/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.analysis;
+import jalview.datamodel.AlignedCodon;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.datamodel.FeatureProperties;
+import jalview.datamodel.IncompleteCodonException;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
+import jalview.io.gff.SequenceOntologyFactory;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.Comparison;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
+import jalview.util.MappingUtils;
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.TreeMap;
/**
* grab bag of useful alignment manipulation operations Expect these to be
for (SequenceI s : core.getSequences())
{
SequenceI newSeq = s.deriveSequence();
- if (newSeq.getStart() > maxoffset
+ final int newSeqStart = newSeq.getStart() - 1;
+ if (newSeqStart > maxoffset
&& newSeq.getDatasetSequence().getStart() < s.getStart())
{
- maxoffset = newSeq.getStart();
+ maxoffset = newSeqStart;
}
sq.add(newSeq);
}
if (flankSize > -1)
{
- maxoffset = flankSize;
+ maxoffset = Math.min(maxoffset, flankSize);
}
- // now add offset to create a new expanded alignment
+
+ /*
+ * now add offset left and right to create an expanded alignment
+ */
for (SequenceI s : sq)
{
SequenceI ds = s;
}
int s_end = s.findPosition(s.getStart() + s.getLength());
// find available flanking residues for sequence
- int ustream_ds = s.getStart() - ds.getStart(), dstream_ds = ds
- .getEnd() - s_end;
+ int ustream_ds = s.getStart() - ds.getStart();
+ int dstream_ds = ds.getEnd() - s_end;
// build new flanked sequence
offset = maxoffset - flankSize;
ustream_ds = flankSize;
}
- if (flankSize < dstream_ds)
+ if (flankSize <= dstream_ds)
{
- dstream_ds = flankSize;
+ dstream_ds = flankSize - 1;
}
}
+ // TODO use Character.toLowerCase to avoid creating String objects?
char[] upstream = new String(ds.getSequence(s.getStart() - 1
- ustream_ds, s.getStart() - 1)).toLowerCase().toCharArray();
- char[] downstream = new String(ds.getSequence(s_end - 1, s_end + 1
+ char[] downstream = new String(ds.getSequence(s_end - 1, s_end
+ dstream_ds)).toLowerCase().toCharArray();
char[] coreseq = s.getSequence();
char[] nseq = new char[offset + upstream.length + downstream.length
+ coreseq.length];
char c = core.getGapCharacter();
- // TODO could lowercase the flanking regions
+
int p = 0;
for (; p < offset; p++)
{
nseq[p] = c;
}
- // s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) +
- // new String(downstream).toLowerCase());
+
System.arraycopy(upstream, 0, nseq, p, upstream.length);
System.arraycopy(coreseq, 0, nseq, p + upstream.length,
coreseq.length);
{
for (AlignmentAnnotation aa : s.getAnnotation())
{
+ aa.adjustForAlignment(); // JAL-1712 fix
newAl.addAnnotation(aa);
}
}
}
return result;
}
+
+ /**
+ * Returns a map of lists of sequences in the alignment, keyed by sequence
+ * name. For use in mapping between different alignment views of the same
+ * sequences.
+ *
+ * @see jalview.datamodel.AlignmentI#getSequencesByName()
+ */
+ public static Map<String, List<SequenceI>> getSequencesByName(
+ AlignmentI al)
+ {
+ Map<String, List<SequenceI>> theMap = new LinkedHashMap<String, List<SequenceI>>();
+ for (SequenceI seq : al.getSequences())
+ {
+ String name = seq.getName();
+ if (name != null)
+ {
+ List<SequenceI> seqs = theMap.get(name);
+ if (seqs == null)
+ {
+ seqs = new ArrayList<SequenceI>();
+ theMap.put(name, seqs);
+ }
+ seqs.add(seq);
+ }
+ }
+ return theMap;
+ }
+
+ /**
+ * Build mapping of protein to cDNA alignment. Mappings are made between
+ * sequences where the cDNA translates to the protein sequence. Any new
+ * mappings are added to the protein alignment. Returns true if any mappings
+ * either already exist or were added, else false.
+ *
+ * @param proteinAlignment
+ * @param cdnaAlignment
+ * @return
+ */
+ public static boolean mapProteinAlignmentToCdna(
+ final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment)
+ {
+ if (proteinAlignment == null || cdnaAlignment == null)
+ {
+ return false;
+ }
+
+ Set<SequenceI> mappedDna = new HashSet<SequenceI>();
+ Set<SequenceI> mappedProtein = new HashSet<SequenceI>();
+
+ /*
+ * First pass - map sequences where cross-references exist. This include
+ * 1-to-many mappings to support, for example, variant cDNA.
+ */
+ boolean mappingPerformed = mapProteinToCdna(proteinAlignment,
+ cdnaAlignment, mappedDna, mappedProtein, true);
+
+ /*
+ * Second pass - map sequences where no cross-references exist. This only
+ * does 1-to-1 mappings and assumes corresponding sequences are in the same
+ * order in the alignments.
+ */
+ mappingPerformed |= mapProteinToCdna(proteinAlignment, cdnaAlignment,
+ mappedDna, mappedProtein, false);
+ return mappingPerformed;
+ }
+
+ /**
+ * Make mappings between compatible sequences (where the cDNA translation
+ * matches the protein).
+ *
+ * @param proteinAlignment
+ * @param cdnaAlignment
+ * @param mappedDna
+ * a set of mapped DNA sequences (to add to)
+ * @param mappedProtein
+ * a set of mapped Protein sequences (to add to)
+ * @param xrefsOnly
+ * if true, only map sequences where xrefs exist
+ * @return
+ */
+ protected static boolean mapProteinToCdna(
+ final AlignmentI proteinAlignment,
+ final AlignmentI cdnaAlignment, Set<SequenceI> mappedDna,
+ Set<SequenceI> mappedProtein, boolean xrefsOnly)
+ {
+ boolean mappingExistsOrAdded = false;
+ List<SequenceI> thisSeqs = proteinAlignment.getSequences();
+ for (SequenceI aaSeq : thisSeqs)
+ {
+ boolean proteinMapped = false;
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ for (SequenceI cdnaSeq : cdnaAlignment.getSequences())
+ {
+ /*
+ * Always try to map if sequences have xref to each other; this supports
+ * variant cDNA or alternative splicing for a protein sequence.
+ *
+ * If no xrefs, try to map progressively, assuming that alignments have
+ * mappable sequences in corresponding order. These are not
+ * many-to-many, as that would risk mixing species with similar cDNA
+ * sequences.
+ */
+ if (xrefsOnly && !AlignmentUtils.haveCrossRef(aaSeq, cdnaSeq))
+ {
+ continue;
+ }
+
+ /*
+ * Don't map non-xrefd sequences more than once each. This heuristic
+ * allows us to pair up similar sequences in ordered alignments.
+ */
+ if (!xrefsOnly
+ && (mappedProtein.contains(aaSeq) || mappedDna
+ .contains(cdnaSeq)))
+ {
+ continue;
+ }
+ if (mappingExists(proteinAlignment.getCodonFrames(),
+ aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
+ {
+ mappingExistsOrAdded = true;
+ }
+ else
+ {
+ MapList map = mapProteinSequenceToCdna(aaSeq, cdnaSeq);
+ if (map != null)
+ {
+ acf.addMap(cdnaSeq, aaSeq, map);
+ mappingExistsOrAdded = true;
+ proteinMapped = true;
+ mappedDna.add(cdnaSeq);
+ mappedProtein.add(aaSeq);
+ }
+ }
+ }
+ if (proteinMapped)
+ {
+ proteinAlignment.addCodonFrame(acf);
+ }
+ }
+ return mappingExistsOrAdded;
+ }
+
+ /**
+ * Answers true if the mappings include one between the given (dataset)
+ * sequences.
+ */
+ public static boolean mappingExists(List<AlignedCodonFrame> mappings,
+ SequenceI aaSeq, SequenceI cdnaSeq)
+ {
+ if (mappings != null)
+ {
+ for (AlignedCodonFrame acf : mappings)
+ {
+ if (cdnaSeq == acf.getDnaForAaSeq(aaSeq))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Build a mapping (if possible) of a protein to a cDNA sequence. The cDNA
+ * must be three times the length of the protein, possibly after ignoring
+ * start and/or stop codons, and must translate to the protein. Returns null
+ * if no mapping is determined.
+ *
+ * @param proteinSeqs
+ * @param cdnaSeq
+ * @return
+ */
+ public static MapList mapProteinSequenceToCdna(SequenceI proteinSeq,
+ SequenceI cdnaSeq)
+ {
+ /*
+ * Here we handle either dataset sequence set (desktop) or absent (applet).
+ * Use only the char[] form of the sequence to avoid creating possibly large
+ * String objects.
+ */
+ final SequenceI proteinDataset = proteinSeq.getDatasetSequence();
+ char[] aaSeqChars = proteinDataset != null ? proteinDataset
+ .getSequence() : proteinSeq.getSequence();
+ final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence();
+ char[] cdnaSeqChars = cdnaDataset != null ? cdnaDataset.getSequence()
+ : cdnaSeq.getSequence();
+ if (aaSeqChars == null || cdnaSeqChars == null)
+ {
+ return null;
+ }
+
+ /*
+ * cdnaStart/End, proteinStartEnd are base 1 (for dataset sequence mapping)
+ */
+ final int mappedLength = 3 * aaSeqChars.length;
+ int cdnaLength = cdnaSeqChars.length;
+ int cdnaStart = cdnaSeq.getStart();
+ int cdnaEnd = cdnaSeq.getEnd();
+ final int proteinStart = proteinSeq.getStart();
+ final int proteinEnd = proteinSeq.getEnd();
+
+ /*
+ * If lengths don't match, try ignoring stop codon.
+ */
+ if (cdnaLength != mappedLength && cdnaLength > 2)
+ {
+ String lastCodon = String.valueOf(cdnaSeqChars, cdnaLength - 3, 3)
+ .toUpperCase();
+ for (String stop : ResidueProperties.STOP)
+ {
+ if (lastCodon.equals(stop))
+ {
+ cdnaEnd -= 3;
+ cdnaLength -= 3;
+ break;
+ }
+ }
+ }
+
+ /*
+ * If lengths still don't match, try ignoring start codon.
+ */
+ int startOffset = 0;
+ if (cdnaLength != mappedLength
+ && cdnaLength > 2
+ && String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
+ .equals(ResidueProperties.START))
+ {
+ startOffset += 3;
+ cdnaStart += 3;
+ cdnaLength -= 3;
+ }
+
+ if (cdnaLength != mappedLength)
+ {
+ return null;
+ }
+ if (!translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
+ {
+ return null;
+ }
+ MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, new int[] {
+ proteinStart, proteinEnd }, 3, 1);
+ return map;
+ }
+
+ /**
+ * Test whether the given cdna sequence, starting at the given offset,
+ * translates to the given amino acid sequence, using the standard translation
+ * table. Designed to fail fast i.e. as soon as a mismatch position is found.
+ *
+ * @param cdnaSeqChars
+ * @param cdnaStart
+ * @param aaSeqChars
+ * @return
+ */
+ protected static boolean translatesAs(char[] cdnaSeqChars, int cdnaStart,
+ char[] aaSeqChars)
+ {
+ if (cdnaSeqChars == null || aaSeqChars == null)
+ {
+ return false;
+ }
+
+ int aaResidue = 0;
+ for (int i = cdnaStart; i < cdnaSeqChars.length - 2
+ && aaResidue < aaSeqChars.length; i += 3, aaResidue++)
+ {
+ String codon = String.valueOf(cdnaSeqChars, i, 3);
+ final String translated = ResidueProperties.codonTranslate(codon);
+ /*
+ * allow * in protein to match untranslatable in dna
+ */
+ final char aaRes = aaSeqChars[aaResidue];
+ if ((translated == null || "STOP".equals(translated)) && aaRes == '*')
+ {
+ continue;
+ }
+ if (translated == null || !(aaRes == translated.charAt(0)))
+ {
+ // debug
+ // System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
+ // + codon + "(" + translated + ") != " + aaRes));
+ return false;
+ }
+ }
+ // fail if we didn't match all of the aa sequence
+ return (aaResidue == aaSeqChars.length);
+ }
+
+ /**
+ * Align sequence 'seq' to match the alignment of a mapped sequence. Note this
+ * currently assumes that we are aligning cDNA to match protein.
+ *
+ * @param seq
+ * the sequence to be realigned
+ * @param al
+ * the alignment whose sequence alignment is to be 'copied'
+ * @param gap
+ * character string represent a gap in the realigned sequence
+ * @param preserveUnmappedGaps
+ * @param preserveMappedGaps
+ * @return true if the sequence was realigned, false if it could not be
+ */
+ public static boolean alignSequenceAs(SequenceI seq, AlignmentI al,
+ String gap, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ /*
+ * Get any mappings from the source alignment to the target (dataset)
+ * sequence.
+ */
+ // TODO there may be one AlignedCodonFrame per dataset sequence, or one with
+ // all mappings. Would it help to constrain this?
+ List<AlignedCodonFrame> mappings = al.getCodonFrame(seq);
+ if (mappings == null || mappings.isEmpty())
+ {
+ return false;
+ }
+
+ /*
+ * Locate the aligned source sequence whose dataset sequence is mapped. We
+ * just take the first match here (as we can't align like more than one
+ * sequence).
+ */
+ SequenceI alignFrom = null;
+ AlignedCodonFrame mapping = null;
+ for (AlignedCodonFrame mp : mappings)
+ {
+ alignFrom = mp.findAlignedSequence(seq.getDatasetSequence(), al);
+ if (alignFrom != null)
+ {
+ mapping = mp;
+ break;
+ }
+ }
+
+ if (alignFrom == null)
+ {
+ return false;
+ }
+ alignSequenceAs(seq, alignFrom, mapping, gap, al.getGapCharacter(),
+ preserveMappedGaps, preserveUnmappedGaps);
+ return true;
+ }
+
+ /**
+ * Align sequence 'alignTo' the same way as 'alignFrom', using the mapping to
+ * match residues and codons. Flags control whether existing gaps in unmapped
+ * (intron) and mapped (exon) regions are preserved or not. Gaps between
+ * intron and exon are only retained if both flags are set.
