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.datamodel.AlignedCodon;
24 import jalview.datamodel.AlignedCodonFrame;
25 import jalview.datamodel.Alignment;
26 import jalview.datamodel.AlignmentAnnotation;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.DBRefEntry;
29 import jalview.datamodel.DBRefSource;
30 import jalview.datamodel.FeatureProperties;
31 import jalview.datamodel.Mapping;
32 import jalview.datamodel.SearchResults;
33 import jalview.datamodel.Sequence;
34 import jalview.datamodel.SequenceGroup;
35 import jalview.datamodel.SequenceI;
36 import jalview.schemes.ResidueProperties;
37 import jalview.util.DBRefUtils;
38 import jalview.util.MapList;
39 import jalview.util.MappingUtils;
41 import java.util.ArrayList;
42 import java.util.Arrays;
43 import java.util.Collection;
44 import java.util.HashMap;
45 import java.util.HashSet;
46 import java.util.Iterator;
47 import java.util.LinkedHashMap;
48 import java.util.LinkedHashSet;
49 import java.util.List;
51 import java.util.Map.Entry;
53 import java.util.TreeMap;
56 * grab bag of useful alignment manipulation operations Expect these to be
57 * refactored elsewhere at some point.
62 public class AlignmentUtils
66 * given an existing alignment, create a new alignment including all, or up to
67 * flankSize additional symbols from each sequence's dataset sequence
73 public static AlignmentI expandContext(AlignmentI core, int flankSize)
75 List<SequenceI> sq = new ArrayList<SequenceI>();
77 for (SequenceI s : core.getSequences())
79 SequenceI newSeq = s.deriveSequence();
80 final int newSeqStart = newSeq.getStart() - 1;
81 if (newSeqStart > maxoffset
82 && newSeq.getDatasetSequence().getStart() < s.getStart())
84 maxoffset = newSeqStart;
90 maxoffset = Math.min(maxoffset, flankSize);
94 * now add offset left and right to create an expanded alignment
96 for (SequenceI s : sq)
99 while (ds.getDatasetSequence() != null)
101 ds = ds.getDatasetSequence();
103 int s_end = s.findPosition(s.getStart() + s.getLength());
104 // find available flanking residues for sequence
105 int ustream_ds = s.getStart() - ds.getStart();
106 int dstream_ds = ds.getEnd() - s_end;
108 // build new flanked sequence
110 // compute gap padding to start of flanking sequence
111 int offset = maxoffset - ustream_ds;
113 // padding is gapChar x ( maxoffset - min(ustream_ds, flank)
116 if (flankSize < ustream_ds)
118 // take up to flankSize residues
119 offset = maxoffset - flankSize;
120 ustream_ds = flankSize;
122 if (flankSize <= dstream_ds)
124 dstream_ds = flankSize - 1;
127 // TODO use Character.toLowerCase to avoid creating String objects?
128 char[] upstream = new String(ds.getSequence(s.getStart() - 1
129 - ustream_ds, s.getStart() - 1)).toLowerCase().toCharArray();
130 char[] downstream = new String(ds.getSequence(s_end - 1, s_end
131 + dstream_ds)).toLowerCase().toCharArray();
132 char[] coreseq = s.getSequence();
133 char[] nseq = new char[offset + upstream.length + downstream.length
135 char c = core.getGapCharacter();
138 for (; p < offset; p++)
143 System.arraycopy(upstream, 0, nseq, p, upstream.length);
144 System.arraycopy(coreseq, 0, nseq, p + upstream.length,
146 System.arraycopy(downstream, 0, nseq, p + coreseq.length
147 + upstream.length, downstream.length);
148 s.setSequence(new String(nseq));
149 s.setStart(s.getStart() - ustream_ds);
150 s.setEnd(s_end + downstream.length);
152 AlignmentI newAl = new Alignment(sq.toArray(new SequenceI[0]));
153 for (SequenceI s : sq)
155 if (s.getAnnotation() != null)
157 for (AlignmentAnnotation aa : s.getAnnotation())
159 aa.adjustForAlignment(); // JAL-1712 fix
160 newAl.addAnnotation(aa);
164 newAl.setDataset(core.getDataset());
169 * Returns the index (zero-based position) of a sequence in an alignment, or
176 public static int getSequenceIndex(AlignmentI al, SequenceI seq)
180 for (SequenceI alSeq : al.getSequences())
193 * Returns a map of lists of sequences in the alignment, keyed by sequence
194 * name. For use in mapping between different alignment views of the same
197 * @see AlignmentI#getSequencesByName()
199 public static Map<String, List<SequenceI>> getSequencesByName(
202 Map<String, List<SequenceI>> theMap = new LinkedHashMap<String, List<SequenceI>>();
203 for (SequenceI seq : al.getSequences())
205 String name = seq.getName();
208 List<SequenceI> seqs = theMap.get(name);
211 seqs = new ArrayList<SequenceI>();
212 theMap.put(name, seqs);
221 * Build mapping of protein to cDNA alignment. Mappings are made between
222 * sequences where the cDNA translates to the protein sequence. Any new
223 * mappings are added to the protein alignment. Returns true if any mappings
224 * either already exist or were added, else false.
226 * @param proteinAlignment
227 * @param cdnaAlignment
230 public static boolean mapProteinToCdna(
231 final AlignmentI proteinAlignment,
232 final AlignmentI cdnaAlignment)
234 if (proteinAlignment == null || cdnaAlignment == null)
239 Set<SequenceI> mappedDna = new HashSet<SequenceI>();
240 Set<SequenceI> mappedProtein = new HashSet<SequenceI>();
243 * First pass - map sequences where cross-references exist. This include
244 * 1-to-many mappings to support, for example, variant cDNA.
246 boolean mappingPerformed = mapProteinToCdna(proteinAlignment,
247 cdnaAlignment, mappedDna, mappedProtein, true);
250 * Second pass - map sequences where no cross-references exist. This only
251 * does 1-to-1 mappings and assumes corresponding sequences are in the same
252 * order in the alignments.
254 mappingPerformed |= mapProteinToCdna(proteinAlignment, cdnaAlignment,
255 mappedDna, mappedProtein, false);
256 return mappingPerformed;
260 * Make mappings between compatible sequences (where the cDNA translation
261 * matches the protein).
263 * @param proteinAlignment
264 * @param cdnaAlignment
266 * a set of mapped DNA sequences (to add to)
267 * @param mappedProtein
268 * a set of mapped Protein sequences (to add to)
270 * if true, only map sequences where xrefs exist
273 protected static boolean mapProteinToCdna(
274 final AlignmentI proteinAlignment,
275 final AlignmentI cdnaAlignment, Set<SequenceI> mappedDna,
276 Set<SequenceI> mappedProtein, boolean xrefsOnly)
278 boolean mappingPerformed = false;
279 List<SequenceI> thisSeqs = proteinAlignment.getSequences();
280 for (SequenceI aaSeq : thisSeqs)
282 boolean proteinMapped = false;
283 AlignedCodonFrame acf = new AlignedCodonFrame();
285 for (SequenceI cdnaSeq : cdnaAlignment.getSequences())
288 * Always try to map if sequences have xref to each other; this supports
289 * variant cDNA or alternative splicing for a protein sequence.
291 * If no xrefs, try to map progressively, assuming that alignments have
292 * mappable sequences in corresponding order. These are not
293 * many-to-many, as that would risk mixing species with similar cDNA
296 if (xrefsOnly && !AlignmentUtils.haveCrossRef(aaSeq, cdnaSeq))
302 * Don't map non-xrefd sequences more than once each. This heuristic
303 * allows us to pair up similar sequences in ordered alignments.
306 && (mappedProtein.contains(aaSeq) || mappedDna
311 if (!mappingExists(proteinAlignment.getCodonFrames(),
312 aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
314 MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
317 acf.addMap(cdnaSeq, aaSeq, map);
318 mappingPerformed = true;
319 proteinMapped = true;
320 mappedDna.add(cdnaSeq);
321 mappedProtein.add(aaSeq);
327 proteinAlignment.addCodonFrame(acf);
330 return mappingPerformed;
334 * Answers true if the mappings include one between the given (dataset)
337 public static boolean mappingExists(Set<AlignedCodonFrame> set,
338 SequenceI aaSeq, SequenceI cdnaSeq)
342 for (AlignedCodonFrame acf : set)
344 if (cdnaSeq == acf.getDnaForAaSeq(aaSeq))
354 * Build a mapping (if possible) of a protein to a cDNA sequence. The cDNA
355 * must be three times the length of the protein, possibly after ignoring
356 * start and/or stop codons, and must translate to the protein. Returns null
357 * if no mapping is determined.
363 public static MapList mapProteinToCdna(SequenceI proteinSeq,
367 * Here we handle either dataset sequence set (desktop) or absent (applet).
368 * Use only the char[] form of the sequence to avoid creating possibly large
371 final SequenceI proteinDataset = proteinSeq.getDatasetSequence();
372 char[] aaSeqChars = proteinDataset != null ? proteinDataset
373 .getSequence() : proteinSeq.getSequence();
374 final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence();
375 char[] cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence()
376 : cdnaSeq.getSequence();
377 if (aaSeqChars == null || cdnaSeqChars == null)
383 * cdnaStart/End, proteinStartEnd are base 1 (for dataset sequence mapping)
385 final int mappedLength = 3 * aaSeqChars.length;
386 int cdnaLength = cdnaSeqChars.length;
388 int cdnaEnd = cdnaLength;
389 final int proteinStart = 1;
390 final int proteinEnd = aaSeqChars.length;
393 * If lengths don't match, try ignoring stop codon.
395 if (cdnaLength != mappedLength && cdnaLength > 2)
397 String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - 3, 3)
399 for (String stop : ResidueProperties.STOP)
401 if (lastCodon.equals(stop))
411 * If lengths still don't match, try ignoring start codon.
413 if (cdnaLength != mappedLength
415 && String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
417 ResidueProperties.START))
423 if (cdnaLength != mappedLength)
427 if (!translatesAs(cdnaSeqChars, cdnaStart - 1, aaSeqChars))
431 MapList map = new MapList(new int[]
432 { cdnaStart, cdnaEnd }, new int[]
433 { proteinStart, proteinEnd }, 3, 1);
438 * Test whether the given cdna sequence, starting at the given offset,
439 * translates to the given amino acid sequence, using the standard translation
440 * table. Designed to fail fast i.e. as soon as a mismatch position is found.
442 * @param cdnaSeqChars
447 protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,
451 for (int i = cdnaStart; i < cdnaSeqChars.length - 2
452 && aaResidue < aaSeqChars.length; i += 3, aaResidue++)
454 String codon = String.valueOf(cdnaSeqChars, i, 3);
455 final String translated = ResidueProperties.codonTranslate(
458 * ? allow X in protein to match untranslatable in dna ?
460 final char aaRes = aaSeqChars[aaResidue];
461 if ((translated == null || "STOP".equals(translated)) && aaRes == 'X')
465 if (translated == null
466 || !(aaRes == translated.charAt(0)))
469 // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
470 // + codon + "(" + translated + ") != " + aaRes));
474 // fail if we didn't match all of the aa sequence
475 return (aaResidue == aaSeqChars.length);
479 * Align sequence 'seq' to match the alignment of a mapped sequence. Note this
480 * currently assumes that we are aligning cDNA to match protein.
483 * the sequence to be realigned
485 * the alignment whose sequence alignment is to be 'copied'
487 * character string represent a gap in the realigned sequence
488 * @param preserveUnmappedGaps
489 * @param preserveMappedGaps
490 * @return true if the sequence was realigned, false if it could not be
492 public static boolean alignSequenceAs(SequenceI seq, AlignmentI al,
493 String gap, boolean preserveMappedGaps,
494 boolean preserveUnmappedGaps)
497 * Get any mappings from the source alignment to the target (dataset) sequence.
499 // TODO there may be one AlignedCodonFrame per dataset sequence, or one with
500 // all mappings. Would it help to constrain this?
501 List<AlignedCodonFrame> mappings = al.getCodonFrame(seq);
502 if (mappings == null || mappings.isEmpty())
508 * Locate the aligned source sequence whose dataset sequence is mapped. We
509 * just take the first match here (as we can't align cDNA like more than one
512 SequenceI alignFrom = null;
513 AlignedCodonFrame mapping = null;
514 for (AlignedCodonFrame mp : mappings)
516 alignFrom = mp.findAlignedSequence(seq.getDatasetSequence(), al);
517 if (alignFrom != null)
524 if (alignFrom == null)
528 alignSequenceAs(seq, alignFrom, mapping, gap, al.getGapCharacter(),
529 preserveMappedGaps, preserveUnmappedGaps);
534 * Align sequence 'alignTo' the same way as 'alignFrom', using the mapping to
535 * match residues and codons. Flags control whether existing gaps in unmapped
536 * (intron) and mapped (exon) regions are preserved or not. Gaps linking intro
537 * and exon are only retained if both flags are set.
544 * @param preserveUnmappedGaps
545 * @param preserveMappedGaps
547 public static void alignSequenceAs(SequenceI alignTo,
549 AlignedCodonFrame mapping, String myGap, char sourceGap,
550 boolean preserveMappedGaps, boolean preserveUnmappedGaps)
552 // TODO generalise to work for Protein-Protein, dna-dna, dna-protein
553 final char[] thisSeq = alignTo.getSequence();
554 final char[] thatAligned = alignFrom.getSequence();
555 StringBuilder thisAligned = new StringBuilder(2 * thisSeq.length);
557 // aligned and dataset sequence positions, all base zero
561 int basesWritten = 0;
562 char myGapChar = myGap.charAt(0);
563 int ratio = myGap.length();
566 * Traverse the aligned protein sequence.
568 int sourceGapMappedLength = 0;
569 boolean inExon = false;
570 for (char sourceChar : thatAligned)
572 if (sourceChar == sourceGap)
574 sourceGapMappedLength += ratio;
579 * Found a residue. Locate its mapped codon (start) position.
582 // Note mapping positions are base 1, our sequence positions base 0
583 int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom,
585 if (mappedPos == null)
588 * Abort realignment if unmapped protein. Or could ignore it??
590 System.err.println("Can't align: no codon mapping to residue "
591 + sourceDsPos + "(" + sourceChar + ")");
595 int mappedCodonStart = mappedPos[0]; // position (1...) of codon start
596 int mappedCodonEnd = mappedPos[mappedPos.length - 1]; // codon end pos
597 StringBuilder trailingCopiedGap = new StringBuilder();
600 * Copy dna sequence up to and including this codon. Optionally, include
601 * gaps before the codon starts (in introns) and/or after the codon starts
604 * Note this only works for 'linear' splicing, not reverse or interleaved.
605 * But then 'align dna as protein' doesn't make much sense otherwise.
607 int intronLength = 0;
608 while (basesWritten < mappedCodonEnd && thisSeqPos < thisSeq.length)
610 final char c = thisSeq[thisSeqPos++];
615 if (basesWritten < mappedCodonStart)
618 * Found an unmapped (intron) base. First add in any preceding gaps
621 if (preserveUnmappedGaps && trailingCopiedGap.length() > 0)
623 thisAligned.append(trailingCopiedGap.toString());
624 intronLength += trailingCopiedGap.length();
625 trailingCopiedGap = new StringBuilder();
632 final boolean startOfCodon = basesWritten == mappedCodonStart;
633 int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
634 preserveUnmappedGaps, sourceGapMappedLength, inExon,
635 trailingCopiedGap.length(), intronLength, startOfCodon);
636 for (int i = 0; i < gapsToAdd; i++)
638 thisAligned.append(myGapChar);
640 sourceGapMappedLength = 0;
643 thisAligned.append(c);
644 trailingCopiedGap = new StringBuilder();
648 if (inExon && preserveMappedGaps)
650 trailingCopiedGap.append(myGapChar);
652 else if (!inExon && preserveUnmappedGaps)
654 trailingCopiedGap.append(myGapChar);
661 * At end of protein sequence. Copy any remaining dna sequence, optionally
662 * including (intron) gaps. We do not copy trailing gaps in protein.
664 while (thisSeqPos < thisSeq.length)
666 final char c = thisSeq[thisSeqPos++];
667 if (c != myGapChar || preserveUnmappedGaps)
669 thisAligned.append(c);
674 * All done aligning, set the aligned sequence.
676 alignTo.setSequence(new String(thisAligned));
680 * Helper method to work out how many gaps to insert when realigning.
682 * @param preserveMappedGaps
683 * @param preserveUnmappedGaps
684 * @param sourceGapMappedLength
686 * @param trailingCopiedGap
687 * @param intronLength
688 * @param startOfCodon
691 protected static int calculateGapsToInsert(boolean preserveMappedGaps,
692 boolean preserveUnmappedGaps, int sourceGapMappedLength,
693 boolean inExon, int trailingGapLength,
694 int intronLength, final boolean startOfCodon)
700 * Reached start of codon. Ignore trailing gaps in intron unless we are
701 * preserving gaps in both exon and intron. Ignore them anyway if the
702 * protein alignment introduces a gap at least as large as the intronic
705 if (inExon && !preserveMappedGaps)
707 trailingGapLength = 0;
709 if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps))
711 trailingGapLength = 0;
715 gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
719 if (intronLength + trailingGapLength <= sourceGapMappedLength)
721 gapsToAdd = sourceGapMappedLength - intronLength;
725 gapsToAdd = Math.min(intronLength + trailingGapLength
726 - sourceGapMappedLength, trailingGapLength);
733 * second or third base of codon; check for any gaps in dna
735 if (!preserveMappedGaps)
737 trailingGapLength = 0;
739 gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
745 * Returns a list of sequences mapped from the given sequences and aligned
746 * (gapped) in the same way. For example, the cDNA for aligned protein, where
747 * a single gap in protein generates three gaps in cDNA.
750 * @param gapCharacter
754 public static List<SequenceI> getAlignedTranslation(
755 List<SequenceI> sequences, char gapCharacter,
756 Set<AlignedCodonFrame> mappings)
758 List<SequenceI> alignedSeqs = new ArrayList<SequenceI>();
760 for (SequenceI seq : sequences)
762 List<SequenceI> mapped = getAlignedTranslation(seq, gapCharacter,
764 alignedSeqs.addAll(mapped);
770 * Returns sequences aligned 'like' the source sequence, as mapped by the
771 * given mappings. Normally we expect zero or one 'mapped' sequences, but this
772 * will support 1-to-many as well.
775 * @param gapCharacter
779 protected static List<SequenceI> getAlignedTranslation(SequenceI seq,
780 char gapCharacter, Set<AlignedCodonFrame> mappings)
782 List<SequenceI> result = new ArrayList<SequenceI>();
783 for (AlignedCodonFrame mapping : mappings)
785 if (mapping.involvesSequence(seq))
787 SequenceI mapped = getAlignedTranslation(seq, gapCharacter, mapping);
798 * Returns the translation of 'seq' (as held in the mapping) with
799 * corresponding alignment (gaps).
802 * @param gapCharacter
806 protected static SequenceI getAlignedTranslation(SequenceI seq,
807 char gapCharacter, AlignedCodonFrame mapping)
809 String gap = String.valueOf(gapCharacter);
810 boolean toDna = false;
812 SequenceI mapTo = mapping.getDnaForAaSeq(seq);
815 // mapping is from protein to nucleotide
817 // should ideally get gap count ratio from mapping
818 gap = String.valueOf(new char[]
819 { gapCharacter, gapCharacter, gapCharacter });
823 // mapping is from nucleotide to protein
824 mapTo = mapping.getAaForDnaSeq(seq);
827 StringBuilder newseq = new StringBuilder(seq.getLength()
830 int residueNo = 0; // in seq, base 1
831 int[] phrase = new int[fromRatio];
832 int phraseOffset = 0;
834 boolean first = true;
835 final Sequence alignedSeq = new Sequence("", "");
837 for (char c : seq.getSequence())
839 if (c == gapCharacter)
842 if (gapWidth >= fromRatio)
850 phrase[phraseOffset++] = residueNo + 1;
851 if (phraseOffset == fromRatio)
854 * Have read a whole codon (or protein residue), now translate: map
855 * source phrase to positions in target sequence add characters at
856 * these positions to newseq Note mapping positions are base 1, our
857 * sequence positions base 0.
859 SearchResults sr = new SearchResults();
860 for (int pos : phrase)
862 mapping.markMappedRegion(seq, pos, sr);
864 newseq.append(sr.toString());
868 // Hack: Copy sequence dataset, name and description from
869 // SearchResults.match[0].sequence
870 // TODO? carry over sequence names from original 'complement'
872 SequenceI mappedTo = sr.getResultSequence(0);
873 alignedSeq.setName(mappedTo.getName());
874 alignedSeq.setDescription(mappedTo.getDescription());
875 alignedSeq.setDatasetSequence(mappedTo);
882 alignedSeq.setSequence(newseq.toString());
887 * Realigns the given protein to match the alignment of the dna, using codon
888 * mappings to translate aligned codon positions to protein residues.
891 * the alignment whose sequences are realigned by this method
893 * the dna alignment whose alignment we are 'copying'
894 * @return the number of sequences that were realigned
896 public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)
898 Set<AlignedCodonFrame> mappings = protein.getCodonFrames();
901 * Map will hold, for each aligned codon position e.g. [3, 5, 6], a map of
902 * {dnaSequence, {proteinSequence, codonProduct}} at that position. The
903 * comparator keeps the codon positions ordered.
905 Map<AlignedCodon, Map<SequenceI, String>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, String>>(
906 new CodonComparator());
907 for (SequenceI dnaSeq : dna.getSequences())
909 for (AlignedCodonFrame mapping : mappings)
911 Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
912 SequenceI prot = mapping.findAlignedSequence(
913 dnaSeq.getDatasetSequence(), protein);
916 addCodonPositions(dnaSeq, prot, protein.getGapCharacter(),
917 seqMap, alignedCodons);
921 return alignProteinAs(protein, alignedCodons);
925 * Update the aligned protein sequences to match the codon alignments given in
929 * @param alignedCodons
930 * an ordered map of codon positions (columns), with sequence/peptide
931 * values present in each column
934 protected static int alignProteinAs(AlignmentI protein,
935 Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
938 * Prefill aligned sequences with gaps before inserting aligned protein
941 int alignedWidth = alignedCodons.size();
942 char[] gaps = new char[alignedWidth];
943 Arrays.fill(gaps, protein.getGapCharacter());
944 String allGaps = String.valueOf(gaps);
945 for (SequenceI seq : protein.getSequences())
947 seq.setSequence(allGaps);
951 for (AlignedCodon codon : alignedCodons.keySet())
953 final Map<SequenceI, String> columnResidues = alignedCodons.get(codon);
954 for (Entry<SequenceI, String> entry : columnResidues
957 // place translated codon at its column position in sequence
958 entry.getKey().getSequence()[column] = entry.getValue().charAt(0);
966 * Populate the map of aligned codons by traversing the given sequence
967 * mapping, locating the aligned positions of mapped codons, and adding those
968 * positions and their translation products to the map.
971 * the aligned sequence we are mapping from
973 * the sequence to be aligned to the codons
975 * the gap character in the dna sequence
977 * a mapping to a sequence translation
978 * @param alignedCodons
979 * the map we are building up
981 static void addCodonPositions(SequenceI dna, SequenceI protein,
984 Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
986 Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
987 while (codons.hasNext())
989 AlignedCodon codon = codons.next();
990 Map<SequenceI, String> seqProduct = alignedCodons.get(codon);
991 if (seqProduct == null)
993 seqProduct = new HashMap<SequenceI, String>();
994 alignedCodons.put(codon, seqProduct);
996 seqProduct.put(protein, codon.product);
1001 * Returns true if a cDNA/Protein mapping either exists, or could be made,
1002 * between at least one pair of sequences in the two alignments. Currently,
1005 * <li>One alignment must be nucleotide, and the other protein</li>
1006 * <li>At least one pair of sequences must be already mapped, or mappable</li>
1007 * <li>Mappable means the nucleotide translation matches the protein sequence</li>
1008 * <li>The translation may ignore start and stop codons if present in the
1016 public static boolean isMappable(AlignmentI al1, AlignmentI al2)
1019 * Require one nucleotide and one protein
1021 if (al1.isNucleotide() == al2.isNucleotide())
1025 AlignmentI dna = al1.isNucleotide() ? al1 : al2;
1026 AlignmentI protein = dna == al1 ? al2 : al1;
1027 Set<AlignedCodonFrame> mappings = protein.getCodonFrames();
1028 for (SequenceI dnaSeq : dna.getSequences())
1030 for (SequenceI proteinSeq : protein.getSequences())
1032 if (isMappable(dnaSeq, proteinSeq, mappings))
1042 * Returns true if the dna sequence is mapped, or could be mapped, to the
1050 public static boolean isMappable(SequenceI dnaSeq, SequenceI proteinSeq,
1051 Set<AlignedCodonFrame> mappings)
1053 SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
1054 SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
1055 : proteinSeq.getDatasetSequence();
1060 for (AlignedCodonFrame mapping : mappings) {
1061 if ( proteinDs == mapping.getAaForDnaSeq(dnaDs)) {
1067 * Just try to make a mapping (it is not yet stored), test whether
1070 return mapProteinToCdna(proteinDs, dnaDs) != null;
1074 * Finds any reference annotations associated with the sequences in
1075 * sequenceScope, that are not already added to the alignment, and adds them
1076 * to the 'candidates' map. Also populates a lookup table of annotation
1077 * labels, keyed by calcId, for use in constructing tooltips or the like.
1079 * @param sequenceScope
1080 * the sequences to scan for reference annotations
1081 * @param labelForCalcId
1082 * (optional) map to populate with label for calcId
1084 * map to populate with annotations for sequence
1086 * the alignment to check for presence of annotations
1088 public static void findAddableReferenceAnnotations(
1089 List<SequenceI> sequenceScope, Map<String, String> labelForCalcId,
1090 final Map<SequenceI, List<AlignmentAnnotation>> candidates,
1093 if (sequenceScope == null)
1099 * For each sequence in scope, make a list of any annotations on the
1100 * underlying dataset sequence which are not already on the alignment.
1102 * Add to a map of { alignmentSequence, <List of annotations to add> }
1104 for (SequenceI seq : sequenceScope)
1106 SequenceI dataset = seq.getDatasetSequence();
1107 if (dataset == null)
1111 AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
1112 if (datasetAnnotations == null)
1116 final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
1117 for (AlignmentAnnotation dsann : datasetAnnotations)
1120 * Find matching annotations on the alignment. If none is found, then
1121 * add this annotation to the list of 'addable' annotations for this
1124 final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
1125 .findAnnotations(seq, dsann.getCalcId(),
1127 if (!matchedAlignmentAnnotations.iterator().hasNext())
1130 if (labelForCalcId != null)
1132 labelForCalcId.put(dsann.getCalcId(), dsann.label);
1137 * Save any addable annotations for this sequence
1139 if (!result.isEmpty())
1141 candidates.put(seq, result);
1147 * Adds annotations to the top of the alignment annotations, in the same order
1148 * as their related sequences.
1150 * @param annotations
1151 * the annotations to add
1153 * the alignment to add them to
1154 * @param selectionGroup
1155 * current selection group (or null if none)
1157 public static void addReferenceAnnotations(
1158 Map<SequenceI, List<AlignmentAnnotation>> annotations,
1159 final AlignmentI alignment, final SequenceGroup selectionGroup)
1161 for (SequenceI seq : annotations.keySet())
1163 for (AlignmentAnnotation ann : annotations.get(seq))
1165 AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
1167 int endRes = ann.annotations.length;
1168 if (selectionGroup != null)
1170 startRes = selectionGroup.getStartRes();
1171 endRes = selectionGroup.getEndRes();
1173 copyAnn.restrict(startRes, endRes);
1176 * Add to the sequence (sets copyAnn.datasetSequence), unless the
1177 * original annotation is already on the sequence.
1179 if (!seq.hasAnnotation(ann))
1181 seq.addAlignmentAnnotation(copyAnn);
1184 copyAnn.adjustForAlignment();
1185 // add to the alignment and set visible
1186 alignment.addAnnotation(copyAnn);
1187 copyAnn.visible = true;
1193 * Set visibility of alignment annotations of specified types (labels), for
1194 * specified sequences. This supports controls like
1195 * "Show all secondary structure", "Hide all Temp factor", etc.
1197 * @al the alignment to scan for annotations
1199 * the types (labels) of annotations to be updated
1200 * @param forSequences
1201 * if not null, only annotations linked to one of these sequences are
1202 * in scope for update; if null, acts on all sequence annotations
1204 * if this flag is true, 'types' is ignored (label not checked)
1206 * if true, set visibility on, else set off
1208 public static void showOrHideSequenceAnnotations(AlignmentI al,
1209 Collection<String> types, List<SequenceI> forSequences,
1210 boolean anyType, boolean doShow)
1212 for (AlignmentAnnotation aa : al
1213 .getAlignmentAnnotation())
1215 if (anyType || types.contains(aa.label))
1217 if ((aa.sequenceRef != null)
1218 && (forSequences == null || forSequences
1219 .contains(aa.sequenceRef)))
1221 aa.visible = doShow;
1228 * Returns true if either sequence has a cross-reference to the other
1234 public static boolean haveCrossRef(SequenceI seq1, SequenceI seq2)
1236 // Note: moved here from class CrossRef as the latter class has dependencies
1237 // not availability to the applet's classpath
1238 return hasCrossRef(seq1, seq2) || hasCrossRef(seq2, seq1);
1242 * Returns true if seq1 has a cross-reference to seq2. Currently this assumes
1243 * that sequence name is structured as Source|AccessionId.
1249 public static boolean hasCrossRef(SequenceI seq1, SequenceI seq2)
1251 if (seq1 == null || seq2 == null)
1255 String name = seq2.getName();
1256 final DBRefEntry[] xrefs = seq1.getDBRef();
1259 for (DBRefEntry xref : xrefs)
1261 String xrefName = xref.getSource() + "|" + xref.getAccessionId();
1262 // case-insensitive test, consistent with DBRefEntry.equalRef()
1263 if (xrefName.equalsIgnoreCase(name))
1273 * Constructs an alignment consisting of the mapped exon regions in the given
1274 * nucleotide sequences, and updates mappings to match.
1277 * aligned dna sequences
1279 * from dna to protein; these are replaced with new mappings
1280 * @return an alignment whose sequences are the exon-only parts of the dna
1281 * sequences (or null if no exons are found)
1283 public static AlignmentI makeExonAlignment(SequenceI[] dna,
1284 Set<AlignedCodonFrame> mappings)
1286 Set<AlignedCodonFrame> newMappings = new LinkedHashSet<AlignedCodonFrame>();
1287 List<SequenceI> exonSequences = new ArrayList<SequenceI>();
1289 for (SequenceI dnaSeq : dna)
1291 final SequenceI ds = dnaSeq.getDatasetSequence();
1292 List<AlignedCodonFrame> seqMappings = MappingUtils
1293 .findMappingsForSequence(ds, mappings);
1294 for (AlignedCodonFrame acf : seqMappings)
1296 AlignedCodonFrame newMapping = new AlignedCodonFrame();
1297 final List<SequenceI> mappedExons = makeExonSequences(ds, acf,
1299 if (!mappedExons.isEmpty())
1301 exonSequences.addAll(mappedExons);
1302 newMappings.add(newMapping);
1306 AlignmentI al = new Alignment(
1307 exonSequences.toArray(new SequenceI[exonSequences.size()]));
1308 al.setDataset(null);
1311 * Replace the old mappings with the new ones
1314 mappings.addAll(newMappings);
1320 * Helper method to make exon-only sequences and populate their mappings to
1323 * For example, if ggCCaTTcGAg has mappings [3, 4, 6, 7, 9, 10] to protein
1324 * then generate a sequence CCTTGA with mapping [1, 6] to the same protein
1327 * Typically eukaryotic dna will include exons encoding for a single peptide
1328 * sequence i.e. return a single result. Bacterial dna may have overlapping
1329 * exon mappings coding for multiple peptides so return multiple results
1330 * (example EMBL KF591215).
1333 * a dna dataset sequence
1335 * containing one or more mappings of the sequence to protein
1337 * the new mapping to populate, from the exon-only sequences to their
1338 * mapped protein sequences
1341 protected static List<SequenceI> makeExonSequences(SequenceI dnaSeq,
1342 AlignedCodonFrame mapping, AlignedCodonFrame newMapping)
1344 List<SequenceI> exonSequences = new ArrayList<SequenceI>();
1345 List<Mapping> seqMappings = mapping.getMappingsForSequence(dnaSeq);
1346 final char[] dna = dnaSeq.getSequence();
1347 for (Mapping seqMapping : seqMappings)
1349 StringBuilder newSequence = new StringBuilder(dnaSeq.getLength());
1352 * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
1354 final List<int[]> dnaExonRanges = seqMapping.getMap().getFromRanges();
1355 for (int[] range : dnaExonRanges)
1357 for (int pos = range[0]; pos <= range[1]; pos++)
1359 newSequence.append(dna[pos - 1]);
1363 SequenceI exon = new Sequence(dnaSeq.getName(),
1364 newSequence.toString());
1367 * Locate any xrefs to CDS database on the protein product and attach to
1368 * the CDS sequence. Also add as a sub-token of the sequence name.
1370 // default to "CDS" if we can't locate an actual gene id
1371 String cdsAccId = FeatureProperties
1372 .getCodingFeature(DBRefSource.EMBL);
1373 DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(seqMapping.getTo()
1374 .getDBRef(), DBRefSource.CODINGDBS);
1375 if (cdsRefs != null)
1377 for (DBRefEntry cdsRef : cdsRefs)
1379 exon.addDBRef(new DBRefEntry(cdsRef));
1380 cdsAccId = cdsRef.getAccessionId();
1383 exon.setName(exon.getName() + "|" + cdsAccId);
1384 exon.createDatasetSequence();
1387 * Build new mappings - from the same protein regions, but now to
1390 List<int[]> exonRange = new ArrayList<int[]>();
1391 exonRange.add(new int[]
1392 { 1, newSequence.length() });
1393 MapList map = new MapList(exonRange, seqMapping.getMap()
1396 newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
1397 MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
1398 newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);
1400 exonSequences.add(exon);
1402 return exonSequences;