+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis;
+import jalview.datamodel.AlignedCodon;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Mapping;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+import jalview.util.MapList;
+
import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
import java.util.List;
-
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.AlignmentI;
+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 refactored elsewhere at some point.
+ * grab bag of useful alignment manipulation operations Expect these to be
+ * refactored elsewhere at some point.
+ *
* @author jimp
- *
+ *
*/
public class AlignmentUtils
{
/**
- * given an existing alignment, create a new alignment including all, or up to flankSize additional symbols from each sequence's dataset sequence
+ * Represents the 3 possible results of trying to map one alignment to
+ * another.
+ */
+ public enum MappingResult
+ {
+ Mapped, NotMapped, AlreadyMapped
+ }
+
+ /**
+ * given an existing alignment, create a new alignment including all, or up to
+ * flankSize additional symbols from each sequence's dataset sequence
+ *
* @param core
* @param flankSize
* @return AlignmentI
{
List<SequenceI> sq = new ArrayList<SequenceI>();
int maxoffset = 0;
- for (SequenceI s:core.getSequences())
+ for (SequenceI s : core.getSequences())
{
SequenceI newSeq = s.deriveSequence();
- if (newSeq.getStart()>maxoffset)
+ if (newSeq.getStart() > maxoffset
+ && newSeq.getDatasetSequence().getStart() < s.getStart())
{
maxoffset = newSeq.getStart();
}
sq.add(newSeq);
}
- if (flankSize>-1) {
+ if (flankSize > -1)
+ {
maxoffset = flankSize;
}
// now add offset to create a new expanded alignment
- for (SequenceI s:sq)
+ for (SequenceI s : sq)
{
SequenceI ds = s;
- while (ds.getDatasetSequence()!=null) {
- ds=ds.getDatasetSequence();
+ while (ds.getDatasetSequence() != null)
+ {
+ ds = ds.getDatasetSequence();
}
+ 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.getEnd();
-
+ int ustream_ds = s.getStart() - ds.getStart(), dstream_ds = ds
+ .getEnd() - s_end;
+
// build new flanked sequence
-
+
// compute gap padding to start of flanking sequence
- int offset=maxoffset - ustream_ds;
-
+ int offset = maxoffset - ustream_ds;
+
// padding is gapChar x ( maxoffset - min(ustream_ds, flank)
- if (flankSize>=0) {
- if (flankSize<ustream_ds)
+ if (flankSize >= 0)
+ {
+ if (flankSize < ustream_ds)
{
- // take up to flankSize residues
- offset = maxoffset-flankSize;
- ustream_ds = flankSize;
- }
- if (flankSize<dstream_ds)
+ // take up to flankSize residues
+ offset = maxoffset - flankSize;
+ ustream_ds = flankSize;
+ }
+ if (flankSize < dstream_ds)
{
- dstream_ds=flankSize;
+ dstream_ds = flankSize;
}
}
- char[] upstream = new String(ds.getSequence(s.getStart()-1-ustream_ds, s.getStart()-1)).toLowerCase().toCharArray();
- char[] downstream = new String(ds.getSequence(s.getEnd()+1,s.getEnd()+1+dstream_ds)).toLowerCase().toCharArray();
- char[] coreseq=s.getSequence();
- char[] nseq = new char[offset+upstream.length+downstream.length+coreseq.length];
+ 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
+ + 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++)
+ int p = 0;
+ for (; p < offset; p++)
{
nseq[p] = c;
}
-// s.setSequence(new String(upstream).toLowerCase()+new String(coreseq) + new String(downstream).toLowerCase());
+ // 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);
- System.arraycopy(downstream, 0, nseq, p+coreseq.length+upstream.length, downstream.length);
+ System.arraycopy(coreseq, 0, nseq, p + upstream.length,
+ coreseq.length);
+ System.arraycopy(downstream, 0, nseq, p + coreseq.length
+ + upstream.length, downstream.length);
s.setSequence(new String(nseq));
- s.setStart(s.getStart()-ustream_ds);
- s.setEnd(s.getEnd()+downstream.length);
+ s.setStart(s.getStart() - ustream_ds);
+ s.setEnd(s_end + downstream.length);
+ }
+ AlignmentI newAl = new jalview.datamodel.Alignment(
+ sq.toArray(new SequenceI[0]));
+ for (SequenceI s : sq)
+ {
+ if (s.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : s.getAnnotation())
+ {
+ newAl.addAnnotation(aa);
+ }
+ }
}
- AlignmentI newAl = new jalview.datamodel.Alignment(sq.toArray(new SequenceI[0]));
newAl.setDataset(core.getDataset());
return newAl;
}
+
+ /**
+ * Returns the index (zero-based position) of a sequence in an alignment, or
+ * -1 if not found.