+ *
+ * @param alignTo
+ * @param alignFrom
+ * @param mapping
+ * @param myGap
+ * @param sourceGap
+ * @param preserveUnmappedGaps
+ * @param preserveMappedGaps
+ */
+ public static void alignSequenceAs(SequenceI alignTo,
+ SequenceI alignFrom, AlignedCodonFrame mapping, String myGap,
+ char sourceGap, boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps)
+ {
+ // TODO generalise to work for Protein-Protein, dna-dna, dna-protein
+
+ // aligned and dataset sequence positions, all base zero
+ int thisSeqPos = 0;
+ int sourceDsPos = 0;
+
+ int basesWritten = 0;
+ char myGapChar = myGap.charAt(0);
+ int ratio = myGap.length();
+
+ int fromOffset = alignFrom.getStart() - 1;
+ int toOffset = alignTo.getStart() - 1;
+ int sourceGapMappedLength = 0;
+ boolean inExon = false;
+ final char[] thisSeq = alignTo.getSequence();
+ final char[] thatAligned = alignFrom.getSequence();
+ StringBuilder thisAligned = new StringBuilder(2 * thisSeq.length);
+
+ /*
+ * Traverse the 'model' aligned sequence
+ */
+ for (char sourceChar : thatAligned)
+ {
+ if (sourceChar == sourceGap)
+ {
+ sourceGapMappedLength += ratio;
+ continue;
+ }
+
+ /*
+ * Found a non-gap character. Locate its mapped region if any.
+ */
+ sourceDsPos++;
+ // Note mapping positions are base 1, our sequence positions base 0
+ int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom,
+ sourceDsPos + fromOffset);
+ if (mappedPos == null)
+ {
+ /*
+ * unmapped position; treat like a gap
+ */
+ sourceGapMappedLength += ratio;
+ // System.err.println("Can't align: no codon mapping to residue "
+ // + sourceDsPos + "(" + sourceChar + ")");
+ // return;
+ continue;
+ }
+
+ int mappedCodonStart = mappedPos[0]; // position (1...) of codon start
+ int mappedCodonEnd = mappedPos[mappedPos.length - 1]; // codon end pos
+ StringBuilder trailingCopiedGap = new StringBuilder();
+
+ /*
+ * Copy dna sequence up to and including this codon. Optionally, include
+ * gaps before the codon starts (in introns) and/or after the codon starts
+ * (in exons).
+ *
+ * Note this only works for 'linear' splicing, not reverse or interleaved.
+ * But then 'align dna as protein' doesn't make much sense otherwise.
+ */
+ int intronLength = 0;
+ while (basesWritten + toOffset < mappedCodonEnd
+ && thisSeqPos < thisSeq.length)
+ {
+ final char c = thisSeq[thisSeqPos++];
+ if (c != myGapChar)
+ {
+ basesWritten++;
+ int sourcePosition = basesWritten + toOffset;
+ if (sourcePosition < mappedCodonStart)
+ {
+ /*
+ * Found an unmapped (intron) base. First add in any preceding gaps
+ * (if wanted).
+ */
+ if (preserveUnmappedGaps && trailingCopiedGap.length() > 0)
+ {
+ thisAligned.append(trailingCopiedGap.toString());
+ intronLength += trailingCopiedGap.length();
+ trailingCopiedGap = new StringBuilder();
+ }
+ intronLength++;
+ inExon = false;
+ }
+ else
+ {
+ final boolean startOfCodon = sourcePosition == mappedCodonStart;
+ int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
+ preserveUnmappedGaps, sourceGapMappedLength, inExon,
+ trailingCopiedGap.length(), intronLength, startOfCodon);
+ for (int i = 0; i < gapsToAdd; i++)
+ {
+ thisAligned.append(myGapChar);
+ }
+ sourceGapMappedLength = 0;
+ inExon = true;
+ }
+ thisAligned.append(c);
+ trailingCopiedGap = new StringBuilder();
+ }
+ else
+ {
+ if (inExon && preserveMappedGaps)
+ {
+ trailingCopiedGap.append(myGapChar);
+ }
+ else if (!inExon && preserveUnmappedGaps)
+ {
+ trailingCopiedGap.append(myGapChar);
+ }
+ }
+ }
+ }
+
+ /*
+ * At end of model aligned sequence. Copy any remaining target sequence, optionally
+ * including (intron) gaps.
+ */
+ while (thisSeqPos < thisSeq.length)
+ {
+ final char c = thisSeq[thisSeqPos++];
+ if (c != myGapChar || preserveUnmappedGaps)
+ {
+ thisAligned.append(c);
+ }
+ sourceGapMappedLength--;
+ }
+
+ /*
+ * finally add gaps to pad for any trailing source gaps or
+ * unmapped characters
+ */
+ if (preserveUnmappedGaps)
+ {
+ while (sourceGapMappedLength > 0)
+ {
+ thisAligned.append(myGapChar);
+ sourceGapMappedLength--;
+ }
+ }
+
+ /*
+ * All done aligning, set the aligned sequence.
+ */
+ alignTo.setSequence(new String(thisAligned));
+ }
+
+ /**
+ * Helper method to work out how many gaps to insert when realigning.
+ *
+ * @param preserveMappedGaps
+ * @param preserveUnmappedGaps
+ * @param sourceGapMappedLength
+ * @param inExon
+ * @param trailingCopiedGap
+ * @param intronLength
+ * @param startOfCodon
+ * @return
+ */
+ protected static int calculateGapsToInsert(boolean preserveMappedGaps,
+ boolean preserveUnmappedGaps, int sourceGapMappedLength,
+ boolean inExon, int trailingGapLength, int intronLength,
+ final boolean startOfCodon)
+ {
+ int gapsToAdd = 0;
+ if (startOfCodon)
+ {
+ /*
+ * Reached start of codon. Ignore trailing gaps in intron unless we are
+ * preserving gaps in both exon and intron. Ignore them anyway if the
+ * protein alignment introduces a gap at least as large as the intronic
+ * region.
+ */
+ if (inExon && !preserveMappedGaps)
+ {
+ trailingGapLength = 0;
+ }
+ if (!inExon && !(preserveMappedGaps && preserveUnmappedGaps))
+ {
+ trailingGapLength = 0;
+ }
+ if (inExon)
+ {
+ gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
+ }
+ else
+ {
+ if (intronLength + trailingGapLength <= sourceGapMappedLength)
+ {
+ gapsToAdd = sourceGapMappedLength - intronLength;
+ }
+ else
+ {
+ gapsToAdd = Math.min(intronLength + trailingGapLength
+ - sourceGapMappedLength, trailingGapLength);
+ }
+ }
+ }
+ else
+ {
+ /*
+ * second or third base of codon; check for any gaps in dna
+ */
+ if (!preserveMappedGaps)
+ {
+ trailingGapLength = 0;
+ }
+ gapsToAdd = Math.max(sourceGapMappedLength, trailingGapLength);
+ }
+ return gapsToAdd;
+ }
+
+ /**
+ * Returns a list of sequences mapped from the given sequences and aligned
+ * (gapped) in the same way. For example, the cDNA for aligned protein, where
+ * a single gap in protein generates three gaps in cDNA.
+ *
+ * @param sequences
+ * @param gapCharacter
+ * @param mappings
+ * @return
+ */
+ public static List<SequenceI> getAlignedTranslation(
+ List<SequenceI> sequences, char gapCharacter,
+ Set<AlignedCodonFrame> mappings)
+ {
+ List<SequenceI> alignedSeqs = new ArrayList<SequenceI>();
+
+ for (SequenceI seq : sequences)
+ {
+ List<SequenceI> mapped = getAlignedTranslation(seq, gapCharacter,
+ mappings);
+ alignedSeqs.addAll(mapped);
+ }
+ return alignedSeqs;
+ }
+
+ /**
+ * Returns sequences aligned 'like' the source sequence, as mapped by the
+ * given mappings. Normally we expect zero or one 'mapped' sequences, but this
+ * will support 1-to-many as well.
+ *
+ * @param seq
+ * @param gapCharacter
+ * @param mappings
+ * @return
+ */
+ protected static List<SequenceI> getAlignedTranslation(SequenceI seq,
+ char gapCharacter, Set<AlignedCodonFrame> mappings)
+ {
+ List<SequenceI> result = new ArrayList<SequenceI>();
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (mapping.involvesSequence(seq))
+ {
+ SequenceI mapped = getAlignedTranslation(seq, gapCharacter, mapping);
+ if (mapped != null)
+ {
+ result.add(mapped);
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Returns the translation of 'seq' (as held in the mapping) with
+ * corresponding alignment (gaps).
+ *
+ * @param seq
+ * @param gapCharacter
+ * @param mapping
+ * @return
+ */
+ protected static SequenceI getAlignedTranslation(SequenceI seq,
+ char gapCharacter, AlignedCodonFrame mapping)
+ {
+ String gap = String.valueOf(gapCharacter);
+ boolean toDna = false;
+ int fromRatio = 1;
+ SequenceI mapTo = mapping.getDnaForAaSeq(seq);
+ if (mapTo != null)
+ {
+ // mapping is from protein to nucleotide
+ toDna = true;
+ // should ideally get gap count ratio from mapping
+ gap = String.valueOf(new char[] { gapCharacter, gapCharacter,
+ gapCharacter });
+ }
+ else
+ {
+ // mapping is from nucleotide to protein
+ mapTo = mapping.getAaForDnaSeq(seq);
+ fromRatio = 3;
+ }
+ StringBuilder newseq = new StringBuilder(seq.getLength()
+ * (toDna ? 3 : 1));
+
+ int residueNo = 0; // in seq, base 1
+ int[] phrase = new int[fromRatio];
+ int phraseOffset = 0;
+ int gapWidth = 0;
+ boolean first = true;
+ final Sequence alignedSeq = new Sequence("", "");
+
+ for (char c : seq.getSequence())
+ {
+ if (c == gapCharacter)
+ {
+ gapWidth++;
+ if (gapWidth >= fromRatio)
+ {
+ newseq.append(gap);
+ gapWidth = 0;
+ }
+ }
+ else
+ {
+ phrase[phraseOffset++] = residueNo + 1;
+ if (phraseOffset == fromRatio)
+ {
+ /*
+ * Have read a whole codon (or protein residue), now translate: map
+ * source phrase to positions in target sequence add characters at
+ * these positions to newseq Note mapping positions are base 1, our
+ * sequence positions base 0.
+ */
+ SearchResults sr = new SearchResults();
+ for (int pos : phrase)
+ {
+ mapping.markMappedRegion(seq, pos, sr);
+ }
+ newseq.append(sr.getCharacters());
+ if (first)
+ {
+ first = false;
+ // Hack: Copy sequence dataset, name and description from
+ // SearchResults.match[0].sequence
+ // TODO? carry over sequence names from original 'complement'
+ // alignment
+ SequenceI mappedTo = sr.getResultSequence(0);
+ alignedSeq.setName(mappedTo.getName());
+ alignedSeq.setDescription(mappedTo.getDescription());
+ alignedSeq.setDatasetSequence(mappedTo);
+ }
+ phraseOffset = 0;
+ }
+ residueNo++;
+ }
+ }
+ alignedSeq.setSequence(newseq.toString());
+ return alignedSeq;
+ }
+
+ /**
+ * Realigns the given protein to match the alignment of the dna, using codon
+ * mappings to translate aligned codon positions to protein residues.
+ *
+ * @param protein
+ * the alignment whose sequences are realigned by this method
+ * @param dna
+ * the dna alignment whose alignment we are 'copying'
+ * @return the number of sequences that were realigned
+ */
+ public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)
+ {
+ List<SequenceI> unmappedProtein = new ArrayList<SequenceI>();
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = buildCodonColumnsMap(
+ protein, dna, unmappedProtein);
+ return alignProteinAs(protein, alignedCodons, unmappedProtein);
+ }
+
+ /**
+ * Builds a map whose key is an aligned codon position (3 alignment column
+ * numbers base 0), and whose value is a map from protein sequence to each
+ * protein's peptide residue for that codon. The map generates an ordering of
+ * the codons, and allows us to read off the peptides at each position in
+ * order to assemble 'aligned' protein sequences.
+ *
+ * @param protein
+ * the protein alignment
+ * @param dna
+ * the coding dna alignment
+ * @param unmappedProtein
+ * any unmapped proteins are added to this list
+ * @return
+ */
+ protected static Map<AlignedCodon, Map<SequenceI, AlignedCodon>> buildCodonColumnsMap(
+ AlignmentI protein, AlignmentI dna,
+ List<SequenceI> unmappedProtein)
+ {
+ /*
+ * maintain a list of any proteins with no mappings - these will be
+ * rendered 'as is' in the protein alignment as we can't align them
+ */
+ unmappedProtein.addAll(protein.getSequences());
+
+ List<AlignedCodonFrame> mappings = protein.getCodonFrames();
+
+ /*
+ * Map will hold, for each aligned codon position e.g. [3, 5, 6], a map of
+ * {dnaSequence, {proteinSequence, codonProduct}} at that position. The
+ * comparator keeps the codon positions ordered.
