/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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.Mapping;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.ResidueProperties;
+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.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
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.
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);
}
}
* @param cdnaAlignment
* @return
*/
- public static boolean mapProteinToCdna(
- final AlignmentI proteinAlignment,
- final AlignmentI cdnaAlignment)
+ public static boolean mapProteinAlignmentToCdna(
+ final AlignmentI proteinAlignment, final AlignmentI cdnaAlignment)
{
if (proteinAlignment == null || cdnaAlignment == null)
{
final AlignmentI cdnaAlignment, Set<SequenceI> mappedDna,
Set<SequenceI> mappedProtein, boolean xrefsOnly)
{
- boolean mappingPerformed = false;
+ boolean mappingExistsOrAdded = false;
List<SequenceI> thisSeqs = proteinAlignment.getSequences();
for (SequenceI aaSeq : thisSeqs)
{
* many-to-many, as that would risk mixing species with similar cDNA
* sequences.
*/
- if (xrefsOnly && !CrossRef.haveCrossRef(aaSeq, cdnaSeq))
+ if (xrefsOnly && !AlignmentUtils.haveCrossRef(aaSeq, cdnaSeq))
{
continue;
}
{
continue;
}
- if (!mappingExists(proteinAlignment.getCodonFrames(),
+ if (mappingExists(proteinAlignment.getCodonFrames(),
aaSeq.getDatasetSequence(), cdnaSeq.getDatasetSequence()))
{
- MapList map = mapProteinToCdna(aaSeq, cdnaSeq);
+ mappingExistsOrAdded = true;
+ }
+ else
+ {
+ MapList map = mapProteinSequenceToCdna(aaSeq, cdnaSeq);
if (map != null)
{
acf.addMap(cdnaSeq, aaSeq, map);
- mappingPerformed = true;
+ mappingExistsOrAdded = true;
proteinMapped = true;
mappedDna.add(cdnaSeq);
mappedProtein.add(aaSeq);
proteinAlignment.addCodonFrame(acf);
}
}
- return mappingPerformed;
+ return mappingExistsOrAdded;
}
/**
* @param cdnaSeq
* @return
*/
- public static MapList mapProteinToCdna(SequenceI proteinSeq,
+ public static MapList mapProteinSequenceToCdna(SequenceI proteinSeq,
SequenceI cdnaSeq)
{
/*
*/
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;
+ 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 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))
+ .equals(ResidueProperties.START))
{
+ startOffset += 3;
cdnaStart += 3;
cdnaLength -= 3;
}
{
return null;
}
- if (!translatesAs(cdnaSeqChars, cdnaStart - 1, aaSeqChars))
+ if (!translatesAs(cdnaSeqChars, startOffset, aaSeqChars))
{
return null;
}
- MapList map = new MapList(new int[]
- { cdnaStart, cdnaEnd }, new int[]
- { proteinStart, proteinEnd }, 3, 1);
+ MapList map = new MapList(new int[] { cdnaStart, cdnaEnd }, new int[] {
+ proteinStart, proteinEnd }, 3, 1);
return map;
}
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);
+ final String translated = ResidueProperties.codonTranslate(codon);
/*
- * ? allow X in protein to match untranslatable in dna ?
+ * allow * in protein to match untranslatable in dna
*/
final char aaRes = aaSeqChars[aaResidue];
- if ((translated == null || "STOP".equals(translated)) && aaRes == 'X')
+ if ((translated == null || "STOP".equals(translated)) && aaRes == '*')
{
continue;
}
- if (translated == null
- || !(aaRes == translated.charAt(0)))
+ if (translated == null || !(aaRes == translated.charAt(0)))
{
// debug
// System.out.println(("Mismatch at " + i + "/" + aaResidue + ": "
boolean preserveUnmappedGaps)
{
/*
- * Get any mappings from the source alignment to the target (dataset) sequence.
+ * 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?
{
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
break;
}
}
-
+
if (alignFrom == null)
{
return false;
* @param preserveMappedGaps
*/
public static void alignSequenceAs(SequenceI alignTo,
- SequenceI alignFrom,
- AlignedCodonFrame mapping, String myGap, char sourceGap,
- boolean preserveMappedGaps, boolean preserveUnmappedGaps)
+ 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;
/*
* Traverse the aligned protein sequence.
*/
+ int fromOffset = alignFrom.getStart() - 1;
+ int toOffset = alignTo.getStart() - 1;
int sourceGapMappedLength = 0;
boolean inExon = false;
for (char sourceChar : thatAligned)
sourceDsPos++;
// Note mapping positions are base 1, our sequence positions base 0
int[] mappedPos = mapping.getMappedRegion(alignTo, alignFrom,
- sourceDsPos);
+ sourceDsPos + fromOffset);
if (mappedPos == null)
{
/*
* But then 'align dna as protein' doesn't make much sense otherwise.
*/
int intronLength = 0;
- while (basesWritten < mappedCodonEnd && thisSeqPos < thisSeq.length)
+ while (basesWritten + toOffset < mappedCodonEnd
+ && thisSeqPos < thisSeq.length)
{
final char c = thisSeq[thisSeqPos++];
if (c != myGapChar)
{
basesWritten++;
-
- if (basesWritten < mappedCodonStart)
+ int sourcePosition = basesWritten + toOffset;
+ if (sourcePosition < mappedCodonStart)
{
/*
* Found an unmapped (intron) base. First add in any preceding gaps
}
else
{
- final boolean startOfCodon = basesWritten == mappedCodonStart;
+ final boolean startOfCodon = sourcePosition == mappedCodonStart;
int gapsToAdd = calculateGapsToInsert(preserveMappedGaps,
preserveUnmappedGaps, sourceGapMappedLength, inExon,
trailingCopiedGap.length(), intronLength, startOfCodon);
*/
protected static int calculateGapsToInsert(boolean preserveMappedGaps,
boolean preserveUnmappedGaps, int sourceGapMappedLength,
- boolean inExon, int trailingGapLength,
- int intronLength, final boolean startOfCodon)
+ boolean inExon, int trailingGapLength, int intronLength,
+ final boolean startOfCodon)
{
int gapsToAdd = 0;
if (startOfCodon)
// mapping is from protein to nucleotide
toDna = true;
// should ideally get gap count ratio from mapping
- gap = String.valueOf(new char[]
- { gapCharacter, gapCharacter, gapCharacter });
+ gap = String.valueOf(new char[] { gapCharacter, gapCharacter,
+ gapCharacter });
}
else
{
{
mapping.markMappedRegion(seq, pos, sr);
}
- newseq.append(sr.toString());
+ newseq.append(sr.getCharacters());
if (first)
{
first = false;
*/
public static int alignProteinAsDna(AlignmentI protein, AlignmentI dna)
{
+ List<SequenceI> unmappedProtein = new ArrayList<SequenceI>();
+ unmappedProtein.addAll(protein.getSequences());
+
Set<AlignedCodonFrame> mappings = protein.getCodonFrames();
/*
{
addCodonPositions(dnaSeq, prot, protein.getGapCharacter(),
seqMap, alignedCodons);
+ unmappedProtein.remove(prot);
}
}
}
- return alignProteinAs(protein, alignedCodons);
+ return alignProteinAs(protein, alignedCodons, unmappedProtein);
}
/**
* @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, String>> alignedCodons)
+ Map<AlignedCodon, Map<SequenceI, String>> alignedCodons,
+ List<SequenceI> unmappedProtein)
{
/*
* Prefill aligned sequences with gaps before inserting aligned protein
String allGaps = String.valueOf(gaps);
for (SequenceI seq : protein.getSequences())
{
- seq.setSequence(allGaps);
+ if (!unmappedProtein.contains(seq))
+ {
+ 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())
+ 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);
* the map we are building up
*/
static void addCodonPositions(SequenceI dna, SequenceI protein,
- char gapChar,
- Mapping seqMap,
+ char gapChar, Mapping seqMap,
Map<AlignedCodon, Map<SequenceI, String>> alignedCodons)
{
Iterator<AlignedCodon> codons = seqMap.getCodonIterator(dna, gapChar);
*/
public static boolean isMappable(AlignmentI al1, AlignmentI al2)
{
+ if (al1 == null || al2 == null)
+ {
+ return false;
+ }
+
/*
* Require one nucleotide and one protein
*/
* @param mappings
* @return
*/
- public static boolean isMappable(SequenceI dnaSeq, SequenceI proteinSeq,
- Set<AlignedCodonFrame> mappings)
+ protected static boolean isMappable(SequenceI dnaSeq,
+ SequenceI proteinSeq, Set<AlignedCodonFrame> mappings)
{
- SequenceI dnaDs = dnaSeq.getDatasetSequence() == null ? dnaSeq : dnaSeq.getDatasetSequence();
+ if (dnaSeq == null || proteinSeq == null)
+ {
+ return false;
+ }
+
+ 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)) {
+ 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;
+ return mapProteinSequenceToCdna(proteinDs, dnaDs) != null;
}
/**
* the alignment to check for presence of annotations
*/
public static void findAddableReferenceAnnotations(
- List<SequenceI> sequenceScope, Map<String, String> labelForCalcId,
+ List<SequenceI> sequenceScope,
+ Map<String, String> labelForCalcId,
final Map<SequenceI, List<AlignmentAnnotation>> candidates,
AlignmentI al)
{
{
return;
}
-
+
/*
* For each sequence in scope, make a list of any annotations on the
* underlying dataset sequence which are not already on the alignment.
* sequence.
*/
final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
- .findAnnotations(seq, dsann.getCalcId(),
- dsann.label);
+ .findAnnotations(seq, dsann.getCalcId(), dsann.label);
if (!matchedAlignmentAnnotations.iterator().hasNext())
{
result.add(dsann);
endRes = selectionGroup.getEndRes();
}
copyAnn.restrict(startRes, endRes);
-
+
/*
* Add to the sequence (sets copyAnn.datasetSequence), unless the
* original annotation is already on the sequence.
Collection<String> types, List<SequenceI> forSequences,
boolean anyType, boolean doShow)
{
- for (AlignmentAnnotation aa : al
- .getAlignmentAnnotation())
+ for (AlignmentAnnotation aa : al.getAlignmentAnnotation())
{
if (anyType || types.contains(aa.label))
{
}
}
}
+
+ /**
+ * 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.getDBRef();
+ 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 exon regions in the given
+ * nucleotide sequences, and updates mappings to match.
+ *
+ * @param dna
+ * aligned dna sequences
+ * @param mappings
+ * from dna to protein; these are replaced with new mappings
+ * @return an alignment whose sequences are the exon-only parts of the dna
+ * sequences (or null if no exons are found)
+ */
+ public static AlignmentI makeExonAlignment(SequenceI[] dna,
+ Set<AlignedCodonFrame> mappings)
+ {
+ Set<AlignedCodonFrame> newMappings = new LinkedHashSet<AlignedCodonFrame>();
+ List<SequenceI> exonSequences = 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> mappedExons = makeExonSequences(ds, acf,
+ newMapping);
+ if (!mappedExons.isEmpty())
+ {
+ exonSequences.addAll(mappedExons);
+ newMappings.add(newMapping);
+ }
+ }
+ }
+ AlignmentI al = new Alignment(
+ exonSequences.toArray(new SequenceI[exonSequences.size()]));
+ al.setDataset(null);
+
+ /*
+ * Replace the old mappings with the new ones
+ */
+ mappings.clear();
+ mappings.addAll(newMappings);
+
+ return al;
+ }
+
+ /**
+ * Helper method to make exon-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 exons encoding for a single peptide
+ * sequence i.e. return a single result. Bacterial dna may have overlapping
+ * exon mappings coding for multiple peptides so return multiple results
+ * (example EMBL KF591215).
+ *
+ * @param dnaSeq
+ * a dna dataset sequence
+ * @param mapping
+ * containing one or more mappings of the sequence to protein
+ * @param newMapping
+ * the new mapping to populate, from the exon-only sequences to their
+ * mapped protein sequences
+ * @return
+ */
+ protected static List<SequenceI> makeExonSequences(SequenceI dnaSeq,
+ AlignedCodonFrame mapping, AlignedCodonFrame newMapping)
+ {
+ List<SequenceI> exonSequences = new ArrayList<SequenceI>();
+ List<Mapping> seqMappings = mapping.getMappingsForSequence(dnaSeq);
+ final char[] dna = dnaSeq.getSequence();
+ for (Mapping seqMapping : seqMappings)
+ {
+ StringBuilder newSequence = new StringBuilder(dnaSeq.getLength());
+
+ /*
+ * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
+ */
+ final List<int[]> dnaExonRanges = seqMapping.getMap().getFromRanges();
+ for (int[] range : dnaExonRanges)
+ {
+ for (int pos = range[0]; pos <= range[1]; pos++)
+ {
+ newSequence.append(dna[pos - 1]);
+ }
+ }
+
+ SequenceI exon = new Sequence(dnaSeq.getName(),
+ newSequence.toString());
+
+ /*
+ * Locate any xrefs to CDS database on the protein product and attach to
+ * the CDS sequence. Also add as a sub-token of the sequence name.
+ */
+ // default to "CDS" if we can't locate an actual gene id
+ String cdsAccId = FeatureProperties
+ .getCodingFeature(DBRefSource.EMBL);
+ DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(seqMapping.getTo()
+ .getDBRef(), DBRefSource.CODINGDBS);
+ if (cdsRefs != null)
+ {
+ for (DBRefEntry cdsRef : cdsRefs)
+ {
+ exon.addDBRef(new DBRefEntry(cdsRef));
+ cdsAccId = cdsRef.getAccessionId();
+ }
+ }
+ exon.setName(exon.getName() + "|" + cdsAccId);
+ exon.createDatasetSequence();
+
+ /*
+ * Build new mappings - from the same protein regions, but now to
+ * contiguous exons
+ */
+ List<int[]> exonRange = new ArrayList<int[]>();
+ exonRange.add(new int[] { 1, newSequence.length() });
+ MapList map = new MapList(exonRange, seqMapping.getMap()
+ .getToRanges(), 3, 1);
+ newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
+ MapList cdsToDnaMap = new MapList(dnaExonRanges, exonRange, 1, 1);
+ newMapping.addMap(dnaSeq, exon.getDatasetSequence(), cdsToDnaMap);
+
+ exonSequences.add(exon);
+ }
+ return exonSequences;
+ }
}
git://source.jalview.org / jalview.git / blobdiff