+ *
+ * @param al
+ * @param seq
+ * @return
+ */
+ public static int getSequenceIndex(AlignmentI al, SequenceI seq)
+ {
+ int result = -1;
+ int pos = 0;
+ for (SequenceI alSeq : al.getSequences())
+ {
+ if (alSeq == seq)
+ {
+ result = pos;
+ break;
+ }
+ pos++;
+ }
+ 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. Has a 3-valued result: either
+ * Mapped (at least one sequence mapping was created), AlreadyMapped (all
+ * possible sequence mappings already exist), or NotMapped (no possible
+ * sequence mappings exist).
+ *
+ * @param proteinAlignment
+ * @param cdnaAlignment
+ * @return
+ */
+ public static MappingResult mapProteinToCdna(
+ final AlignmentI proteinAlignment,
+ final AlignmentI cdnaAlignment)
+ {
+ if (proteinAlignment == null || cdnaAlignment == null)
+ {
+ return MappingResult.NotMapped;
+ }
+
+ boolean mappingPossible = false;
+ boolean mappingPerformed = false;
+
+ List<SequenceI> mapped = new ArrayList<SequenceI>();
+
+ List<SequenceI> thisSeqs = proteinAlignment.getSequences();
+
+ for (SequenceI aaSeq : thisSeqs)
+ {
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+
+ for (SequenceI cdnaSeq : cdnaAlignment.getSequences())
+ {
+ /*
+ * Heuristic rule: don't map more than one AA sequence to the same cDNA;
+ * map progressively assuming that alignments have mappable sequences in
+ * the same respective order
+ */
+ if (mapped.contains(cdnaSeq))
+ {
+ continue;
+ }
+ if (!mappingExists(proteinAlignment.getCodonFrames(),
+ aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
+ {
+ MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
+ if (map != null)
+ {
+ acf.addMap(cdnaSeq, aaSeq, map);
+ mappingPerformed = true;
+ mapped.add(cdnaSeq);
+
+ /*
+ * Heuristic rule #2: don't map AA sequence to more than one cDNA
+ */
+ break;
+ }
+ }
+ }
+ proteinAlignment.addCodonFrame(acf);
+ }
+
+ /*
+ * If at least one mapping was possible but none was done, then the
+ * alignments are already as mapped as they can be.
+ */
+ if (mappingPossible && !mappingPerformed)
+ {
+ return MappingResult.AlreadyMapped;
+ }
+ else
+ {
+ return mappingPerformed ? MappingResult.Mapped
+ : MappingResult.NotMapped;
+ }
+ }
+
+ /**
+ * Answers true if the mappings include one between the given (dataset)
+ * sequences.
+ */
+ public static boolean mappingExists(Set<AlignedCodonFrame> set,
+ SequenceI aaSeq, SequenceI cdnaSeq)
+ {
+ if (set != null)
+ {
+ for (AlignedCodonFrame acf : set)
+ {
+ 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 mapProteinToCdna(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 = 1;
+ int cdnaEnd = cdnaLength;
+ final int proteinStart = 1;
+ final int proteinEnd = aaSeqChars.length;
+
+ /*
+ * 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.