+ */
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, AlignedCodon>>(
+ new CodonComparator());
+
+ for (SequenceI dnaSeq : dna.getSequences())
+ {
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ SequenceI prot = mapping.findAlignedSequence(
+ dnaSeq.getDatasetSequence(), protein);
+ if (prot != null)
+ {
+ Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
+ addCodonPositions(dnaSeq, prot, protein.getGapCharacter(),
+ seqMap, alignedCodons);
+ unmappedProtein.remove(prot);
+ }
+ }
+ }
+
+ /*
+ * Finally add any unmapped peptide start residues (e.g. for incomplete
+ * codons) as if at the codon position before the second residue
+ */
+ int mappedSequenceCount = protein.getHeight() - unmappedProtein.size();
+ addUnmappedPeptideStarts(alignedCodons, mappedSequenceCount);
+
+ return alignedCodons;
+ }
+
+ /**
+ * Scans for any protein mapped from position 2 (meaning unmapped start
+ * position e.g. an incomplete codon), and synthesizes a 'codon' for it at the
+ * preceding position in the alignment
+ *
+ * @param alignedCodons
+ * the codon-to-peptide map
+ * @param mappedSequenceCount
+ * the number of distinct sequences in the map
+ */
+ protected static void addUnmappedPeptideStarts(
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
+ int mappedSequenceCount)
+ {
+ // TODO there must be an easier way! root problem is that our mapping data
+ // model does not include phase so can't map part of a codon to a peptide
+ List<SequenceI> sequencesChecked = new ArrayList<SequenceI>();
+ AlignedCodon lastCodon = null;
+ Map<SequenceI, AlignedCodon> toAdd = new HashMap<SequenceI, AlignedCodon>();
+
+ for (Entry<AlignedCodon, Map<SequenceI, AlignedCodon>> entry : alignedCodons
+ .entrySet())
+ {
+ for (Entry<SequenceI, AlignedCodon> sequenceCodon : entry.getValue()
+ .entrySet())
+ {
+ SequenceI seq = sequenceCodon.getKey();
+ if (sequencesChecked.contains(seq))
+ {
+ continue;
+ }
+ sequencesChecked.add(seq);
+ AlignedCodon codon = sequenceCodon.getValue();
+ if (codon.peptideCol > 1)
+ {
+ System.err
+ .println("Problem mapping protein with >1 unmapped start positions: "
+ + seq.getName());
+ }
+ else if (codon.peptideCol == 1)
+ {
+ /*
+ * first position (peptideCol == 0) was unmapped - add it
+ */
+ if (lastCodon != null)
+ {
+ AlignedCodon firstPeptide = new AlignedCodon(lastCodon.pos1,
+ lastCodon.pos2, lastCodon.pos3, String.valueOf(seq
+ .getCharAt(0)), 0);
+ toAdd.put(seq, firstPeptide);
+ }
+ else
+ {
+ /*
+ * unmapped residue at start of alignment (no prior column) -
+ * 'insert' at nominal codon [0, 0, 0]
+ */
+ AlignedCodon firstPeptide = new AlignedCodon(0, 0, 0,
+ String.valueOf(seq.getCharAt(0)), 0);
+ toAdd.put(seq, firstPeptide);
+ }
+ }
+ if (sequencesChecked.size() == mappedSequenceCount)
+ {
+ // no need to check past first mapped position in all sequences
+ break;
+ }
+ }
+ lastCodon = entry.getKey();
+ }
+
+ /*
+ * add any new codons safely after iterating over the map
+ */
+ for (Entry<SequenceI, AlignedCodon> startCodon : toAdd.entrySet())
+ {
+ addCodonToMap(alignedCodons, startCodon.getValue(),
+ startCodon.getKey());
+ }
+ }
+
+ /**
+ * Update the aligned protein sequences to match the codon alignments given in
+ * the map.
+ *
+ * @param protein
+ * @param alignedCodons
+ * an ordered map of codon positions (columns), with sequence/peptide
+ * values present in each column
+ * @param unmappedProtein
+ * @return
+ */
+ protected static int alignProteinAs(AlignmentI protein,
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
+ List<SequenceI> unmappedProtein)
+ {
+ /*
+ * Prefill aligned sequences with gaps before inserting aligned protein
+ * residues.
+ */
+ int alignedWidth = alignedCodons.size();
+ char[] gaps = new char[alignedWidth];
+ Arrays.fill(gaps, protein.getGapCharacter());
+ String allGaps = String.valueOf(gaps);
+ for (SequenceI seq : protein.getSequences())
+ {
+ if (!unmappedProtein.contains(seq))
+ {
+ seq.setSequence(allGaps);
+ }
+ }
+
+ int column = 0;
+ for (AlignedCodon codon : alignedCodons.keySet())
+ {
+ final Map<SequenceI, AlignedCodon> columnResidues = alignedCodons
+ .get(codon);
+ for (Entry<SequenceI, AlignedCodon> entry : columnResidues.entrySet())
+ {
+ // place translated codon at its column position in sequence
+ entry.getKey().getSequence()[column] = entry.getValue().product
+ .charAt(0);
+ }
+ column++;
+ }
+ return 0;
+ }
+
+ /**
+ * Populate the map of aligned codons by traversing the given sequence
+ * mapping, locating the aligned positions of mapped codons, and adding those
+ * positions and their translation products to the map.
+ *
+ * @param dna
+ * the aligned sequence we are mapping from
+ * @param protein
+ * the sequence to be aligned to the codons
+ * @param gapChar
+ * the gap character in the dna sequence
+ * @param seqMap
+ * a mapping to a sequence translation
+ * @param alignedCodons
+ * the map we are building up
+ */
+ static void addCodonPositions(SequenceI dna, SequenceI protein,
+ char gapChar, Mapping seqMap,
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons)
+ {
+ Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
+
+ /*
+ * add codon positions, and their peptide translations, to the alignment
+ * map, while remembering the first codon mapped
+ */
+ while (codons.hasNext())
+ {
+ try
+ {
+ AlignedCodon codon = codons.next();
+ addCodonToMap(alignedCodons, codon, protein);
+ } catch (IncompleteCodonException e)
+ {
+ // possible incomplete trailing codon - ignore
+ }
+ }
+ }
+
+ /**
+ * Helper method to add a codon-to-peptide entry to the aligned codons map
+ *
+ * @param alignedCodons
+ * @param codon
+ * @param protein
+ */
+ protected static void addCodonToMap(
+ Map<AlignedCodon, Map<SequenceI, AlignedCodon>> alignedCodons,
+ AlignedCodon codon, SequenceI protein)
+ {
+ Map<SequenceI, AlignedCodon> seqProduct = alignedCodons.get(codon);
+ if (seqProduct == null)
+ {
+ seqProduct = new HashMap<SequenceI, AlignedCodon>();
+ alignedCodons.put(codon, seqProduct);
+ }
+ seqProduct.put(protein, codon);
+ }
+
+ /**
+ * Returns true if a cDNA/Protein mapping either exists, or could be made,
+ * between at least one pair of sequences in the two alignments. Currently,
+ * the logic is:
+ * <ul>
+ * <li>One alignment must be nucleotide, and the other protein</li>
+ * <li>At least one pair of sequences must be already mapped, or mappable</li>
+ * <li>Mappable means the nucleotide translation matches the protein sequence</li>
+ * <li>The translation may ignore start and stop codons if present in the
+ * nucleotide</li>
+ * </ul>
+ *
+ * @param al1
+ * @param al2
+ * @return
+ */
+ public static boolean isMappable(AlignmentI al1, AlignmentI al2)
+ {
+ if (al1 == null || al2 == null)
+ {
+ return false;
+ }
+
+ /*
+ * Require one nucleotide and one protein
+ */
+ if (al1.isNucleotide() == al2.isNucleotide())
+ {
+ return false;
+ }
+ AlignmentI dna = al1.isNucleotide() ? al1 : al2;
+ AlignmentI protein = dna == al1 ? al2 : al1;
+ List<AlignedCodonFrame> mappings = protein.getCodonFrames();
+ for (SequenceI dnaSeq : dna.getSequences())
+ {
+ for (SequenceI proteinSeq : protein.getSequences())
+ {
+ if (isMappable(dnaSeq, proteinSeq, mappings))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Returns true if the dna sequence is mapped, or could be mapped, to the
+ * protein sequence.
+ *
+ * @param dnaSeq
+ * @param proteinSeq
+ * @param mappings
+ * @return
+ */
+ protected static boolean isMappable(SequenceI dnaSeq,
+ SequenceI proteinSeq, List<AlignedCodonFrame> mappings)
+ {
+ if (dnaSeq == null || proteinSeq == null)
+ {
+ return false;
+ }
+
+ SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq
+ .getDatasetSequence();
+ SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
+ : proteinSeq.getDatasetSequence();
+
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ if (proteinDs == mapping.getAaForDnaSeq(dnaDs))
+ {
+ /*
+ * already mapped
+ */
+ return true;
+ }
+ }
+
+ /*
+ * Just try to make a mapping (it is not yet stored), test whether
+ * successful.
+ */
+ return mapProteinSequenceToCdna(proteinDs, dnaDs) != null;
+ }
+
+ /**
+ * Finds any reference annotations associated with the sequences in
+ * sequenceScope, that are not already added to the alignment, and adds them
+ * to the 'candidates' map. Also populates a lookup table of annotation
+ * labels, keyed by calcId, for use in constructing tooltips or the like.
+ *
+ * @param sequenceScope
+ * the sequences to scan for reference annotations
+ * @param labelForCalcId
+ * (optional) map to populate with label for calcId
+ * @param candidates
+ * map to populate with annotations for sequence
+ * @param al
+ * the alignment to check for presence of annotations
+ */
+ public static void findAddableReferenceAnnotations(
+ List<SequenceI> sequenceScope,
+ Map<String, String> labelForCalcId,
+ final Map<SequenceI, List<AlignmentAnnotation>> candidates,
+ AlignmentI al)
+ {
+ if (sequenceScope == null)
+ {
+ return;
+ }
+
+ /*
+ * For each sequence in scope, make a list of any annotations on the
+ * underlying dataset sequence which are not already on the alignment.
+ *
+ * Add to a map of { alignmentSequence, <List of annotations to add> }
+ */
+ for (SequenceI seq : sequenceScope)
+ {
+ SequenceI dataset = seq.getDatasetSequence();
+ if (dataset == null)
+ {
+ continue;
+ }
+ AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
+ if (datasetAnnotations == null)
+ {
+ continue;
+ }
+ final List<AlignmentAnnotation> result = new ArrayList<AlignmentAnnotation>();
+ for (AlignmentAnnotation dsann : datasetAnnotations)
+ {
+ /*
+ * Find matching annotations on the alignment. If none is found, then
+ * add this annotation to the list of 'addable' annotations for this
+ * sequence.
+ */
+ final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
+ .findAnnotations(seq, dsann.getCalcId(), dsann.label);
+ if (!matchedAlignmentAnnotations.iterator().hasNext())
+ {
+ result.add(dsann);
+ if (labelForCalcId != null)
+ {
+ labelForCalcId.put(dsann.getCalcId(), dsann.label);
+ }
+ }
+ }
+ /*
+ * Save any addable annotations for this sequence
+ */
+ if (!result.isEmpty())
+ {
+ candidates.put(seq, result);
+ }
+ }
+ }
+
+ /**
+ * Adds annotations to the top of the alignment annotations, in the same order
+ * as their related sequences.
+ *
+ * @param annotations
+ * the annotations to add
+ * @param alignment
+ * the alignment to add them to
+ * @param selectionGroup
+ * current selection group (or null if none)
+ */
+ public static void addReferenceAnnotations(
+ Map<SequenceI, List<AlignmentAnnotation>> annotations,
+ final AlignmentI alignment, final SequenceGroup selectionGroup)
+ {
+ for (SequenceI seq : annotations.keySet())
+ {
+ for (AlignmentAnnotation ann : annotations.get(seq))
+ {
+ AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann);
+ int startRes = 0;
+ int endRes = ann.annotations.length;
+ if (selectionGroup != null)
+ {
+ startRes = selectionGroup.getStartRes();
+ endRes = selectionGroup.getEndRes();
+ }
+ copyAnn.restrict(startRes, endRes);
+
+ /*
+ * Add to the sequence (sets copyAnn.datasetSequence), unless the
+ * original annotation is already on the sequence.
+ */
+ if (!seq.hasAnnotation(ann))
+ {
+ seq.addAlignmentAnnotation(copyAnn);
+ }
+ // adjust for gaps
+ copyAnn.adjustForAlignment();
+ // add to the alignment and set visible
+ alignment.addAnnotation(copyAnn);
+ copyAnn.visible = true;
+ }
+ }
+ }
+
+ /**
+ * Set visibility of alignment annotations of specified types (labels), for
+ * specified sequences. This supports controls like
+ * "Show all secondary structure", "Hide all Temp factor", etc.
+ *
+ * @al the alignment to scan for annotations
+ * @param types
+ * the types (labels) of annotations to be updated
+ * @param forSequences
+ * if not null, only annotations linked to one of these sequences are
+ * in scope for update; if null, acts on all sequence annotations
+ * @param anyType
+ * if this flag is true, 'types' is ignored (label not checked)
+ * @param doShow
+ * if true, set visibility on, else set off
+ */
+ public static void showOrHideSequenceAnnotations(AlignmentI al,
+ Collection<String> types, List<SequenceI> forSequences,
+ boolean anyType, boolean doShow)
+ {
+ for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
+ {
+ if (anyType || types.contains(aa.label))
+ {
+ if ((aa.sequenceRef != null)
+ && (forSequences == null || forSequences
+ .contains(aa.sequenceRef)))
+ {
+ aa.visible = doShow;
+ }
+ }
+ }
+ }
+
+ /**
+ * Returns true if either sequence has a cross-reference to the other
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ public static boolean haveCrossRef(SequenceI seq1, SequenceI seq2)
+ {
+ // Note: moved here from class CrossRef as the latter class has dependencies
+ // not availability to the applet's classpath
+ return hasCrossRef(seq1, seq2) || hasCrossRef(seq2, seq1);
+ }
+
+ /**
+ * Returns true if seq1 has a cross-reference to seq2. Currently this assumes
+ * that sequence name is structured as Source|AccessionId.
+ *
+ * @param seq1
+ * @param seq2
+ * @return
+ */
+ public static boolean hasCrossRef(SequenceI seq1, SequenceI seq2)
+ {
+ if (seq1 == null || seq2 == null)
+ {
+ return false;
+ }
+ String name = seq2.getName();
+ final DBRefEntry[] xrefs = seq1.getDBRefs();
+ if (xrefs != null)
+ {
+ for (DBRefEntry xref : xrefs)
+ {
+ String xrefName = xref.getSource() + "|" + xref.getAccessionId();
+ // case-insensitive test, consistent with DBRefEntry.equalRef()
+ if (xrefName.equalsIgnoreCase(name))
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
+
+ /**
+ * Constructs an alignment consisting of the mapped (CDS) regions in the given
+ * nucleotide sequences, and updates mappings to match. The new sequences are
+ * aligned as per the original sequences (with gapped columns omitted).
+ *
+ * @param dna
+ * aligned dna sequences
+ * @param mappings
+ * from dna to protein; these are replaced with new mappings
+ * @param gapChar
+ * @return an alignment whose sequences are the cds-only parts of the dna
+ * sequences (or null if no mappings are found)
+ */
+ public static AlignmentI makeCdsAlignment(SequenceI[] dna,
+ List<AlignedCodonFrame> mappings, char gapChar)
+ {
+ List<int[]> cdsColumns = findCdsColumns(dna);
+
+ /*
+ * create CDS sequences and new mappings
+ * (from cdna to cds, and cds to peptide)
+ */
+ List<AlignedCodonFrame> newMappings = new ArrayList<AlignedCodonFrame>();
+ List<SequenceI> cdsSequences = new ArrayList<SequenceI>();
+
+ for (SequenceI dnaSeq : dna)
+ {
+ final SequenceI ds = dnaSeq.getDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = MappingUtils
+ .findMappingsForSequence(ds, mappings);
+ for (AlignedCodonFrame acf : seqMappings)
+ {
+ AlignedCodonFrame newMapping = new AlignedCodonFrame();
+ final List<SequenceI> mappedCds = makeCdsSequences(dnaSeq, acf,
+ cdsColumns, newMapping, gapChar);
+ if (!mappedCds.isEmpty())
+ {
+ cdsSequences.addAll(mappedCds);
+ newMappings.add(newMapping);
+ }
+ }
+ }
+ AlignmentI al = new Alignment(
+ cdsSequences.toArray(new SequenceI[cdsSequences.size()]));
+ al.setGapCharacter(gapChar);
+ al.setDataset(null);
+
+ /*
+ * Replace the old mappings with the new ones
+ */
+ mappings.clear();
+ mappings.addAll(newMappings);
+
+ return al;
+ }
+
+ /**
+ * Returns a consolidated list of column ranges where at least one sequence
+ * has a CDS feature. This assumes CDS features are on genomic sequence i.e.
+ * are for contiguous CDS ranges (no gaps).
+ *
+ * @param seqs
+ * @return
+ */
+ public static List<int[]> findCdsColumns(SequenceI[] seqs)
+ {
+ // TODO use refactored code from AlignViewController
+ // markColumnsContainingFeatures, not reinvent the wheel!
+
+ List<int[]> result = new ArrayList<int[]>();
+ for (SequenceI seq : seqs)
+ {
+ result.addAll(findCdsColumns(seq));
+ }
+
+ /*
+ * sort and compact the list into ascending, non-overlapping ranges
+ */
+ Collections.sort(result, new Comparator<int[]>()
+ {
+ @Override
+ public int compare(int[] o1, int[] o2)
+ {
+ return Integer.compare(o1[0], o2[0]);
+ }
+ });
+ result = MapList.coalesceRanges(result);
+
+ return result;
+ }
+
+ public static List<int[]> findCdsColumns(SequenceI seq)
+ {
+ List<int[]> result = new ArrayList<int[]>();
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ SequenceFeature[] sfs = seq.getSequenceFeatures();
+ if (sfs != null)
+ {
+ for (SequenceFeature sf : sfs)
+ {
+ if (so.isA(sf.getType(), SequenceOntologyI.CDS))
+ {
+ int colStart = seq.findIndex(sf.getBegin());
+ int colEnd = seq.findIndex(sf.getEnd());
+ result.add(new int[] { colStart, colEnd });
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Answers true if all sequences have a gap at (or do not extend to) the
+ * specified column position (base 1)
+ *
+ * @param seqs
+ * @param col
+ * @return
+ */
+ public static boolean isGappedColumn(List<SequenceI> seqs, int col)
+ {
+ if (seqs != null)
+ {
+ for (SequenceI seq : seqs)
+ {
+ if (!Comparison.isGap(seq.getCharAt(col - 1)))
+ {
+ return false;
+ }
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Returns the column ranges (base 1) of each aligned sequence that are
+ * involved in any mapping. This is a helper method for aligning protein
+ * products of aligned transcripts.
+ *
+ * @param mappedSequences
+ * (possibly gapped) dna sequences
+ * @param mappings
+ * @return
+ */
+ protected static List<List<int[]>> getMappedColumns(
+ List<SequenceI> mappedSequences, List<AlignedCodonFrame> mappings)
+ {
+ List<List<int[]>> result = new ArrayList<List<int[]>>();
+ for (SequenceI seq : mappedSequences)
+ {
+ List<int[]> columns = new ArrayList<int[]>();
+ List<AlignedCodonFrame> seqMappings = MappingUtils
+ .findMappingsForSequence(seq, mappings);
+ for (AlignedCodonFrame mapping : seqMappings)
+ {
+ List<Mapping> maps = mapping.getMappingsForSequence(seq);
+ for (Mapping map : maps)
+ {
+ /*
+ * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
+ * Find and add the overall aligned column range for each
+ */
+ for (int[] cdsRange : map.getMap().getFromRanges())
+ {
+ int startPos = cdsRange[0];
+ int endPos = cdsRange[1];
+ int startCol = seq.findIndex(startPos);
+ int endCol = seq.findIndex(endPos);
+ columns.add(new int[] { startCol, endCol });
+ }
+ }
+ }
+ result.add(columns);
+ }
+ return result;
+ }
+
+ /**
+ * Helper method to make cds-only sequences and populate their mappings to
+ * protein products
+ * <p>
+ * For example, if ggCCaTTcGAg has mappings [3, 4, 6, 7, 9, 10] to protein
+ * then generate a sequence CCTTGA with mapping [1, 6] to the same protein
+ * residues
+ * <p>
+ * Typically eukaryotic dna will include cds encoding for a single peptide
+ * sequence i.e. return a single result. Bacterial dna may have overlapping
+ * cds mappings coding for multiple peptides so return multiple results
+ * (example EMBL KF591215).
+ *
+ * @param dnaSeq
+ * a dna aligned sequence
+ * @param mapping
+ * containing one or more mappings of the sequence to protein
+ * @param ungappedCdsColumns
+ * @param newMappings
+ * the new mapping to populate, from the cds-only sequences to their
+ * mapped protein sequences
+ * @return
+ */
+ protected static List<SequenceI> makeCdsSequences(SequenceI dnaSeq,
+ AlignedCodonFrame mapping, List<int[]> ungappedCdsColumns,
+ AlignedCodonFrame newMappings, char gapChar)
+ {
+ List<SequenceI> cdsSequences = new ArrayList<SequenceI>();
+ List<Mapping> seqMappings = mapping.getMappingsForSequence(dnaSeq);
+
+ for (Mapping seqMapping : seqMappings)
+ {
+ SequenceI cds = makeCdsSequence(dnaSeq, seqMapping,
+ ungappedCdsColumns, gapChar);
+ cdsSequences.add(cds);
+
+ /*
+ * add new mappings, from dna to cds, and from cds to peptide
+ */
+ MapList dnaToCds = addCdsMappings(dnaSeq.getDatasetSequence(), cds,
+ seqMapping, newMappings);
+
+ /*
+ * transfer any features on dna that overlap the CDS
+ */
+ transferFeatures(dnaSeq, cds, dnaToCds, null, SequenceOntologyI.CDS);
+ }
+ return cdsSequences;
+ }
+
+ /**
+ * Transfers co-located features on 'fromSeq' to 'toSeq', adjusting the
+ * feature start/end ranges, optionally omitting specified feature types.
