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.commands.RemoveGapColCommand;
24 import jalview.datamodel.AlignedCodon;
25 import jalview.datamodel.AlignedCodonFrame;
26 import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
27 import jalview.datamodel.Alignment;
28 import jalview.datamodel.AlignmentAnnotation;
29 import jalview.datamodel.AlignmentI;
30 import jalview.datamodel.DBRefEntry;
31 import jalview.datamodel.GeneLociI;
32 import jalview.datamodel.IncompleteCodonException;
33 import jalview.datamodel.Mapping;
34 import jalview.datamodel.Sequence;
35 import jalview.datamodel.SequenceFeature;
36 import jalview.datamodel.SequenceGroup;
37 import jalview.datamodel.SequenceI;
38 import jalview.datamodel.features.SequenceFeatures;
39 import jalview.io.gff.SequenceOntologyI;
40 import jalview.schemes.ResidueProperties;
41 import jalview.util.Comparison;
42 import jalview.util.DBRefUtils;
43 import jalview.util.IntRangeComparator;
44 import jalview.util.MapList;
45 import jalview.util.MappingUtils;
47 import java.util.ArrayList;
48 import java.util.Arrays;
49 import java.util.Collection;
50 import java.util.Collections;
51 import java.util.HashMap;
52 import java.util.HashSet;
53 import java.util.Iterator;
54 import java.util.LinkedHashMap;
55 import java.util.List;
57 import java.util.Map.Entry;
58 import java.util.NoSuchElementException;
60 import java.util.SortedMap;
61 import java.util.TreeMap;
64 * grab bag of useful alignment manipulation operations Expect these to be
65 * refactored elsewhere at some point.
70 public class AlignmentUtils
72 private static final int CODON_LENGTH = 3;
74 private static final String SEQUENCE_VARIANT = "sequence_variant:";
77 * the 'id' attribute is provided for variant features fetched from
78 * Ensembl using its REST service with JSON format
80 public static final String VARIANT_ID = "id";
83 * A data model to hold the 'normal' base value at a position, and an optional
84 * sequence variant feature
86 static final class DnaVariant
90 SequenceFeature variant;
92 DnaVariant(String nuc)
98 DnaVariant(String nuc, SequenceFeature var)
104 public String getSource()
106 return variant == null ? null : variant.getFeatureGroup();
110 * toString for aid in the debugger only
113 public String toString()
115 return base + ":" + (variant == null ? "" : variant.getDescription());
120 * given an existing alignment, create a new alignment including all, or up to
121 * flankSize additional symbols from each sequence's dataset sequence
127 public static AlignmentI expandContext(AlignmentI core, int flankSize)
129 List<SequenceI> sq = new ArrayList<>();
131 for (SequenceI s : core.getSequences())
133 SequenceI newSeq = s.deriveSequence();
134 final int newSeqStart = newSeq.getStart() - 1;
135 if (newSeqStart > maxoffset
136 && newSeq.getDatasetSequence().getStart() < s.getStart())
138 maxoffset = newSeqStart;
144 maxoffset = Math.min(maxoffset, flankSize);
148 * now add offset left and right to create an expanded alignment
150 for (SequenceI s : sq)
153 while (ds.getDatasetSequence() != null)
155 ds = ds.getDatasetSequence();
157 int s_end = s.findPosition(s.getStart() + s.getLength());
158 // find available flanking residues for sequence
159 int ustream_ds = s.getStart() - ds.getStart();
160 int dstream_ds = ds.getEnd() - s_end;
162 // build new flanked sequence
164 // compute gap padding to start of flanking sequence
165 int offset = maxoffset - ustream_ds;
167 // padding is gapChar x ( maxoffset - min(ustream_ds, flank)
170 if (flankSize < ustream_ds)
172 // take up to flankSize residues
173 offset = maxoffset - flankSize;
174 ustream_ds = flankSize;
176 if (flankSize <= dstream_ds)
178 dstream_ds = flankSize - 1;
181 // TODO use Character.toLowerCase to avoid creating String objects?
182 char[] upstream = new String(ds
183 .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
184 .toLowerCase().toCharArray();
185 char[] downstream = new String(
186 ds.getSequence(s_end - 1, s_end + dstream_ds)).toLowerCase()
188 char[] coreseq = s.getSequence();
189 char[] nseq = new char[offset + upstream.length + downstream.length
191 char c = core.getGapCharacter();
194 for (; p < offset; p++)
199 System.arraycopy(upstream, 0, nseq, p, upstream.length);
200 System.arraycopy(coreseq, 0, nseq, p + upstream.length,
202 System.arraycopy(downstream, 0, nseq,
203 p + coreseq.length + upstream.length, downstream.length);
204 s.setSequence(new String(nseq));
205 s.setStart(s.getStart() - ustream_ds);
206 s.setEnd(s_end + downstream.length);
208 AlignmentI newAl = new jalview.datamodel.Alignment(
209 sq.toArray(new SequenceI[0]));
210 for (SequenceI s : sq)
212 if (s.getAnnotation() != null)
214 for (AlignmentAnnotation aa : s.getAnnotation())
216 aa.adjustForAlignment(); // JAL-1712 fix
217 newAl.addAnnotation(aa);
221 newAl.setDataset(core.getDataset());
226 * Returns the index (zero-based position) of a sequence in an alignment, or
233 public static int getSequenceIndex(AlignmentI al, SequenceI seq)
237 for (SequenceI alSeq : al.getSequences())
250 * Returns a map of lists of sequences in the alignment, keyed by sequence
251 * name. For use in mapping between different alignment views of the same
254 * @see jalview.datamodel.AlignmentI#getSequencesByName()
256 public static Map<String, List<SequenceI>> getSequencesByName(
259 Map<String, List<SequenceI>> theMap = new LinkedHashMap<>();
260 for (SequenceI seq : al.getSequences())
262 String name = seq.getName();
265 List<SequenceI> seqs = theMap.get(name);
268 seqs = new ArrayList<>();
269 theMap.put(name, seqs);
278 * Build mapping of protein to cDNA alignment. Mappings are made between
279 * sequences where the cDNA translates to the protein sequence. Any new
280 * mappings are added to the protein alignment. Returns true if any mappings
281 * either already exist or were added, else false.
283 * @param proteinAlignment
284 * @param cdnaAlignment
287 public static boolean mapProteinAlignmentToCdna(
288 final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment)
290 if (proteinAlignment == null || cdnaAlignment == null)
295 Set<SequenceI> mappedDna = new HashSet<>();
296 Set<SequenceI> mappedProtein = new HashSet<>();
299 * First pass - map sequences where cross-references exist. This include
300 * 1-to-many mappings to support, for example, variant cDNA.
302 boolean mappingPerformed = mapProteinToCdna(proteinAlignment,
303 cdnaAlignment, mappedDna, mappedProtein, true);
306 * Second pass - map sequences where no cross-references exist. This only
307 * does 1-to-1 mappings and assumes corresponding sequences are in the same
308 * order in the alignments.
310 mappingPerformed |= mapProteinToCdna(proteinAlignment, cdnaAlignment,
311 mappedDna, mappedProtein, false);
312 return mappingPerformed;
316 * Make mappings between compatible sequences (where the cDNA translation
317 * matches the protein).
319 * @param proteinAlignment
320 * @param cdnaAlignment
322 * a set of mapped DNA sequences (to add to)
323 * @param mappedProtein
324 * a set of mapped Protein sequences (to add to)
326 * if true, only map sequences where xrefs exist
329 protected static boolean mapProteinToCdna(
330 final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment,
331 Set<SequenceI> mappedDna, Set<SequenceI> mappedProtein,
334 boolean mappingExistsOrAdded = false;
335 List<SequenceI> thisSeqs = proteinAlignment.getSequences();
336 for (SequenceI aaSeq : thisSeqs)
338 boolean proteinMapped = false;
339 AlignedCodonFrame acf = new AlignedCodonFrame();
341 for (SequenceI cdnaSeq : cdnaAlignment.getSequences())
344 * Always try to map if sequences have xref to each other; this supports
345 * variant cDNA or alternative splicing for a protein sequence.
347 * If no xrefs, try to map progressively, assuming that alignments have
348 * mappable sequences in corresponding order. These are not
349 * many-to-many, as that would risk mixing species with similar cDNA
352 if (xrefsOnly && !AlignmentUtils.haveCrossRef(aaSeq, cdnaSeq))
358 * Don't map non-xrefd sequences more than once each. This heuristic
359 * allows us to pair up similar sequences in ordered alignments.
361 if (!xrefsOnly && (mappedProtein.contains(aaSeq)
362 || mappedDna.contains(cdnaSeq)))
366 if (mappingExists(proteinAlignment.getCodonFrames(),
367 aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
369 mappingExistsOrAdded = true;
373 MapList map = mapCdnaToProtein(aaSeq, cdnaSeq);
376 acf.addMap(cdnaSeq, aaSeq, map);
377 mappingExistsOrAdded = true;
378 proteinMapped = true;
379 mappedDna.add(cdnaSeq);
380 mappedProtein.add(aaSeq);
386 proteinAlignment.addCodonFrame(acf);
389 return mappingExistsOrAdded;
393 * Answers true if the mappings include one between the given (dataset)
396 protected static boolean mappingExists(List<AlignedCodonFrame> mappings,
397 SequenceI aaSeq, SequenceI cdnaSeq)
399 if (mappings != null)
401 for (AlignedCodonFrame acf : mappings)
403 if (cdnaSeq == acf.getDnaForAaSeq(aaSeq))
413 * Builds a mapping (if possible) of a cDNA to a protein sequence.