+ */
+ if (cdnaLength != mappedLength
+ && cdnaLength > 2
+ && String.valueOf(cdnaSeqChars, 0, 3).toUpperCase()
+ .equals(
+ ResidueProperties.START))
+ {
+ cdnaStart += 3;
+ cdnaLength -= 3;
+ }
+
+ if (cdnaLength != mappedLength)
+ {
+ return null;
+ }
+ if (!translatesAs(cdnaSeqChars, cdnaStart - 1, 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)
+ {
+ int aaResidue = 0;
+ for (int i = cdnaStart; i < cdnaSeqChars.length - 2
+ && aaResidue < aaSeqChars.length; i += 3)
+ {
+ String codon = String.valueOf(cdnaSeqChars, i, 3);
+ final String translated = ResidueProperties.codonTranslate(
+ codon);
+ if (translated == null
+ || !(aaSeqChars[aaResidue] == translated.charAt(0)))
+ {
+ return false;
+ }
+ aaResidue++;
+ }
+ // 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 cDNA like more than one
+ * protein 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 linking intro
+ * 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
+ final char[] thisSeq = alignTo.getSequence();
+ final char[] thatAligned = alignFrom.getSequence();
+ StringBuilder thisAligned = new StringBuilder(2 * thisSeq.length);
+
+ // 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();
+
+ /*
+ * Traverse the aligned protein sequence.
+ */
+ int sourceGapMappedLength = 0;
+ boolean inExon = false;
+ for (char sourceChar : thatAligned)
+ {
+ if (sourceChar == sourceGap)
+ {
+ sourceGapMappedLength += ratio;
+ continue;
+ }
+
+ /*
+ * Found a residue. Locate its mapped codon (start) position.
+ */
+ sourceDsPos++;
+ // Note mapping positions are base 1, our sequence positions base 0
+ int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom,
+ sourceDsPos);
+ if (mappedPos == null)
+ {
+ /*
+ * Abort realignment if unmapped protein. Or could ignore it??
+ */
+ System.err.println("Can't align: no codon mapping to residue "
+ + sourceDsPos + "(" + sourceChar + ")");
+ return;
+ }
+
+ 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 < mappedCodonEnd && thisSeqPos < thisSeq.length)
+ {
+ final char c = thisSeq[thisSeqPos++];
+ if (c != myGapChar)
+ {
+ basesWritten++;
+
+ if (basesWritten < 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 = basesWritten == 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 protein sequence. Copy any remaining dna sequence, optionally
+ * including (intron) gaps. We do not copy trailing gaps in protein.
+ */
+ while (thisSeqPos < thisSeq.length)
+ {
+ final char c = thisSeq[thisSeqPos++];
+ if (c != myGapChar || preserveUnmappedGaps)
+ {
+ thisAligned.append(c);
+ }
+ }
+
+ /*
+ * 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.toString());
+ 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)
+ {
+ Set<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, String>> alignedCodons = new TreeMap<AlignedCodon, Map<SequenceI, String>>(
+ new CodonComparator());
+ for (SequenceI dnaSeq : dna.getSequences())
+ {
+ for (AlignedCodonFrame mapping : mappings)
+ {
+ Mapping seqMap = mapping.getMappingForSequence(dnaSeq);
+ SequenceI prot = mapping.findAlignedSequence(
+ dnaSeq.getDatasetSequence(), protein);
+ if (prot != null)
+ {
+ addCodonPositions(dnaSeq, prot, protein.getGapCharacter(),
+ seqMap, alignedCodons);
+ }
+ }
+ }
+ return alignProteinAs(protein, alignedCodons);
+ }
+
+ /**
+ * 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
+ * @return
+ */
+ protected static int alignProteinAs(AlignmentI protein,
+ Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
+ {
+ /*
+ * 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())
+ {
+ seq.setSequence(allGaps);
+ }
+
+ int column = 0;
+ for (AlignedCodon codon : alignedCodons.keySet())
+ {
+ final Map<SequenceI, String> columnResidues = alignedCodons.get(codon);
+ for (Entry<SequenceI, String> entry : columnResidues
+ .entrySet())
+ {
+ // place translated codon at its column position in sequence
+ entry.getKey().getSequence()[column] = entry.getValue().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, String>> alignedCodons)
+ {
+ Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
+ while (codons.hasNext())
+ {
+ AlignedCodon codon = codons.next();
+ Map<SequenceI, String> seqProduct = alignedCodons.get(codon);
+ if (seqProduct == null)
+ {
+ seqProduct = new HashMap<SequenceI, String>();
+ alignedCodons.put(codon, seqProduct);
+ }
+ seqProduct.put(protein, codon.product);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff