/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
import jalview.util.MapList;
import java.util.ArrayList;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
/**
* grab bag of useful alignment manipulation operations Expect these to be
* refactored elsewhere at some point.
*
* @author jimp
*
*/
public class AlignmentUtils
{
/**
* 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
*/
public static AlignmentI expandContext(AlignmentI core, int flankSize)
{
List sq = new ArrayList();
int maxoffset = 0;
for (SequenceI s : core.getSequences())
{
SequenceI newSeq = s.deriveSequence();
if (newSeq.getStart() > maxoffset
&& newSeq.getDatasetSequence().getStart() < s.getStart())
{
maxoffset = newSeq.getStart();
}
sq.add(newSeq);
}
if (flankSize > -1)
{
maxoffset = flankSize;
}
// now add offset to create a new expanded alignment
for (SequenceI s : sq)
{
SequenceI ds = s;
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_end;
// build new flanked sequence
// compute gap padding to start of flanking sequence
int offset = maxoffset - ustream_ds;
// padding is gapChar x ( maxoffset - min(ustream_ds, flank)
if (flankSize >= 0)
{
if (flankSize < ustream_ds)
{
// take up to flankSize residues
offset = maxoffset - flankSize;
ustream_ds = flankSize;
}
if (flankSize < dstream_ds)
{
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_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++)
{
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);
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_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);
}
}
}
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> getSequencesByName(
AlignmentI al)
{
Map> theMap = new LinkedHashMap>();
for (SequenceI seq : al.getSequences())
{
String name = seq.getName();
if (name != null)
{
List seqs = theMap.get(name);
if (seqs == null)
{
seqs = new ArrayList();
theMap.put(name, seqs);
}
seqs.add(seq);
}
}
return theMap;
}
/**
* Build mapping of protein to cDNA alignment. Mappings are made between
* sequences which have the same name and compatible lengths. 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 thisSeqs = proteinAlignment.getSequences();
/*
* Build a look-up of cDNA sequences by name, for matching purposes.
*/
Map> cdnaSeqs = cdnaAlignment
.getSequencesByName();
for (SequenceI aaSeq : thisSeqs)
{
AlignedCodonFrame acf = new AlignedCodonFrame();
List candidates = cdnaSeqs.get(aaSeq.getName());
if (candidates == null)
{
/*
* No cDNA sequence with matching name, so no mapping possible for this
* protein sequence
*/
continue;
}
mappingPossible = true;
for (SequenceI cdnaSeq : candidates)
{
if (!mappingExists(proteinAlignment.getCodonFrames(),
aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
{
MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
if (map != null)
{
acf.addMap(cdnaSeq, aaSeq, map);
mappingPerformed = true;
}
}
}
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 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. 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)
*/
final SequenceI proteinDataset = proteinSeq.getDatasetSequence();
String aaSeqString = proteinDataset != null ? proteinDataset
.getSequenceAsString() : proteinSeq.getSequenceAsString();
final SequenceI cdnaDataset = cdnaSeq.getDatasetSequence();
String cdnaSeqString = cdnaDataset != null ? cdnaDataset
.getSequenceAsString() : cdnaSeq.getSequenceAsString();
if (aaSeqString == null || cdnaSeqString == null)
{
return null;
}
final int mappedLength = 3 * aaSeqString.length();
int cdnaLength = cdnaSeqString.length();
int cdnaStart = 1;
int cdnaEnd = cdnaLength;
final int proteinStart = 1;
final int proteinEnd = aaSeqString.length();
/*
* If lengths don't match, try ignoring stop codon.
*/
if (cdnaLength != mappedLength)
{
for (Object stop : ResidueProperties.STOP)
{
if (cdnaSeqString.toUpperCase().endsWith((String) stop))
{
cdnaEnd -= 3;
cdnaLength -= 3;
break;
}
}
}
/*
* If lengths still don't match, try ignoring start codon.
*/
if (cdnaLength != mappedLength
&& cdnaSeqString.toUpperCase().startsWith(
ResidueProperties.START))
{
cdnaStart += 3;
cdnaLength -= 3;
}
if (cdnaLength == mappedLength)
{
MapList map = new MapList(new int[]
{ cdnaStart, cdnaEnd }, new int[]
{ proteinStart, proteinEnd }, 3, 1);
return map;
}
else
{
return null;
}
}
/**
* 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 mappings = al.getCodonFrame(seq);
if (mappings == null)
{
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;
}
}