415 * <li>first checks if the cdna translates exactly to the protein
417 * <li>else checks for translation after removing a STOP codon</li>
418 * <li>else checks for translation after removing a START codon</li>
419 * <li>if that fails, inspect CDS features on the cDNA sequence</li>
421 * Returns null if no mapping is determined.
424 * the aligned protein sequence
426 * the aligned cdna sequence
429 public static MapList mapCdnaToProtein(SequenceI proteinSeq,
433 * Here we handle either dataset sequence set (desktop) or absent (applet).
434 * Use only the char[] form of the sequence to avoid creating possibly large
437 final SequenceI proteinDataset = proteinSeq.getDatasetSequence();
438 char[] aaSeqChars = proteinDataset != null
439 ? proteinDataset.getSequence()
440 : proteinSeq.getSequence();
441 final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence();
442 char[] cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence()
443 : cdnaSeq.getSequence();
444 if (aaSeqChars == null || cdnaSeqChars == null)
450 * cdnaStart/End, proteinStartEnd are base 1 (for dataset sequence mapping)
452 final int mappedLength = CODON_LENGTH * aaSeqChars.length;
453 int cdnaLength = cdnaSeqChars.length;
454 int cdnaStart = cdnaSeq.getStart();
455 int cdnaEnd = cdnaSeq.getEnd();
456 final int proteinStart = proteinSeq.getStart();
457 final int proteinEnd = proteinSeq.getEnd();
460 * If lengths don't match, try ignoring stop codon (if present)
462 if (cdnaLength != mappedLength && cdnaLength > 2)
464 String lastCodon = String.valueOf(cdnaSeqChars,
465 cdnaLength - CODON_LENGTH, CODON_LENGTH).toUpperCase();
466 for (String stop : ResidueProperties.STOP_CODONS)
468 if (lastCodon.equals(stop))
470 cdnaEnd -= CODON_LENGTH;
471 cdnaLength -= CODON_LENGTH;
478 * If lengths still don't match, try ignoring start codon.
481 if (cdnaLength != mappedLength && cdnaLength > 2
482 && String.valueOf(cdnaSeqChars, 0, CODON_LENGTH).toUpperCase()
483 .equals(ResidueProperties.START))
485 startOffset += CODON_LENGTH;
486 cdnaStart += CODON_LENGTH;
487 cdnaLength -= CODON_LENGTH;
490 if (translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
493 * protein is translation of dna (+/- start/stop codons)
495 MapList map = new MapList(new int[] { cdnaStart, cdnaEnd },
497 { proteinStart, proteinEnd }, CODON_LENGTH, 1);
502 * translation failed - try mapping CDS annotated regions of dna
504 return mapCdsToProtein(cdnaSeq, proteinSeq);
508 * Test whether the given cdna sequence, starting at the given offset,
509 * translates to the given amino acid sequence, using the standard translation
510 * table. Designed to fail fast i.e. as soon as a mismatch position is found.
512 * @param cdnaSeqChars
517 protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,
520 if (cdnaSeqChars == null || aaSeqChars == null)
526 int dnaPos = cdnaStart;
527 for (; dnaPos < cdnaSeqChars.length - 2
528 && aaPos < aaSeqChars.length; dnaPos += CODON_LENGTH, aaPos++)
530 String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
531 final String translated = ResidueProperties.codonTranslate(codon);
534 * allow * in protein to match untranslatable in dna
536 final char aaRes = aaSeqChars[aaPos];
537 if ((translated == null || ResidueProperties.STOP.equals(translated))
542 if (translated == null || !(aaRes == translated.charAt(0)))
545 // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
546 // + codon + "(" + translated + ") != " + aaRes));
552 * check we matched all of the protein sequence
554 if (aaPos != aaSeqChars.length)
560 * check we matched all of the dna except
561 * for optional trailing STOP codon
563 if (dnaPos == cdnaSeqChars.length)
567 if (dnaPos == cdnaSeqChars.length - CODON_LENGTH)
569 String codon = String.valueOf(cdnaSeqChars, dnaPos, CODON_LENGTH);
570 if (ResidueProperties.STOP
571 .equals(ResidueProperties.codonTranslate(codon)))
580 * Align sequence 'seq' to match the alignment of a mapped sequence. Note this
581 * currently assumes that we are aligning cDNA to match protein.
584 * the sequence to be realigned
586 * the alignment whose sequence alignment is to be 'copied'
588 * character string represent a gap in the realigned sequence
589 * @param preserveUnmappedGaps
590 * @param preserveMappedGaps
591 * @return true if the sequence was realigned, false if it could not be
593 public static boolean alignSequenceAs(SequenceI seq, AlignmentI al,
594 String gap, boolean preserveMappedGaps,
595 boolean preserveUnmappedGaps)
598 * Get any mappings from the source alignment to the target (dataset)
601 // TODO there may be one AlignedCodonFrame per dataset sequence, or one with
602 // all mappings. Would it help to constrain this?
603 List<AlignedCodonFrame> mappings = al.getCodonFrame(seq);
604 if (mappings == null || mappings.isEmpty())
610 * Locate the aligned source sequence whose dataset sequence is mapped. We
611 * just take the first match here (as we can't align like more than one
614 SequenceI alignFrom = null;
615 AlignedCodonFrame mapping = null;
616 for (AlignedCodonFrame mp : mappings)
618 alignFrom = mp.findAlignedSequence(seq, al);
619 if (alignFrom != null)
626 if (alignFrom == null)
630 alignSequenceAs(seq, alignFrom, mapping, gap, al.getGapCharacter(),
631 preserveMappedGaps, preserveUnmappedGaps);
636 * Align sequence 'alignTo' the same way as 'alignFrom', using the mapping to
637 * match residues and codons. Flags control whether existing gaps in unmapped
638 * (intron) and mapped (exon) regions are preserved or not. Gaps between
639 * intron and exon are only retained if both flags are set.
646 * @param preserveUnmappedGaps
647 * @param preserveMappedGaps
649 public static void alignSequenceAs(SequenceI alignTo, SequenceI alignFrom,
650 AlignedCodonFrame mapping, String myGap, char sourceGap,
651 boolean preserveMappedGaps, boolean preserveUnmappedGaps)
653 // TODO generalise to work for Protein-Protein, dna-dna, dna-protein
655 // aligned and dataset sequence positions, all base zero
659 int basesWritten = 0;
660 char myGapChar = myGap.charAt(0);
661 int ratio = myGap.length();
663 int fromOffset = alignFrom.getStart() - 1;
664 int toOffset = alignTo.getStart() - 1;
665 int sourceGapMappedLength = 0;
666 boolean inExon = false;
667 final int toLength = alignTo.getLength();
668 final int fromLength = alignFrom.getLength();
669 StringBuilder thisAligned = new StringBuilder(2 * toLength);
672 * Traverse the 'model' aligned sequence
674 for (int i = 0; i < fromLength; i++)
676 char sourceChar = alignFrom.getCharAt(i);
677 if (sourceChar == sourceGap)
679 sourceGapMappedLength += ratio;
684 * Found a non-gap character. Locate its mapped region if any.
687 // Note mapping positions are base 1, our sequence positions base 0
688 int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom,
689 sourceDsPos + fromOffset);
690 if (mappedPos == null)
693 * unmapped position; treat like a gap
695 sourceGapMappedLength += ratio;
696 // System.err.println("Can't align: no codon mapping to residue "
697 // + sourceDsPos + "(" + sourceChar + ")");
702 int mappedCodonStart = mappedPos[0]; // position (1...) of codon start
703 int mappedCodonEnd = mappedPos[mappedPos.length - 1]; // codon end pos
704 StringBuilder trailingCopiedGap = new StringBuilder();
707 * Copy dna sequence up to and including this codon. Optionally, include
708 * gaps before the codon starts (in introns) and/or after the codon starts
711 * Note this only works for 'linear' splicing, not reverse or interleaved.
712 * But then 'align dna as protein' doesn't make much sense otherwise.
714 int intronLength = 0;
715 while (basesWritten + toOffset < mappedCodonEnd
716 && thisSeqPos < toLength)
718 final char c = alignTo.getCharAt(thisSeqPos++);
722 int sourcePosition = basesWritten + toOffset;
723 if (sourcePosition < mappedCodonStart)
726 * Found an unmapped (intron) base. First add in any preceding gaps
729 if (preserveUnmappedGaps && trailingCopiedGap.length() > 0)
731 thisAligned.append(trailingCopiedGap.toString());
732 intronLength += trailingCopiedGap.length();
733 trailingCopiedGap = new StringBuilder();
740 final boolean startOfCodon = sourcePosition == mappedCodonStart;
741 int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
742 preserveUnmappedGaps, sourceGapMappedLength, inExon,
743 trailingCopiedGap.length(), intronLength, startOfCodon);
744 for (int k = 0; k < gapsToAdd; k++)
746 thisAligned.append(myGapChar);
748 sourceGapMappedLength = 0;
751 thisAligned.append(c);
752 trailingCopiedGap = new StringBuilder();
756 if (inExon && preserveMappedGaps)
758 trailingCopiedGap.append(myGapChar);
760 else if (!inExon && preserveUnmappedGaps)
762 trailingCopiedGap.append(myGapChar);
769 * At end of model aligned sequence. Copy any remaining target sequence, optionally
770 * including (intron) gaps.
772 while (thisSeqPos < toLength)
774 final char c = alignTo.getCharAt(thisSeqPos++);
775 if (c != myGapChar || preserveUnmappedGaps)
777 thisAligned.append(c);
779 sourceGapMappedLength--;
783 * finally add gaps to pad for any trailing source gaps or
784 * unmapped characters
786 if (preserveUnmappedGaps)
788 while (sourceGapMappedLength > 0)
790 thisAligned.append(myGapChar);
791 sourceGapMappedLength--;
796 * All done aligning, set the aligned sequence.
798 alignTo.setSequence(new String(thisAligned));
802 * Helper method to work out how many gaps to insert when realigning.
804 * @param preserveMappedGaps
805 * @param preserveUnmappedGaps
806 * @param sourceGapMappedLength
808 * @param trailingCopiedGap
809 * @param intronLength
810 * @param startOfCodon
813 protected static int calculateGapsToInsert(boolean preserveMappedGaps,
814 boolean preserveUnmappedGaps, int sourceGapMappedLength,
815 boolean inExon, int trailingGapLength, int intronLength,
816 final boolean startOfCodon)
822 * Reached start of codon. Ignore trailing gaps in intron unless we are
823 * preserving gaps in both exon and intron. Ignore them anyway if the
824 * protein alignment introduces a gap at least as large as the intronic
827 if (inExon && !preserveMappedGaps)
829 trailingGapLength = 0;
831 if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps))
833 trailingGapLength = 0;
837 gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
841 if (intronLength + trailingGapLength <= sourceGapMappedLength)
843 gapsToAdd = sourceGapMappedLength - intronLength;
847 gapsToAdd = Math.min(
848 intronLength + trailingGapLength - sourceGapMappedLength,
856 * second or third base of codon; check for any gaps in dna
858 if (!preserveMappedGaps)
860 trailingGapLength = 0;
862 gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
868 * Realigns the given protein to match the alignment of the dna, using codon
869 * mappings to translate aligned codon positions to protein residues.
872 * the alignment whose sequences are realigned by this method
874 * the dna alignment whose alignment we are 'copying'
875 * @return the number of sequences that were realigned
877 public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)
879 if (protein.isNucleotide() || !dna.isNucleotide())
881 System.err.println("Wrong alignment type in alignProteinAsDna");
884 List<SequenceI> unmappedProtein = new ArrayList<>();
885 Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = buildCodonColumnsMap(
886 protein, dna, unmappedProtein);
887 return alignProteinAs(protein, alignedCodons, unmappedProtein);
891 * Realigns the given dna to match the alignment of the protein, using codon
892 * mappings to translate aligned peptide positions to codons.
894 * Always produces a padded CDS alignment.
897 * the alignment whose sequences are realigned by this method
899 * the protein alignment whose alignment we are 'copying'
900 * @return the number of sequences that were realigned
902 public static int alignCdsAsProtein(AlignmentI dna, AlignmentI protein)
904 if (protein.isNucleotide() || !dna.isNucleotide())
906 System.err.println("Wrong alignment type in alignProteinAsDna");
909 // todo: implement this
910 List<AlignedCodonFrame> mappings = protein.getCodonFrames();
911 int alignedCount = 0;
912 int width = 0; // alignment width for padding CDS
913 for (SequenceI dnaSeq : dna.getSequences())
915 if (alignCdsSequenceAsProtein(dnaSeq, protein, mappings,
916 dna.getGapCharacter()))
920 width = Math.max(dnaSeq.getLength(), width);
924 for (SequenceI dnaSeq : dna.getSequences())
926 oldwidth = dnaSeq.getLength();
927 diff = width - oldwidth;
930 dnaSeq.insertCharAt(oldwidth, diff, dna.getGapCharacter());
937 * Helper method to align (if possible) the dna sequence to match the
938 * alignment of a mapped protein sequence. This is currently limited to
939 * handling coding sequence only.
947 static boolean alignCdsSequenceAsProtein(SequenceI cdsSeq,
948 AlignmentI protein, List<AlignedCodonFrame> mappings,
951 SequenceI cdsDss = cdsSeq.getDatasetSequence();
955 .println("alignCdsSequenceAsProtein needs aligned sequence!");
959 List<AlignedCodonFrame> dnaMappings = MappingUtils
960 .findMappingsForSequence(cdsSeq, mappings);
961 for (AlignedCodonFrame mapping : dnaMappings)
963 SequenceI peptide = mapping.findAlignedSequence(cdsSeq, protein);
966 final int peptideLength = peptide.getLength();
967 Mapping map = mapping.getMappingBetween(cdsSeq, peptide);
970 MapList mapList = map.getMap();
971 if (map.getTo() == peptide.getDatasetSequence())
973 mapList = mapList.getInverse();
975 final int cdsLength = cdsDss.getLength();
976 int mappedFromLength = MappingUtils.getLength(mapList
978 int mappedToLength = MappingUtils
979 .getLength(mapList.getToRanges());
980 boolean addStopCodon = (cdsLength == mappedFromLength
981 * CODON_LENGTH + CODON_LENGTH)
982 || (peptide.getDatasetSequence()
983 .getLength() == mappedFromLength - 1);
984 if (cdsLength != mappedToLength && !addStopCodon)
986 System.err.println(String.format(
987 "Can't align cds as protein (length mismatch %d/%d): %s",
988 cdsLength, mappedToLength, cdsSeq.getName()));
992 * pre-fill the aligned cds sequence with gaps
994 char[] alignedCds = new char[peptideLength * CODON_LENGTH
995 + (addStopCodon ? CODON_LENGTH : 0)];
996 Arrays.fill(alignedCds, gapChar);
999 * walk over the aligned peptide sequence and insert mapped
1000 * codons for residues in the aligned cds sequence
1002 int copiedBases = 0;
1003 int cdsStart = cdsDss.getStart();
1004 int proteinPos = peptide.getStart() - 1;
1007 for (int col = 0; col < peptideLength; col++)
1009 char residue = peptide.getCharAt(col);
1011 if (Comparison.isGap(residue))
1013 cdsCol += CODON_LENGTH;
1018 int[] codon = mapList.locateInTo(proteinPos, proteinPos);
1021 // e.g. incomplete start codon, X in peptide
1022 cdsCol += CODON_LENGTH;
1026 for (int j = codon[0]; j <= codon[1]; j++)
1028 char mappedBase = cdsDss.getCharAt(j - cdsStart);
1029 alignedCds[cdsCol++] = mappedBase;
1037 * append stop codon if not mapped from protein,
1038 * closing it up to the end of the mapped sequence
1040 if (copiedBases == cdsLength - CODON_LENGTH)
1042 for (int i = alignedCds.length - 1; i >= 0; i--)
1044 if (!Comparison.isGap(alignedCds[i]))
1046 cdsCol = i + 1; // gap just after end of sequence
1050 for (int i = cdsLength - CODON_LENGTH; i < cdsLength; i++)
1052 alignedCds[cdsCol++] = cdsDss.getCharAt(i);
1055 cdsSeq.setSequence(new String(alignedCds));
1064 * Builds a map whose key is an aligned codon position (3 alignment column
1065 * numbers base 0), and whose value is a map from protein sequence to each
1066 * protein's peptide residue for that codon. The map generates an ordering of
1067 * the codons, and allows us to read off the peptides at each position in
1068 * order to assemble 'aligned' protein sequences.
1071 * the protein alignment
1073 * the coding dna alignment
1074 * @param unmappedProtein
1075 * any unmapped proteins are added to this list
1078 protected static Map<AlignedCodon, Map<SequenceI, AlignedCodon>> buildCodonColumnsMap(
1079 AlignmentI protein, AlignmentI dna,
1080 List<SequenceI> unmappedProtein)
1083 * maintain a list of any proteins with no mappings - these will be
1084 * rendered 'as is' in the protein alignment as we can't align them
1086 unmappedProtein.addAll(protein.getSequences());
1088 List<AlignedCodonFrame> mappings = protein.getCodonFrames();
1091 * Map will hold, for each aligned codon position e.g. [3, 5, 6], a map of
1092 * {dnaSequence, {proteinSequence, codonProduct}} at that position. The
1093 * comparator keeps the codon positions ordered.
1095 Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<>(
1096 new CodonComparator());
1098 for (SequenceI dnaSeq : dna.getSequences())
1100 for (AlignedCodonFrame mapping : mappings)
1102 SequenceI prot = mapping.findAlignedSequence(dnaSeq, protein);
1105 Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
1106 addCodonPositions(dnaSeq, prot, protein.getGapCharacter(), seqMap,
1108 unmappedProtein.remove(prot);
1114 * Finally add any unmapped peptide start residues (e.g. for incomplete
1115 * codons) as if at the codon position before the second residue
1117 // TODO resolve JAL-2022 so this fudge can be removed
1118 int mappedSequenceCount = protein.getHeight() - unmappedProtein.size();
1119 addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount);
1121 return alignedCodons;
1125 * Scans for any protein mapped from position 2 (meaning unmapped start
1126 * position e.g. an incomplete codon), and synthesizes a 'codon' for it at the
1127 * preceding position in the alignment
1129 * @param alignedCodons
1130 * the codon-to-peptide map
1131 * @param mappedSequenceCount
1132 * the number of distinct sequences in the map
1134 protected static void addUnmappedPeptideStarts(
1135 Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
1136 int mappedSequenceCount)
1138 // TODO delete this ugly hack once JAL-2022 is resolved
1139 // i.e. we can model startPhase > 0 (incomplete start codon)
1141 List<SequenceI> sequencesChecked = new ArrayList<>();
1142 AlignedCodon lastCodon = null;
1143 Map<SequenceI, AlignedCodon> toAdd = new HashMap<>();
1145 for (Entry<AlignedCodon, Map<SequenceI, AlignedCodon>> entry : alignedCodons
1148 for (Entry<SequenceI, AlignedCodon> sequenceCodon : entry.getValue()
1151 SequenceI seq = sequenceCodon.getKey();
1152 if (sequencesChecked.contains(seq))
1156 sequencesChecked.add(seq);
1157 AlignedCodon codon = sequenceCodon.getValue();
1158 if (codon.peptideCol > 1)
1161 "Problem mapping protein with >1 unmapped start positions: "
1164 else if (codon.peptideCol == 1)
1167 * first position (peptideCol == 0) was unmapped - add it
1169 if (lastCodon != null)
1171 AlignedCodon firstPeptide = new AlignedCodon(lastCodon.pos1,
1172 lastCodon.pos2, lastCodon.pos3,
1173 String.valueOf(seq.getCharAt(0)), 0);
1174 toAdd.put(seq, firstPeptide);
1179 * unmapped residue at start of alignment (no prior column) -
1180 * 'insert' at nominal codon [0, 0, 0]
1182 AlignedCodon firstPeptide = new AlignedCodon(0, 0, 0,
1183 String.valueOf(seq.getCharAt(0)), 0);
1184 toAdd.put(seq, firstPeptide);
1187 if (sequencesChecked.size() == mappedSequenceCount)
1189 // no need to check past first mapped position in all sequences
1193 lastCodon = entry.getKey();
1197 * add any new codons safely after iterating over the map
1199 for (Entry<SequenceI, AlignedCodon> startCodon : toAdd.entrySet())
1201 addCodonToMap(alignedCodons, startCodon.getValue(),
1202 startCodon.getKey());
1207 * Update the aligned protein sequences to match the codon alignments given in
1211 * @param alignedCodons
1212 * an ordered map of codon positions (columns), with sequence/peptide
1213 * values present in each column
1214 * @param unmappedProtein
1217 protected static int alignProteinAs(AlignmentI protein,
1218 Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
1219 List<SequenceI> unmappedProtein)
1222 * prefill peptide sequences with gaps
1224 int alignedWidth = alignedCodons.size();
1225 char[] gaps = new char[alignedWidth];
1226 Arrays.fill(gaps, protein.getGapCharacter());
1227 Map<SequenceI, char[]> peptides = new HashMap<>();
1228 for (SequenceI seq : protein.getSequences())
1230 if (!unmappedProtein.contains(seq))
1232 peptides.put(seq, Arrays.copyOf(gaps, gaps.length));
1237 * Traverse the codons left to right (as defined by CodonComparator)
1238 * and insert peptides in each column where the sequence is mapped.
1239 * This gives a peptide 'alignment' where residues are aligned if their
1240 * corresponding codons occupy the same columns in the cdna alignment.
1243 for (AlignedCodon codon : alignedCodons.keySet())
1245 final Map<SequenceI, AlignedCodon> columnResidues = alignedCodons
1247 for (Entry<SequenceI, AlignedCodon> entry : columnResidues.entrySet())
1249 char residue = entry.getValue().product.charAt(0);
1250 peptides.get(entry.getKey())[column] = residue;
1256 * and finally set the constructed sequences
1258 for (Entry<SequenceI, char[]> entry : peptides.entrySet())
1260 entry.getKey().setSequence(new String(entry.getValue()));
1267 * Populate the map of aligned codons by traversing the given sequence
1268 * mapping, locating the aligned positions of mapped codons, and adding those
1269 * positions and their translation products to the map.
1272 * the aligned sequence we are mapping from
1274 * the sequence to be aligned to the codons
1276 * the gap character in the dna sequence
1278 * a mapping to a sequence translation
1279 * @param alignedCodons
1280 * the map we are building up
1282 static void addCodonPositions(SequenceI dna, SequenceI protein,
1283 char gapChar, Mapping seqMap,
1284 Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons)
1286 Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
1289 * add codon positions, and their peptide translations, to the alignment
1290 * map, while remembering the first codon mapped
1292 while (codons.hasNext())
1296 AlignedCodon codon = codons.next();
1297 addCodonToMap(alignedCodons, codon, protein);
1298 } catch (IncompleteCodonException e)
1300 // possible incomplete trailing codon - ignore
1301 } catch (NoSuchElementException e)
1303 // possibly peptide lacking STOP
1309 * Helper method to add a codon-to-peptide entry to the aligned codons map
1311 * @param alignedCodons
1315 protected static void addCodonToMap(
1316 Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
1317 AlignedCodon codon, SequenceI protein)
1319 Map<SequenceI, AlignedCodon> seqProduct = alignedCodons.get(codon);
1320 if (seqProduct == null)
1322 seqProduct = new HashMap<>();
1323 alignedCodons.put(codon, seqProduct);
1325 seqProduct.put(protein, codon);
1329 * Returns true if a cDNA/Protein mapping either exists, or could be made,
1330 * between at least one pair of sequences in the two alignments. Currently,
1333 * <li>One alignment must be nucleotide, and the other protein</li>
1334 * <li>At least one pair of sequences must be already mapped, or mappable</li>
1335 * <li>Mappable means the nucleotide translation matches the protein
1337 * <li>The translation may ignore start and stop codons if present in the
1345 public static boolean isMappable(AlignmentI al1, AlignmentI al2)
1347 if (al1 == null || al2 == null)
1353 * Require one nucleotide and one protein
1355 if (al1.isNucleotide() == al2.isNucleotide())
1359 AlignmentI dna = al1.isNucleotide() ? al1 : al2;
1360 AlignmentI protein = dna == al1 ? al2 : al1;
1361 List<AlignedCodonFrame> mappings = protein.getCodonFrames();
1362 for (SequenceI dnaSeq : dna.getSequences())
1364 for (SequenceI proteinSeq : protein.getSequences())
1366 if (isMappable(dnaSeq, proteinSeq, mappings))
1376 * Returns true if the dna sequence is mapped, or could be mapped, to the
1384 protected static boolean isMappable(SequenceI dnaSeq,
1385 SequenceI proteinSeq, List<AlignedCodonFrame> mappings)
1387 if (dnaSeq == null || proteinSeq == null)
1392 SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq
1393 : dnaSeq.getDatasetSequence();
1394 SequenceI proteinDs = proteinSeq.getDatasetSequence() == null
1396 : proteinSeq.getDatasetSequence();
1398 for (AlignedCodonFrame mapping : mappings)
1400 if (proteinDs == mapping.getAaForDnaSeq(dnaDs))
1410 * Just try to make a mapping (it is not yet stored), test whether
1413 return mapCdnaToProtein(proteinDs, dnaDs) != null;
1417 * Finds any reference annotations associated with the sequences in
1418 * sequenceScope, that are not already added to the alignment, and adds them
1419 * to the 'candidates' map. Also populates a lookup table of annotation
1420 * labels, keyed by calcId, for use in constructing tooltips or the like.
1422 * @param sequenceScope
1423 * the sequences to scan for reference annotations
1424 * @param labelForCalcId
1425 * (optional) map to populate with label for calcId
1427 * map to populate with annotations for sequence
1429 * the alignment to check for presence of annotations
1431 public static void findAddableReferenceAnnotations(
1432 List<SequenceI> sequenceScope, Map<String, String> labelForCalcId,
1433 final Map<SequenceI, List<AlignmentAnnotation>> candidates,
1436 if (sequenceScope == null)
1442 * For each sequence in scope, make a list of any annotations on the
1443 * underlying dataset sequence which are not already on the alignment.
1445 * Add to a map of { alignmentSequence, <List of annotations to add> }
1447 for (SequenceI seq : sequenceScope)
1449 SequenceI dataset = seq.getDatasetSequence();
1450 if (dataset == null)
1454 AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
1455 if (datasetAnnotations == null)
1459 final List<AlignmentAnnotation> result = new ArrayList<>();
1460 for (AlignmentAnnotation dsann : datasetAnnotations)
1462 if (dsann.annotations != null) // ignore non-positional annotation
1465 * Find matching annotations on the alignment. If none is found, then
1466 * add this annotation to the list of 'addable' annotations for this
1469 final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
1470 .findAnnotations(seq, dsann.getCalcId(), dsann.label);
1471 if (!matchedAlignmentAnnotations.iterator().hasNext())
1474 if (labelForCalcId != null)
1476 labelForCalcId.put(dsann.getCalcId(), dsann.label);
1481 * Save any addable annotations for this sequence
1483 if (!result.isEmpty())
1485 candidates.put(seq, result);
1492 * Adds annotations to the top of the alignment annotations, in the same order
1493 * as their related sequences.
1495 * @param annotations
1496 * the annotations to add
1498 * the alignment to add them to
1499 * @param selectionGroup
1500 * current selection group (or null if none)
1502 public static void addReferenceAnnotations(
1503 Map<SequenceI, List<AlignmentAnnotation>> annotations,
1504 final AlignmentI alignment, final SequenceGroup selectionGroup)
1506 for (SequenceI seq : annotations.keySet())
1508 for (AlignmentAnnotation ann : annotations.get(seq))
1510 AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
1512 int endRes = ann.annotations.length;
1513 if (selectionGroup != null)
1515 startRes = selectionGroup.getStartRes();
1516 endRes = selectionGroup.getEndRes();
1518 copyAnn.restrict(startRes, endRes);
1521 * Add to the sequence (sets copyAnn.datasetSequence), unless the
1522 * original annotation is already on the sequence.
1524 if (!seq.hasAnnotation(ann))
1526 seq.addAlignmentAnnotation(copyAnn);
1529 copyAnn.adjustForAlignment();
1530 // add to the alignment and set visible
1531 alignment.addAnnotation(copyAnn);
1532 copyAnn.visible = true;
1538 * Set visibility of alignment annotations of specified types (labels), for
1539 * specified sequences. This supports controls like "Show all secondary
1540 * structure", "Hide all Temp factor", etc.
1542 * @al the alignment to scan for annotations
1544 * the types (labels) of annotations to be updated
1545 * @param forSequences
1546 * if not null, only annotations linked to one of these sequences are
1547 * in scope for update; if null, acts on all sequence annotations
1549 * if this flag is true, 'types' is ignored (label not checked)
1551 * if true, set visibility on, else set off
1553 public static void showOrHideSequenceAnnotations(AlignmentI al,
1554 Collection<String> types, List<SequenceI> forSequences,
1555 boolean anyType, boolean doShow)
1557 AlignmentAnnotation[] anns = al.getAlignmentAnnotation();
1560 for (AlignmentAnnotation aa : anns)
1562 if (anyType || types.contains(aa.label))
1564 if ((aa.sequenceRef != null) && (forSequences == null
1565 || forSequences.contains(aa.sequenceRef)))
1567 aa.visible = doShow;
1575 * Returns true if either sequence has a cross-reference to the other
1581 public static boolean haveCrossRef(SequenceI seq1, SequenceI seq2)
1583 // Note: moved here from class CrossRef as the latter class has dependencies
1584 // not availability to the applet's classpath
1585 return hasCrossRef(seq1, seq2) || hasCrossRef(seq2, seq1);
1589 * Returns true if seq1 has a cross-reference to seq2. Currently this assumes
1590 * that sequence name is structured as Source|AccessionId.
1596 public static boolean hasCrossRef(SequenceI seq1, SequenceI seq2)
1598 if (seq1 == null || seq2 == null)
1602 String name = seq2.getName();
1603 final List<DBRefEntry> xrefs = seq1.getDBRefs();
1606 for (int ix = 0, nx = xrefs.size(); ix < nx; ix++)
1608 DBRefEntry xref = xrefs.get(ix);
1609 String xrefName = xref.getSource() + "|" + xref.getAccessionId();
1610 // case-insensitive test, consistent with DBRefEntry.equalRef()
1611 if (xrefName.equalsIgnoreCase(name))
1621 * Constructs an alignment consisting of the mapped (CDS) regions in the given
1622 * nucleotide sequences, and updates mappings to match. The CDS sequences are
1623 * added to the original alignment's dataset, which is shared by the new
1624 * alignment. Mappings from nucleotide to CDS, and from CDS to protein, are
1625 * added to the alignment dataset.
1628 * aligned nucleotide (dna or cds) sequences
1630 * the alignment dataset the sequences belong to
1632 * (optional) to restrict results to CDS that map to specified
1634 * @return an alignment whose sequences are the cds-only parts of the dna
1635 * sequences (or null if no mappings are found)
1637 public static AlignmentI makeCdsAlignment(SequenceI[] dna,
1638 AlignmentI dataset, SequenceI[] products)
1640 if (dataset == null || dataset.getDataset() != null)
1642 throw new IllegalArgumentException(
1643 "IMPLEMENTATION ERROR: dataset.getDataset() must be null!");
1645 List<SequenceI> foundSeqs = new ArrayList<>();
1646 List<SequenceI> cdsSeqs = new ArrayList<>();
1647 List<AlignedCodonFrame> mappings = dataset.getCodonFrames();
1648 HashSet<SequenceI> productSeqs = null;
1649 if (products != null)
1651 productSeqs = new HashSet<>();
1652 for (SequenceI seq : products)
1654 productSeqs.add(seq.getDatasetSequence() == null ? seq : seq
1655 .getDatasetSequence());
1660 * Construct CDS sequences from mappings on the alignment dataset.
1662 * - find the protein product(s) mapped to from each dna sequence
1663 * - if the mapping covers the whole dna sequence (give or take start/stop
1664 * codon), take the dna as the CDS sequence
1665 * - else search dataset mappings for a suitable dna sequence, i.e. one
1666 * whose whole sequence is mapped to the protein
1667 * - if no sequence found, construct one from the dna sequence and mapping
1668 * (and add it to dataset so it is found if this is repeated)
1670 for (SequenceI dnaSeq : dna)
1672 SequenceI dnaDss = dnaSeq.getDatasetSequence() == null ? dnaSeq
1673 : dnaSeq.getDatasetSequence();
1675 List<AlignedCodonFrame> seqMappings = MappingUtils
1676 .findMappingsForSequence(dnaSeq, mappings);
1677 for (AlignedCodonFrame mapping : seqMappings)
1679 List<Mapping> mappingsFromSequence = mapping
1680 .getMappingsFromSequence(dnaSeq);
1682 for (Mapping aMapping : mappingsFromSequence)
1684 MapList mapList = aMapping.getMap();
1685 if (mapList.getFromRatio() == 1)
1688 * not a dna-to-protein mapping (likely dna-to-cds)
1694 * skip if mapping is not to one of the target set of proteins
1696 SequenceI proteinProduct = aMapping.getTo();
1697 if (productSeqs != null && !productSeqs.contains(proteinProduct))
1703 * try to locate the CDS from the dataset mappings;
1704 * guard against duplicate results (for the case that protein has
1705 * dbrefs to both dna and cds sequences)
1707 SequenceI cdsSeq = findCdsForProtein(mappings, dnaSeq,
1708 seqMappings, aMapping);
1711 if (!foundSeqs.contains(cdsSeq))
1713 foundSeqs.add(cdsSeq);
1714 SequenceI derivedSequence = cdsSeq.deriveSequence();
1715 cdsSeqs.add(derivedSequence);
1716 if (!dataset.getSequences().contains(cdsSeq))
1718 dataset.addSequence(cdsSeq);
1725 * didn't find mapped CDS sequence - construct it and add
1726 * its dataset sequence to the dataset
1728 cdsSeq = makeCdsSequence(dnaSeq.getDatasetSequence(), aMapping,
1729 dataset).deriveSequence();
1730 // cdsSeq has a name constructed as CDS|<dbref>
1731 // <dbref> will be either the accession for the coding sequence,
1732 // marked in the /via/ dbref to the protein product accession
1733 // or it will be the original nucleotide accession.
1734 SequenceI cdsSeqDss = cdsSeq.getDatasetSequence();
1736 cdsSeqs.add(cdsSeq);
1739 * build the mapping from CDS to protein
1741 List<int[]> cdsRange = Collections
1742 .singletonList(new int[]
1743 { cdsSeq.getStart(),
1744 cdsSeq.getLength() + cdsSeq.getStart() - 1 });
1745 MapList cdsToProteinMap = new MapList(cdsRange,
1746 mapList.getToRanges(), mapList.getFromRatio(),
1747 mapList.getToRatio());
1749 if (!dataset.getSequences().contains(cdsSeqDss))
1752 * if this sequence is a newly created one, add it to the dataset
1753 * and made a CDS to protein mapping (if sequence already exists,
1754 * CDS-to-protein mapping _is_ the transcript-to-protein mapping)
1756 dataset.addSequence(cdsSeqDss);
1757 AlignedCodonFrame cdsToProteinMapping = new AlignedCodonFrame();
1758 cdsToProteinMapping.addMap(cdsSeqDss, proteinProduct,
1762 * guard against duplicating the mapping if repeating this action
1764 if (!mappings.contains(cdsToProteinMapping))
1766 mappings.add(cdsToProteinMapping);
1770 propagateDBRefsToCDS(cdsSeqDss, dnaSeq.getDatasetSequence(),
1771 proteinProduct, aMapping);
1773 * add another mapping from original 'from' range to CDS
1775 AlignedCodonFrame dnaToCdsMapping = new AlignedCodonFrame();
1776 final MapList dnaToCdsMap = new MapList(mapList.getFromRanges(),
1778 dnaToCdsMapping.addMap(dnaSeq.getDatasetSequence(), cdsSeqDss,
1780 if (!mappings.contains(dnaToCdsMapping))
1782 mappings.add(dnaToCdsMapping);
1786 * transfer dna chromosomal loci (if known) to the CDS
1787 * sequence (via the mapping)
1789 final MapList cdsToDnaMap = dnaToCdsMap.getInverse();
1790 transferGeneLoci(dnaSeq, cdsToDnaMap, cdsSeq);
1793 * add DBRef with mapping from protein to CDS
1794 * (this enables Get Cross-References from protein alignment)
1795 * This is tricky because we can't have two DBRefs with the
1796 * same source and accession, so need a different accession for
1797 * the CDS from the dna sequence
1800 // specific use case:
1801 // Genomic contig ENSCHR:1, contains coding regions for ENSG01,
1802 // ENSG02, ENSG03, with transcripts and products similarly named.
1803 // cannot add distinct dbrefs mapping location on ENSCHR:1 to ENSG01
1805 // JBPNote: ?? can't actually create an example that demonstrates we
1807 // synthesize an xref.
1809 List<DBRefEntry> primrefs = dnaDss.getPrimaryDBRefs();
1810 for (int ip = 0, np = primrefs.size(); ip < np; ip++)
1812 DBRefEntry primRef = primrefs.get(ip);
1814 * create a cross-reference from CDS to the source sequence's
1815 * primary reference and vice versa
1817 String source = primRef.getSource();
1818 String version = primRef.getVersion();
1819 DBRefEntry cdsCrossRef = new DBRefEntry(source, source + ":"
1820 + version, primRef.getAccessionId());
1821 cdsCrossRef.setMap(new Mapping(dnaDss, new MapList(cdsToDnaMap)));
1822 cdsSeqDss.addDBRef(cdsCrossRef);
1824 dnaSeq.addDBRef(new DBRefEntry(source, version, cdsSeq
1825 .getName(), new Mapping(cdsSeqDss, dnaToCdsMap)));
1826 // problem here is that the cross-reference is synthesized -
1827 // cdsSeq.getName() may be like 'CDS|dnaaccession' or
1829 // assuming cds version same as dna ?!?
1831 DBRefEntry proteinToCdsRef = new DBRefEntry(source, version,
1834 proteinToCdsRef.setMap(new Mapping(cdsSeqDss, cdsToProteinMap
1836 proteinProduct.addDBRef(proteinToCdsRef);
1839 * transfer any features on dna that overlap the CDS
1841 transferFeatures(dnaSeq, cdsSeq, dnaToCdsMap, null,
1842 SequenceOntologyI.CDS);
1847 AlignmentI cds = new Alignment(cdsSeqs.toArray(new SequenceI[cdsSeqs
1849 cds.setDataset(dataset);
1855 * Tries to transfer gene loci (dbref to chromosome positions) from fromSeq to
1856 * toSeq, mediated by the given mapping between the sequences
1859 * @param targetToFrom
1863 protected static void transferGeneLoci(SequenceI fromSeq,
1864 MapList targetToFrom, SequenceI targetSeq)
1866 if (targetSeq.getGeneLoci() != null)
1868 // already have - don't override
1871 GeneLociI fromLoci = fromSeq.getGeneLoci();
1872 if (fromLoci == null)
1877 MapList newMap = targetToFrom.traverse(fromLoci.getMapping());
1881 targetSeq.setGeneLoci(fromLoci.getSpeciesId(),
1882 fromLoci.getAssemblyId(), fromLoci.getChromosomeId(), newMap);
1887 * A helper method that finds a CDS sequence in the alignment dataset that is
1888 * mapped to the given protein sequence, and either is, or has a mapping from,
1889 * the given dna sequence.
1892 * set of all mappings on the dataset
1894 * a dna (or cds) sequence we are searching from
1895 * @param seqMappings
1896 * the set of mappings involving dnaSeq
1898 * a transcript-to-peptide mapping
1901 static SequenceI findCdsForProtein(List<AlignedCodonFrame> mappings,
1902 SequenceI dnaSeq, List<AlignedCodonFrame> seqMappings,
1906 * TODO a better dna-cds-protein mapping data representation to allow easy
1907 * navigation; until then this clunky looping around lists of mappings
1909 SequenceI seqDss = dnaSeq.getDatasetSequence() == null ? dnaSeq
1910 : dnaSeq.getDatasetSequence();
1911 SequenceI proteinProduct = aMapping.getTo();
1914 * is this mapping from the whole dna sequence (i.e. CDS)?
1915 * allowing for possible stop codon on dna but not peptide
1917 int mappedFromLength = MappingUtils
1918 .getLength(aMapping.getMap().getFromRanges());
1919 int dnaLength = seqDss.getLength();
1920 if (mappedFromLength == dnaLength
1921 || mappedFromLength == dnaLength - CODON_LENGTH)
1924 * if sequence has CDS features, this is a transcript with no UTR
1925 * - do not take this as the CDS sequence! (JAL-2789)
1927 if (seqDss.getFeatures().getFeaturesByOntology(SequenceOntologyI.CDS)
1935 * looks like we found the dna-to-protein mapping; search for the
1936 * corresponding cds-to-protein mapping
1938 List<AlignedCodonFrame> mappingsToPeptide = MappingUtils
1939 .findMappingsForSequence(proteinProduct, mappings);
1940 for (AlignedCodonFrame acf : mappingsToPeptide)
1942 for (SequenceToSequenceMapping map : acf.getMappings())
1944 Mapping mapping = map.getMapping();
1945 if (mapping != aMapping
1946 && mapping.getMap().getFromRatio() == CODON_LENGTH
1947 && proteinProduct == mapping.getTo()
1948 && seqDss != map.getFromSeq())
1950 mappedFromLength = MappingUtils
1951 .getLength(mapping.getMap().getFromRanges());
1952 if (mappedFromLength == map.getFromSeq().getLength())
1955 * found a 3:1 mapping to the protein product which covers
1956 * the whole dna sequence i.e. is from CDS; finally check the CDS
1957 * is mapped from the given dna start sequence
1959 SequenceI cdsSeq = map.getFromSeq();
1960 // todo this test is weak if seqMappings contains multiple mappings;
1961 // we get away with it if transcript:cds relationship is 1:1
1962 List<AlignedCodonFrame> dnaToCdsMaps = MappingUtils
1963 .findMappingsForSequence(cdsSeq, seqMappings);
1964 if (!dnaToCdsMaps.isEmpty())
1976 * Helper method that makes a CDS sequence as defined by the mappings from the
1977 * given sequence i.e. extracts the 'mapped from' ranges (which may be on
1978 * forward or reverse strand).
1983 * - existing dataset. We check for sequences that look like the CDS
1984 * we are about to construct, if one exists already, then we will
1985 * just return that one.
1986 * @return CDS sequence (as a dataset sequence)
1988 static SequenceI makeCdsSequence(SequenceI seq, Mapping mapping,
1992 * construct CDS sequence name as "CDS|" with 'from id' held in the mapping
1993 * if set (e.g. EMBL protein_id), else sequence name appended
1995 String mapFromId = mapping.getMappedFromId();
1996 final String seqId = "CDS|"
1997 + (mapFromId != null ? mapFromId : seq.getName());
1999 SequenceI newSeq = null;
2001 final MapList maplist = mapping.getMap();
2002 if (maplist.isContiguous() && maplist.isFromForwardStrand())
2005 * just a subsequence, keep same dataset sequence
2007 int start = maplist.getFromLowest();
2008 int end = maplist.getFromHighest();
2009 newSeq = seq.getSubSequence(start - 1, end);
2010 newSeq.setName(seqId);
2015 * construct by splicing mapped from ranges
2017 char[] seqChars = seq.getSequence();
2018 List<int[]> fromRanges = maplist.getFromRanges();
2019 int cdsWidth = MappingUtils.getLength(fromRanges);
2020 char[] newSeqChars = new char[cdsWidth];
2023 for (int[] range : fromRanges)
2025 if (range[0] <= range[1])
2027 // forward strand mapping - just copy the range
2028 int length = range[1] - range[0] + 1;
2029 System.arraycopy(seqChars, range[0] - 1, newSeqChars, newPos,
2035 // reverse strand mapping - copy and complement one by one
2036 for (int i = range[0]; i >= range[1]; i--)
2038 newSeqChars[newPos++] = Dna.getComplement(seqChars[i - 1]);
2043 newSeq = new Sequence(seqId, newSeqChars, 1, newPos);
2046 if (dataset != null)
2048 SequenceI[] matches = dataset.findSequenceMatch(newSeq.getName());
2049 if (matches != null)
2051 boolean matched = false;
2052 for (SequenceI mtch : matches)
2054 if (mtch.getStart() != newSeq.getStart())
2058 if (mtch.getEnd() != newSeq.getEnd())
2062 if (!Arrays.equals(mtch.getSequence(), newSeq.getSequence()))
2074 "JAL-2154 regression: warning - found (and ignnored a duplicate CDS sequence):"
2080 // newSeq.setDescription(mapFromId);
2086 * Adds any DBRefEntrys to cdsSeq from contig that have a Mapping congruent to
2087 * the given mapping.
2091 * @param proteinProduct
2093 * @return list of DBRefEntrys added
2095 protected static List<DBRefEntry> propagateDBRefsToCDS(SequenceI cdsSeq,
2096 SequenceI contig, SequenceI proteinProduct, Mapping mapping)
2099 // gather direct refs from contig congruent with mapping
2100 List<DBRefEntry> direct = new ArrayList<>();
2101 HashSet<String> directSources = new HashSet<>();
2103 List<DBRefEntry> refs = contig.getDBRefs();
2106 for (int ib = 0, nb = refs.size(); ib < nb; ib++)
2108 DBRefEntry dbr = refs.get(ib);
2110 if (dbr.hasMap() && (map = dbr.getMap().getMap()).isTripletMap())
2112 // check if map is the CDS mapping
2113 if (mapping.getMap().equals(map))
2116 directSources.add(dbr.getSource());
2121 List<DBRefEntry> onSource = DBRefUtils.selectRefs(
2122 proteinProduct.getDBRefs(),
2123 directSources.toArray(new String[0]));
2124 List<DBRefEntry> propagated = new ArrayList<>();
2126 // and generate appropriate mappings
2127 for (int ic = 0, nc = direct.size(); ic < nc; ic++)
2129 DBRefEntry cdsref = direct.get(ic);
2130 Mapping m = cdsref.getMap();
2131 // clone maplist and mapping
2132 MapList cdsposmap = new MapList(
2133 Arrays.asList(new int[][]
2134 { new int[] { cdsSeq.getStart(), cdsSeq.getEnd() } }),
2135 m.getMap().getToRanges(), 3, 1);
2136 Mapping cdsmap = new Mapping(m.getTo(), m.getMap());
2139 DBRefEntry newref = new DBRefEntry(cdsref.getSource(),
2140 cdsref.getVersion(), cdsref.getAccessionId(),
2141 new Mapping(cdsmap.getTo(), cdsposmap));
2143 // and see if we can map to the protein product for this mapping.
2144 // onSource is the filtered set of accessions on protein that we are
2145 // tranferring, so we assume accession is the same.
2146 if (cdsmap.getTo() == null && onSource != null)
2148 List<DBRefEntry> sourceRefs = DBRefUtils.searchRefs(onSource,
2149 cdsref.getAccessionId());
2150 if (sourceRefs != null)
2152 for (DBRefEntry srcref : sourceRefs)
2154 if (srcref.getSource().equalsIgnoreCase(cdsref.getSource()))
2156 // we have found a complementary dbref on the protein product, so
2157 // update mapping's getTo
2158 newref.getMap().setTo(proteinProduct);
2163 cdsSeq.addDBRef(newref);
2164 propagated.add(newref);
2170 * Transfers co-located features on 'fromSeq' to 'toSeq', adjusting the
2171 * feature start/end ranges, optionally omitting specified feature types.
2172 * Returns the number of features copied.
2177 * the mapping from 'fromSeq' to 'toSeq'
2179 * if not null, only features of this type are copied (including
2180 * subtypes in the Sequence Ontology)
2183 protected static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,
2184 MapList mapping, String select, String... omitting)
2186 SequenceI copyTo = toSeq;
2187 while (copyTo.getDatasetSequence() != null)
2189 copyTo = copyTo.getDatasetSequence();
2191 if (fromSeq == copyTo || fromSeq.getDatasetSequence() == copyTo)
2193 return 0; // shared dataset sequence
2197 * get features, optionally restricted by an ontology term
2199 List<SequenceFeature> sfs = select == null ? fromSeq.getFeatures()
2200 .getPositionalFeatures() : fromSeq.getFeatures()
2201 .getFeaturesByOntology(select);
2204 for (SequenceFeature sf : sfs)
2206 String type = sf.getType();
2207 boolean omit = false;
2208 for (String toOmit : omitting)
2210 if (type.equals(toOmit))
2221 * locate the mapped range - null if either start or end is
2222 * not mapped (no partial overlaps are calculated)
2224 int start = sf.getBegin();
2225 int end = sf.getEnd();
2226 int[] mappedTo = mapping.locateInTo(start, end);
2228 * if whole exon range doesn't map, try interpreting it
2229 * as 5' or 3' exon overlapping the CDS range
2231 if (mappedTo == null)
2233 mappedTo = mapping.locateInTo(end, end);
2234 if (mappedTo != null)
2237 * end of exon is in CDS range - 5' overlap
2238 * to a range from the start of the peptide
2243 if (mappedTo == null)
2245 mappedTo = mapping.locateInTo(start, start);
2246 if (mappedTo != null)
2249 * start of exon is in CDS range - 3' overlap
2250 * to a range up to the end of the peptide
2252 mappedTo[1] = toSeq.getLength();
2255 if (mappedTo != null)
2257 int newBegin = Math.min(mappedTo[0], mappedTo[1]);
2258 int newEnd = Math.max(mappedTo[0], mappedTo[1]);
2259 SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
2260 sf.getFeatureGroup(), sf.getScore());
2261 copyTo.addSequenceFeature(copy);
2269 * Returns a mapping from dna to protein by inspecting sequence features of
2270 * type "CDS" on the dna. A mapping is constructed if the total CDS feature
2271 * length is 3 times the peptide length (optionally after dropping a trailing
2272 * stop codon). This method does not check whether the CDS nucleotide sequence
2273 * translates to the peptide sequence.
2279 public static MapList mapCdsToProtein(SequenceI dnaSeq,
2280 SequenceI proteinSeq)
2282 List<int[]> ranges = findCdsPositions(dnaSeq);
2283 int mappedDnaLength = MappingUtils.getLength(ranges);
2286 * if not a whole number of codons, truncate mapping
2288 int codonRemainder = mappedDnaLength % CODON_LENGTH;
2289 if (codonRemainder > 0)
2291 mappedDnaLength -= codonRemainder;
2292 MappingUtils.removeEndPositions(codonRemainder, ranges);
2295 int proteinLength = proteinSeq.getLength();
2296 int proteinStart = proteinSeq.getStart();
2297 int proteinEnd = proteinSeq.getEnd();
2300 * incomplete start codon may mean X at start of peptide
2301 * we ignore both for mapping purposes
2303 if (proteinSeq.getCharAt(0) == 'X')
2305 // todo JAL-2022 support startPhase > 0
2309 List<int[]> proteinRange = new ArrayList<>();
2312 * dna length should map to protein (or protein plus stop codon)
2314 int codesForResidues = mappedDnaLength / CODON_LENGTH;
2315 if (codesForResidues == (proteinLength + 1))
2317 // assuming extra codon is for STOP and not in peptide
2318 // todo: check trailing codon is indeed a STOP codon
2320 mappedDnaLength -= CODON_LENGTH;
2321 MappingUtils.removeEndPositions(CODON_LENGTH, ranges);
2324 if (codesForResidues == proteinLength)
2326 proteinRange.add(new int[] { proteinStart, proteinEnd });
2327 return new MapList(ranges, proteinRange, CODON_LENGTH, 1);
2333 * Returns a list of CDS ranges found (as sequence positions base 1), i.e. of
2334 * [start, end] positions of sequence features of type "CDS" (or a sub-type of
2335 * CDS in the Sequence Ontology). The ranges are sorted into ascending start
2336 * position order, so this method is only valid for linear CDS in the same
2337 * sense as the protein product.
2342 protected static List<int[]> findCdsPositions(SequenceI dnaSeq)
2344 List<int[]> result = new ArrayList<>();
2346 List<SequenceFeature> sfs = dnaSeq.getFeatures().getFeaturesByOntology(
2347 SequenceOntologyI.CDS);
2352 SequenceFeatures.sortFeatures(sfs, true);
2354 for (SequenceFeature sf : sfs)
2359 String s = sf.getPhase();
2362 phase = Integer.parseInt(s);
2364 } catch (NumberFormatException e)
2369 * phase > 0 on first codon means 5' incomplete - skip to the start
2370 * of the next codon; example ENST00000496384
2372 int begin = sf.getBegin();
2373 int end = sf.getEnd();
2374 if (result.isEmpty() && phase > 0)
2379 // shouldn't happen!
2381 .println("Error: start phase extends beyond start CDS in "
2382 + dnaSeq.getName());
2385 result.add(new int[] { begin, end });
2389 * Finally sort ranges by start position. This avoids a dependency on
2390 * keeping features in order on the sequence (if they are in order anyway,
2391 * the sort will have almost no work to do). The implicit assumption is CDS
2392 * ranges are assembled in order. Other cases should not use this method,
2393 * but instead construct an explicit mapping for CDS (e.g. EMBL parsing).
2395 Collections.sort(result, IntRangeComparator.ASCENDING);
2400 * Makes an alignment with a copy of the given sequences, adding in any
2401 * non-redundant sequences which are mapped to by the cross-referenced
2407 * the alignment dataset shared by the new copy
2410 public static AlignmentI makeCopyAlignment(SequenceI[] seqs,
2411 SequenceI[] xrefs, AlignmentI dataset)
2413 AlignmentI copy = new Alignment(new Alignment(seqs));
2414 copy.setDataset(dataset);
2415 boolean isProtein = !copy.isNucleotide();
2416 SequenceIdMatcher matcher = new SequenceIdMatcher(seqs);
2419 // BH 2019.01.25 recoded to remove iterators
2421 for (int ix = 0, nx = xrefs.length; ix < nx; ix++)
2423 SequenceI xref = xrefs[ix];
2424 List<DBRefEntry> dbrefs = xref.getDBRefs();
2427 for (int ir = 0, nir = dbrefs.size(); ir < nir; ir++)
2429 DBRefEntry dbref = dbrefs.get(ir);
2430 Mapping map = dbref.getMap();
2432 if (map == null || (mto = map.getTo()) == null
2433 || mto.isProtein() != isProtein)
2437 SequenceI mappedTo = mto;
2438 SequenceI match = matcher.findIdMatch(mappedTo);
2441 matcher.add(mappedTo);
2442 copy.addSequence(mappedTo);
2452 * Try to align sequences in 'unaligned' to match the alignment of their
2453 * mapped regions in 'aligned'. For example, could use this to align CDS
2454 * sequences which are mapped to their parent cDNA sequences.
2456 * This method handles 1:1 mappings (dna-to-dna or protein-to-protein). For
2457 * dna-to-protein or protein-to-dna use alternative methods.
2460 * sequences to be aligned
2462 * holds aligned sequences and their mappings
2465 public static int alignAs(AlignmentI unaligned, AlignmentI aligned)
2468 * easy case - aligning a copy of aligned sequences
2470 if (alignAsSameSequences(unaligned, aligned))
2472 return unaligned.getHeight();
2476 * fancy case - aligning via mappings between sequences
2478 List<SequenceI> unmapped = new ArrayList<>();
2479 Map<Integer, Map<SequenceI, Character>> columnMap = buildMappedColumnsMap(
2480 unaligned, aligned, unmapped);
2481 int width = columnMap.size();
2482 char gap = unaligned.getGapCharacter();
2483 int realignedCount = 0;
2484 // TODO: verify this loop scales sensibly for very wide/high alignments
2486 for (SequenceI seq : unaligned.getSequences())
2488 if (!unmapped.contains(seq))
2490 char[] newSeq = new char[width];
2491 Arrays.fill(newSeq, gap); // JBPComment - doubt this is faster than the
2492 // Integer iteration below
2497 * traverse the map to find columns populated
2500 for (Integer column : columnMap.keySet())
2502 Character c = columnMap.get(column).get(seq);
2506 * sequence has a character at this position
2516 * trim trailing gaps
2518 if (lastCol < width)
2520 char[] tmp = new char[lastCol + 1];
2521 System.arraycopy(newSeq, 0, tmp, 0, lastCol + 1);
2524 // TODO: optimise SequenceI to avoid char[]->String->char[]
2525 seq.setSequence(String.valueOf(newSeq));
2529 return realignedCount;
2533 * If unaligned and aligned sequences share the same dataset sequences, then
2534 * simply copies the aligned sequences to the unaligned sequences and returns
2535 * true; else returns false
2538 * - sequences to be aligned based on aligned
2540 * - 'guide' alignment containing sequences derived from same
2541 * dataset as unaligned
2544 static boolean alignAsSameSequences(AlignmentI unaligned,
2547 if (aligned.getDataset() == null || unaligned.getDataset() == null)
2549 return false; // should only pass alignments with datasets here
2552 // map from dataset sequence to alignment sequence(s)
2553 Map<SequenceI, List<SequenceI>> alignedDatasets = new HashMap<>();
2554 for (SequenceI seq : aligned.getSequences())
2556 SequenceI ds = seq.getDatasetSequence();
2557 if (alignedDatasets.get(ds) == null)
2559 alignedDatasets.put(ds, new ArrayList<SequenceI>());
2561 alignedDatasets.get(ds).add(seq);
2565 * first pass - check whether all sequences to be aligned share a
2566 * dataset sequence with an aligned sequence; also note the leftmost
2567 * ungapped column from which to copy
2569 int leftmost = Integer.MAX_VALUE;
2570 for (SequenceI seq : unaligned.getSequences())
2572 final SequenceI ds = seq.getDatasetSequence();
2573 if (!alignedDatasets.containsKey(ds))
2577 SequenceI alignedSeq = alignedDatasets.get(ds)
2579 int startCol = alignedSeq.findIndex(seq.getStart()); // 1..
2580 leftmost = Math.min(leftmost, startCol);
2584 * second pass - copy aligned sequences;
2585 * heuristic rule: pair off sequences in order for the case where
2586 * more than one shares the same dataset sequence
2588 final char gapCharacter = aligned.getGapCharacter();
2589 for (SequenceI seq : unaligned.getSequences())
2591 List<SequenceI> alignedSequences = alignedDatasets
2592 .get(seq.getDatasetSequence());
2593 if (alignedSequences.isEmpty())
2596 * defensive check - shouldn't happen! (JAL-3536)
2600 SequenceI alignedSeq = alignedSequences.get(0);
2603 * gap fill for leading (5') UTR if any
2605 // TODO this copies intron columns - wrong!
2606 int startCol = alignedSeq.findIndex(seq.getStart()); // 1..
2607 int endCol = alignedSeq.findIndex(seq.getEnd());
2608 char[] seqchars = new char[endCol - leftmost + 1];
2609 Arrays.fill(seqchars, gapCharacter);
2610 char[] toCopy = alignedSeq.getSequence(startCol - 1, endCol);
2611 System.arraycopy(toCopy, 0, seqchars, startCol - leftmost,
2613 seq.setSequence(String.valueOf(seqchars));
2614 if (alignedSequences.size() > 0)
2616 // pop off aligned sequences (except the last one)
2617 alignedSequences.remove(0);
2622 * finally remove gapped columns (e.g. introns)
2624 new RemoveGapColCommand("", unaligned.getSequencesArray(), 0,
2625 unaligned.getWidth() - 1, unaligned);
2631 * Returns a map whose key is alignment column number (base 1), and whose
2632 * values are a map of sequence characters in that column.
2639 static SortedMap<Integer, Map<SequenceI, Character>> buildMappedColumnsMap(
2640 AlignmentI unaligned, AlignmentI aligned,
2641 List<SequenceI> unmapped)
2644 * Map will hold, for each aligned column position, a map of
2645 * {unalignedSequence, characterPerSequence} at that position.
2646 * TreeMap keeps the entries in ascending column order.
2648 SortedMap<Integer, Map<SequenceI, Character>> map = new TreeMap<>();
2651 * record any sequences that have no mapping so can't be realigned
2653 unmapped.addAll(unaligned.getSequences());
2655 List<AlignedCodonFrame> mappings = aligned.getCodonFrames();
2657 for (SequenceI seq : unaligned.getSequences())
2659 for (AlignedCodonFrame mapping : mappings)
2661 SequenceI fromSeq = mapping.findAlignedSequence(seq, aligned);
2662 if (fromSeq != null)
2664 Mapping seqMap = mapping.getMappingBetween(fromSeq, seq);
2665 if (addMappedPositions(seq, fromSeq, seqMap, map))
2667 unmapped.remove(seq);
2676 * Helper method that adds to a map the mapped column positions of a sequence.
2678 * For example if aaTT-Tg-gAAA is mapped to TTTAAA then the map should record
2679 * that columns 3,4,6,10,11,12 map to characters T,T,T,A,A,A of the mapped to
2683 * the sequence whose column positions we are recording
2685 * a sequence that is mapped to the first sequence
2687 * the mapping from 'fromSeq' to 'seq'
2689 * a map to add the column positions (in fromSeq) of the mapped
2693 static boolean addMappedPositions(SequenceI seq, SequenceI fromSeq,
2694 Mapping seqMap, Map<Integer, Map<SequenceI, Character>> map)
2702 * invert mapping if it is from unaligned to aligned sequence
2704 if (seqMap.getTo() == fromSeq.getDatasetSequence())
2706 seqMap = new Mapping(seq.getDatasetSequence(),
2707 seqMap.getMap().getInverse());
2710 int toStart = seq.getStart();
2713 * traverse [start, end, start, end...] ranges in fromSeq
2715 for (int[] fromRange : seqMap.getMap().getFromRanges())
2717 for (int i = 0; i < fromRange.length - 1; i += 2)
2719 boolean forward = fromRange[i + 1] >= fromRange[i];
2722 * find the range mapped to (sequence positions base 1)
2724 int[] range = seqMap.locateMappedRange(fromRange[i],
2728 System.err.println("Error in mapping " + seqMap + " from "
2729 + fromSeq.getName());
2732 int fromCol = fromSeq.findIndex(fromRange[i]);
2733 int mappedCharPos = range[0];
2736 * walk over the 'from' aligned sequence in forward or reverse
2737 * direction; when a non-gap is found, record the column position
2738 * of the next character of the mapped-to sequence; stop when all
2739 * the characters of the range have been counted
2741 while (mappedCharPos <= range[1] && fromCol <= fromSeq.getLength()
2744 if (!Comparison.isGap(fromSeq.getCharAt(fromCol - 1)))
2747 * mapped from sequence has a character in this column
2748 * record the column position for the mapped to character
2750 Map<SequenceI, Character> seqsMap = map.get(fromCol);
2751 if (seqsMap == null)
2753 seqsMap = new HashMap<>();
2754 map.put(fromCol, seqsMap);
2756 seqsMap.put(seq, seq.getCharAt(mappedCharPos - toStart));
2759 fromCol += (forward ? 1 : -1);
2766 // strictly temporary hack until proper criteria for aligning protein to cds
2767 // are in place; this is so Ensembl -> fetch xrefs Uniprot aligns the Uniprot
2768 public static boolean looksLikeEnsembl(AlignmentI alignment)
2770 for (SequenceI seq : alignment.getSequences())
2772 String name = seq.getName();
2773 if (!name.startsWith("ENSG") && !name.startsWith("ENST"))