/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ 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 java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
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;
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.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
import jalview.util.MapList;
/**
* 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
*
* @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 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 mapProteinToCdna(
final AlignmentI proteinAlignment,
final AlignmentI cdnaAlignment)
{
if (proteinAlignment == null || cdnaAlignment == null)
{
return false;
}
Set mappedDna = new HashSet();
Set mappedProtein = new HashSet();
/*
* 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 mappedDna,
Set mappedProtein, boolean xrefsOnly)
{
boolean mappingPerformed = false;
List 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 && !CrossRef.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()))
{
MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
if (map != null)
{
acf.addMap(cdnaSeq, aaSeq, map);
mappingPerformed = true;
proteinMapped = true;
mappedDna.add(cdnaSeq);
mappedProtein.add(aaSeq);
}
}
}
if (proteinMapped)
{
proteinAlignment.addCodonFrame(acf);
}
}
return mappingPerformed;
}
/**
* 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, 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, aaResidue++)
{
String codon = String.valueOf(cdnaSeqChars, i, 3);
final String translated = ResidueProperties.codonTranslate(
codon);
/*
* ? allow X in protein to match untranslatable in dna ?
*/
final char aaRes = aaSeqChars[aaResidue];
if ((translated == null || "STOP".equals(translated)) && aaRes == 'X')
{
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 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 getAlignedTranslation(
List sequences, char gapCharacter,
Set mappings)
{
List alignedSeqs = new ArrayList();
for (SequenceI seq : sequences)
{
List 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 getAlignedTranslation(SequenceI seq,
char gapCharacter, Set mappings)
{
List result = new ArrayList();
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 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> alignedCodons = new TreeMap>(
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> 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 columnResidues = alignedCodons.get(codon);
for (Entry 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> alignedCodons)
{
Iterator codons = seqMap.getCodonIterator(dna, gapChar);
while (codons.hasNext())
{
AlignedCodon codon = codons.next();
Map seqProduct = alignedCodons.get(codon);
if (seqProduct == null)
{
seqProduct = new HashMap();
alignedCodons.put(codon, seqProduct);
}
seqProduct.put(protein, codon.product);
}
}
/**
* 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:
*
* - One alignment must be nucleotide, and the other protein
* - At least one pair of sequences must be already mapped, or mappable
* - Mappable means the nucleotide translation matches the protein sequence
* - The translation may ignore start and stop codons if present in the
* nucleotide
*
*
* @param al1
* @param al2
* @return
*/
public static boolean isMappable(AlignmentI al1, AlignmentI al2)
{
/*
* 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;
Set 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
*/
public static boolean isMappable(SequenceI dnaSeq, SequenceI proteinSeq,
Set mappings)
{
SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
SequenceI proteinDs = proteinSeq.getDatasetSequence() == null ? proteinSeq
: proteinSeq.getDatasetSequence();
/*
* Already mapped?
*/
for (AlignedCodonFrame mapping : mappings) {
if ( proteinDs == mapping.getAaForDnaSeq(dnaDs)) {
return true;
}
}
/*
* Just try to make a mapping (it is not yet stored), test whether
* successful.
*/
return mapProteinToCdna(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 sequenceScope, Map labelForCalcId,
final Map> 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, }
*/
for (SequenceI seq : sequenceScope)
{
SequenceI dataset = seq.getDatasetSequence();
if (dataset == null)
{
continue;
}
AlignmentAnnotation[] datasetAnnotations = dataset.getAnnotation();
if (datasetAnnotations == null)
{
continue;
}
final List result = new ArrayList();
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 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> 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 types, List 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;
}
}
}
}
}