+ * Returns the number of features copied.
+ *
+ * @param fromSeq
+ * @param toSeq
+ * @param select
+ * if not null, only features of this type are copied (including
+ * subtypes in the Sequence Ontology)
+ * @param mapping
+ * the mapping from 'fromSeq' to 'toSeq'
+ * @param omitting
+ */
+ public static int transferFeatures(SequenceI fromSeq, SequenceI toSeq,
+ MapList mapping, String select, String... omitting)
+ {
+ SequenceI copyTo = toSeq;
+ while (copyTo.getDatasetSequence() != null)
+ {
+ copyTo = copyTo.getDatasetSequence();
+ }
+
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ int count = 0;
+ SequenceFeature[] sfs = fromSeq.getSequenceFeatures();
+ if (sfs != null)
+ {
+ for (SequenceFeature sf : sfs)
+ {
+ String type = sf.getType();
+ if (select != null && !so.isA(type, select))
+ {
+ continue;
+ }
+ boolean omit = false;
+ for (String toOmit : omitting)
+ {
+ if (type.equals(toOmit))
+ {
+ omit = true;
+ }
+ }
+ if (omit)
+ {
+ continue;
+ }
+
+ /*
+ * locate the mapped range - null if either start or end is
+ * not mapped (no partial overlaps are calculated)
+ */
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ int[] mappedTo = mapping.locateInTo(start, end);
+ /*
+ * if whole exon range doesn't map, try interpreting it
+ * as 5' or 3' exon overlapping the CDS range
+ */
+ if (mappedTo == null)
+ {
+ mappedTo = mapping.locateInTo(end, end);
+ if (mappedTo != null)
+ {
+ /*
+ * end of exon is in CDS range - 5' overlap
+ * to a range from the start of the peptide
+ */
+ mappedTo[0] = 1;
+ }
+ }
+ if (mappedTo == null)
+ {
+ mappedTo = mapping.locateInTo(start, start);
+ if (mappedTo != null)
+ {
+ /*
+ * start of exon is in CDS range - 3' overlap
+ * to a range up to the end of the peptide
+ */
+ mappedTo[1] = toSeq.getLength();
+ }
+ }
+ if (mappedTo != null)
+ {
+ SequenceFeature copy = new SequenceFeature(sf);
+ copy.setBegin(Math.min(mappedTo[0], mappedTo[1]));
+ copy.setEnd(Math.max(mappedTo[0], mappedTo[1]));
+ copyTo.addSequenceFeature(copy);
+ count++;
+ }
+ }
+ }
+ return count;
+ }
+
+ /**
+ * Creates and adds mappings
+ * <ul>
+ * <li>from cds to peptide</li>
+ * <li>from dna to cds</li>
+ * </ul>
+ * and returns the dna-to-cds mapping
+ *
+ * @param dnaSeq
+ * @param cdsSeq
+ * @param dnaMapping
+ * @param newMappings
+ * @return
+ */
+ protected static MapList addCdsMappings(SequenceI dnaSeq,
+ SequenceI cdsSeq, Mapping dnaMapping,
+ AlignedCodonFrame newMappings)
+ {
+ cdsSeq.createDatasetSequence();
+
+ /*
+ * CDS to peptide is just a contiguous 3:1 mapping, with
+ * the peptide ranges taken unchanged from the dna mapping
+ */
+ List<int[]> cdsRanges = new ArrayList<int[]>();
+ SequenceI cdsDataset = cdsSeq.getDatasetSequence();
+ cdsRanges.add(new int[] { 1, cdsDataset.getLength() });
+ MapList cdsToPeptide = new MapList(cdsRanges, dnaMapping.getMap()
+ .getToRanges(), 3, 1);
+ newMappings.addMap(cdsDataset, dnaMapping.getTo(), cdsToPeptide);
+
+ /*
+ * dna 'from' ranges map 1:1 to the contiguous extracted CDS
+ */
+ MapList dnaToCds = new MapList(dnaMapping.getMap().getFromRanges(),
+ cdsRanges, 1, 1);
+ newMappings.addMap(dnaSeq, cdsDataset, dnaToCds);
+ return dnaToCds;
+ }
+
+ /**
+ * Makes and returns a CDS-only sequence, where the CDS regions are identified
+ * as the 'from' ranges of the mapping on the dna.
+ *
+ * @param dnaSeq
+ * nucleotide sequence
+ * @param seqMapping
+ * mappings from CDS regions of nucleotide
+ * @param ungappedCdsColumns
+ * @return
+ */
+ protected static SequenceI makeCdsSequence(SequenceI dnaSeq,
+ Mapping seqMapping, List<int[]> ungappedCdsColumns, char gapChar)
+ {
+ int cdsWidth = MappingUtils.getLength(ungappedCdsColumns);
+
+ /*
+ * populate CDS columns with the aligned
+ * column character if that column is mapped (which may be a gap
+ * if an intron interrupts a codon), else with a gap
+ */
+ List<int[]> fromRanges = seqMapping.getMap().getFromRanges();
+ char[] cdsChars = new char[cdsWidth];
+ int pos = 0;
+ for (int[] columns : ungappedCdsColumns)
+ {
+ for (int i = columns[0]; i <= columns[1]; i++)
+ {
+ char dnaChar = dnaSeq.getCharAt(i - 1);
+ if (Comparison.isGap(dnaChar))
+ {
+ cdsChars[pos] = gapChar;
+ }
+ else
+ {
+ int seqPos = dnaSeq.findPosition(i - 1);
+ if (MappingUtils.contains(fromRanges, seqPos))
+ {
+ cdsChars[pos] = dnaChar;
+ }
+ else
+ {
+ cdsChars[pos] = gapChar;
+ }
+ }
+ pos++;
+ }
+ }
+ SequenceI cdsSequence = new Sequence(dnaSeq.getName(),
+ String.valueOf(cdsChars));
+
+ transferDbRefs(seqMapping.getTo(), cdsSequence);
+
+ return cdsSequence;
+ }
+
+ /**
+ * Locate any xrefs to CDS databases on the protein product and attach to the
+ * CDS sequence. Also add as a sub-token of the sequence name.
+ *
+ * @param from
+ * @param to
+ */
+ protected static void transferDbRefs(SequenceI from, SequenceI to)
+ {
+ String cdsAccId = FeatureProperties.getCodingFeature(DBRefSource.EMBL);
+ DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(from.getDBRefs(),
+ DBRefSource.CODINGDBS);
+ if (cdsRefs != null)
+ {
+ for (DBRefEntry cdsRef : cdsRefs)
+ {
+ to.addDBRef(new DBRefEntry(cdsRef));
+ cdsAccId = cdsRef.getAccessionId();
+ }
+ }
+ if (!to.getName().contains(cdsAccId))
+ {
+ to.setName(to.getName() + "|" + cdsAccId);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff