose keys are the displayed feature type strings
766 * @param featureGroups
767 * hash where keys are feature groups and values are Boolean objects
768 * indicating if they are displayed.
770 private static void transferCodedFeatures(SequenceI dna, SequenceI pep,
771 MapList map, Map<String, Object> featureTypes,
772 Map<String, Boolean> featureGroups)
774 SequenceFeature[] sfs = dna.getSequenceFeatures();
776 DBRefEntry[] dnarefs = DBRefUtils.selectRefs(dna.getDBRef(),
777 DBRefSource.DNACODINGDBS);
780 // intersect with pep
781 for (int d = 0; d < dnarefs.length; d++)
783 Mapping mp = dnarefs[d].getMap();
791 for (SequenceFeature sf : sfs)
793 fgstate = (featureGroups == null) ? null : featureGroups
794 .get(sf.featureGroup);
795 if ((featureTypes == null || featureTypes.containsKey(sf.getType()))
796 && (fgstate == null || fgstate.booleanValue()))
798 if (FeatureProperties.isCodingFeature(null, sf.getType()))
800 // if (map.intersectsFrom(sf[f].begin, sf[f].end))
811 * Returns an alignment consisting of the reversed (and optionally
812 * complemented) sequences set in this object's constructor
817 public AlignmentI reverseCdna(boolean complement)
819 int sSize = selection.size();
820 List<SequenceI> reversed = new ArrayList<SequenceI>();
821 for (int s = 0; s < sSize; s++)
823 SequenceI newseq = reverseSequence(selection.get(s).getName(),
824 seqstring[s], complement);
828 reversed.add(newseq);
832 SequenceI[] newseqs = reversed.toArray(new SequenceI[reversed.size()]);
833 AlignmentI al = new Alignment(newseqs);
834 ((Alignment) al).createDatasetAlignment();
839 * Returns a reversed, and optionally complemented, sequence. The new
840 * sequence's name is the original name with "|rev" or "|revcomp" appended.
841 * aAcCgGtT and DNA ambiguity codes are complemented, any other characters are
848 public static SequenceI reverseSequence(String seqName, String sequence,
851 String newName = seqName + "|rev" + (complement ? "comp" : "");
852 char[] originalSequence = sequence.toCharArray();
853 int length = originalSequence.length;
854 char[] reversedSequence = new char[length];
856 for (int i = 0; i < length; i++)
858 reversedSequence[length - i - 1] = complement ? getComplement(originalSequence[i])
859 : originalSequence[i];
861 SequenceI reversed = new Sequence(newName, reversedSequence, 1, length);
866 * Returns dna complement (preserving case) for aAcCgGtTuU. Ambiguity codes
867 * are treated as on http://reverse-complement.com/. Anything else is left
873 public static char getComplement(char c)