X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=2289ac6314196fe08a62aa4797c8ef5897f0cc58;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=482df7fd0dd6f77f4b92c232132ecc8ef88f24fb;hpb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 482df7f..2289ac6 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -21,14 +21,17 @@ package jalview.datamodel; import jalview.analysis.AlignmentUtils; +import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; import jalview.io.FastaFile; +import jalview.util.Comparison; +import jalview.util.LinkedIdentityHashSet; import jalview.util.MessageManager; import java.util.ArrayList; +import java.util.Collections; import java.util.Enumeration; import java.util.HashSet; import java.util.Hashtable; -import java.util.LinkedHashSet; import java.util.List; import java.util.Map; import java.util.Set; @@ -43,12 +46,11 @@ import java.util.Vector; */ public class Alignment implements AlignmentI { - protected Alignment dataset; + private Alignment dataset; protected List sequences; - protected List groups = java.util.Collections - .synchronizedList(new ArrayList()); + protected List groups; protected char gapCharacter = '-'; @@ -60,20 +62,21 @@ public class Alignment implements AlignmentI public boolean hasRNAStructure = false; - /** DOCUMENT ME!! */ public AlignmentAnnotation[] annotations; - HiddenSequences hiddenSequences = new HiddenSequences(this); + HiddenSequences hiddenSequences; public Hashtable alignmentProperties; - private Set codonFrameList = new LinkedHashSet(); + private List codonFrameList; private void initAlignment(SequenceI[] seqs) { - int i = 0; + groups = Collections.synchronizedList(new ArrayList()); + hiddenSequences = new HiddenSequences(this); + codonFrameList = new ArrayList(); - if (jalview.util.Comparison.isNucleotide(seqs)) + if (Comparison.isNucleotide(seqs)) { type = NUCLEOTIDE; } @@ -82,10 +85,9 @@ public class Alignment implements AlignmentI type = PROTEIN; } - sequences = java.util.Collections - .synchronizedList(new ArrayList()); + sequences = Collections.synchronizedList(new ArrayList()); - for (i = 0; i < seqs.length; i++) + for (int i = 0; i < seqs.length; i++) { sequences.add(seqs[i]); } @@ -104,13 +106,15 @@ public class Alignment implements AlignmentI seqs[i] = new Sequence(seqs[i]); } + initAlignment(seqs); + /* - * Share the same dataset sequence mappings (if any). TODO: find a better - * place for these to live (alignment dataset?). + * Share the same dataset sequence mappings (if any). */ - this.codonFrameList = ((Alignment) al).codonFrameList; - - initAlignment(seqs); + if (dataset == null && al.getDataset() == null) + { + this.setCodonFrames(al.getCodonFrames()); + } } /** @@ -147,7 +151,9 @@ public class Alignment implements AlignmentI */ public static AlignmentI createAlignment(CigarArray compactAlignment) { - throw new Error(MessageManager.getString("error.alignment_cigararray_not_implemented")); + throw new Error( + MessageManager + .getString("error.alignment_cigararray_not_implemented")); // this(compactAlignment.refCigars); } @@ -221,23 +227,25 @@ public class Alignment implements AlignmentI { if (dataset != null) { + // maintain dataset integrity - if (snew.getDatasetSequence() != null) - { - getDataset().addSequence(snew.getDatasetSequence()); - } - else + SequenceI dsseq = snew.getDatasetSequence(); + if (dsseq == null) { // derive new sequence SequenceI adding = snew.deriveSequence(); - getDataset().addSequence(adding.getDatasetSequence()); snew = adding; + dsseq = snew.getDatasetSequence(); } + if (getDataset().findIndex(dsseq) == -1) + { + getDataset().addSequence(dsseq); + } + } if (sequences == null) { - initAlignment(new SequenceI[] - { snew }); + initAlignment(new SequenceI[] { snew }); } else { @@ -252,18 +260,22 @@ public class Alignment implements AlignmentI } } - /** - * Adds a sequence to the alignment. Recalculates maxLength and size. - * - * @param snew - */ @Override - public void setSequenceAt(int i, SequenceI snew) + public SequenceI replaceSequenceAt(int i, SequenceI snew) { synchronized (sequences) { - deleteSequence(i); - sequences.set(i, snew); + if (sequences.size() > i) + { + return sequences.set(i, snew); + + } + else + { + sequences.add(snew); + hiddenSequences.adjustHeightSequenceAdded(); + } + return null; } } @@ -279,13 +291,23 @@ public class Alignment implements AlignmentI } @Override - public void finalize() + public void finalize() throws Throwable { if (getDataset() != null) { getDataset().removeAlignmentRef(); } + nullReferences(); + super.finalize(); + } + + /** + * Defensively nulls out references in case this object is not garbage + * collected + */ + void nullReferences() + { dataset = null; sequences = null; groups = null; @@ -294,14 +316,16 @@ public class Alignment implements AlignmentI } /** - * decrement the alignmentRefs counter by one and call finalize if it goes to - * zero. + * decrement the alignmentRefs counter by one and null references if it goes + * to zero. + * + * @throws Throwable */ - private void removeAlignmentRef() + private void removeAlignmentRef() throws Throwable { if (--alignmentRefs == 0) { - finalize(); + nullReferences(); } } @@ -986,33 +1010,20 @@ public class Alignment implements AlignmentI } @Override - public void setDataset(Alignment data) + public void setDataset(AlignmentI data) { if (dataset == null && data == null) { - // Create a new dataset for this alignment. - // Can only be done once, if dataset is not null - // This will not be performed - SequenceI[] seqs = new SequenceI[getHeight()]; - SequenceI currentSeq; - for (int i = 0; i < getHeight(); i++) - { - currentSeq = getSequenceAt(i); - if (currentSeq.getDatasetSequence() != null) - { - seqs[i] = currentSeq.getDatasetSequence(); - } - else - { - seqs[i] = currentSeq.createDatasetSequence(); - } - } - - dataset = new Alignment(seqs); + createDatasetAlignment(); } else if (dataset == null && data != null) { - dataset = data; + if (!(data instanceof Alignment)) + { + throw new Error( + "Implementation Error: jalview.datamodel.Alignment does not yet support other implementations of AlignmentI as its dataset reference"); + } + dataset = (Alignment) data; for (int i = 0; i < getHeight(); i++) { SequenceI currentSeq = getSequenceAt(i); @@ -1039,6 +1050,111 @@ public class Alignment implements AlignmentI } /** + * add dataset sequences to seq for currentSeq and any sequences it references + */ + private void resolveAndAddDatasetSeq(SequenceI currentSeq, + Set seqs, boolean createDatasetSequence) + { + SequenceI alignedSeq = currentSeq; + if (currentSeq.getDatasetSequence() != null) + { + currentSeq = currentSeq.getDatasetSequence(); + } + else + { + if (createDatasetSequence) + { + currentSeq = currentSeq.createDatasetSequence(); + } + } + if (seqs.contains(currentSeq)) + { + return; + } + List toProcess = new ArrayList(); + toProcess.add(currentSeq); + while (toProcess.size() > 0) + { + // use a queue ? + SequenceI curDs = toProcess.remove(0); + if (seqs.contains(curDs)) + { + continue; + } + seqs.add(curDs); + // iterate over database references, making sure we add forward referenced + // sequences + if (curDs.getDBRefs() != null) + { + for (DBRefEntry dbr : curDs.getDBRefs()) + { + if (dbr.getMap() != null && dbr.getMap().getTo() != null) + { + if (dbr.getMap().getTo() == alignedSeq) + { + /* + * update mapping to be to the newly created dataset sequence + */ + dbr.getMap().setTo(currentSeq); + } + if (dbr.getMap().getTo().getDatasetSequence() != null) + { + throw new Error( + "Implementation error: Map.getTo() for dbref " + dbr + + " from " + curDs.getName() + + " is not a dataset sequence."); + } + // we recurse to add all forward references to dataset sequences via + // DBRefs/etc + toProcess.add(dbr.getMap().getTo()); + } + } + } + } + } + + /** + * Creates a new dataset for this alignment. Can only be done once - if + * dataset is not null this will not be performed. + */ + public void createDatasetAlignment() + { + if (dataset != null) + { + return; + } + // try to avoid using SequenceI.equals at this stage, it will be expensive + Set seqs = new LinkedIdentityHashSet(); + + for (int i = 0; i < getHeight(); i++) + { + SequenceI currentSeq = getSequenceAt(i); + resolveAndAddDatasetSeq(currentSeq, seqs, true); + } + + // verify all mappings are in dataset + for (AlignedCodonFrame cf : codonFrameList) + { + for (SequenceToSequenceMapping ssm : cf.getMappings()) + { + if (!seqs.contains(ssm.getFromSeq())) + { + resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false); + } + if (!seqs.contains(ssm.getMapping().getTo())) + { + resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false); + } + } + } + // finally construct dataset + dataset = new Alignment(seqs.toArray(new SequenceI[seqs.size()])); + // move mappings to the dataset alignment + dataset.codonFrameList = this.codonFrameList; + this.codonFrameList = null; + } + + /** * reference count for number of alignments referencing this one. */ int alignmentRefs = 0; @@ -1260,19 +1376,17 @@ public class Alignment implements AlignmentI return alignmentProperties; } - /* - * (non-Javadoc) - * - * @see - * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame - * ) + /** + * Adds the given mapping to the stored set. Note this may be held on the + * dataset alignment. */ @Override public void addCodonFrame(AlignedCodonFrame codons) { - if (codons != null) + List acfs = getCodonFrames(); + if (codons != null && acfs != null && !acfs.contains(codons)) { - codonFrameList.add(codons); + acfs.add(codons); } } @@ -1290,7 +1404,7 @@ public class Alignment implements AlignmentI return null; } List cframes = new ArrayList(); - for (AlignedCodonFrame acf : codonFrameList) + for (AlignedCodonFrame acf : getCodonFrames()) { if (acf.involvesSequence(seq)) { @@ -1301,52 +1415,60 @@ public class Alignment implements AlignmentI } /** - * Sets the codon frame mappings (replacing any existing mappings). + * Sets the codon frame mappings (replacing any existing mappings). Note the + * mappings are set on the dataset alignment instead if there is one. * * @see jalview.datamodel.AlignmentI#setCodonFrames() */ @Override - public void setCodonFrames(Set acfs) + public void setCodonFrames(List acfs) { - this.codonFrameList = acfs; + if (dataset != null) + { + dataset.setCodonFrames(acfs); + } + else + { + this.codonFrameList = acfs; + } } /** * Returns the set of codon frame mappings. Any changes to the returned set - * will affect the alignment. + * will affect the alignment. The mappings are held on (and read from) the + * dataset alignment if there is one. * * @see jalview.datamodel.AlignmentI#getCodonFrames() */ @Override - public Set getCodonFrames() + public List getCodonFrames() { - return codonFrameList; + // TODO: Fix this method to fix failing AlignedCodonFrame tests + // this behaviour is currently incorrect. method should return codon frames + // for just the alignment, + // selected from dataset + return dataset != null ? dataset.getCodonFrames() : codonFrameList; } - /* - * (non-Javadoc) - * - * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel. - * AlignedCodonFrame) + /** + * Removes the given mapping from the stored set. Note that the mappings are + * held on the dataset alignment if there is one. */ @Override public boolean removeCodonFrame(AlignedCodonFrame codons) { - if (codons == null || codonFrameList == null) + List acfs = getCodonFrames(); + if (codons == null || acfs == null) { return false; } - return codonFrameList.remove(codons); + return acfs.remove(codons); } @Override public void append(AlignmentI toappend) { - if (toappend == this) - { - System.err.println("Self append may cause a deadlock."); - } - // TODO test this method for a future 2.5 release + // TODO JAL-1270 needs test coverage // currently tested for use in jalview.gui.SequenceFetcher boolean samegap = toappend.getGapCharacter() == getGapCharacter(); char oldc = toappend.getGapCharacter(); @@ -1357,6 +1479,8 @@ public class Alignment implements AlignmentI .getFullAlignment().getSequences() : toappend.getSequences(); if (sqs != null) { + // avoid self append deadlock by + List toappendsq = new ArrayList(); synchronized (sqs) { for (SequenceI addedsq : sqs) @@ -1372,9 +1496,13 @@ public class Alignment implements AlignmentI } } } - addSequence(addedsq); + toappendsq.add(addedsq); } } + for (SequenceI addedsq : toappendsq) + { + addSequence(addedsq); + } } AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation(); for (int a = 0; alan != null && a < alan.length; a++) @@ -1382,7 +1510,8 @@ public class Alignment implements AlignmentI addAnnotation(alan[a]); } - this.codonFrameList.addAll(toappend.getCodonFrames()); + // use add method + getCodonFrames().addAll(toappend.getCodonFrames()); List sg = toappend.getGroups(); if (sg != null) @@ -1588,38 +1717,40 @@ public class Alignment implements AlignmentI } } + private SequenceI seqrep = null; - private SequenceI seqrep=null; - - /** - * - * @return the representative sequence for this group - */ - public SequenceI getSeqrep() - { - return seqrep; - } + /** + * + * @return the representative sequence for this group + */ + @Override + public SequenceI getSeqrep() + { + return seqrep; + } - /** - * set the representative sequence for this group. Note - this affects the - * interpretation of the Hidereps attribute. - * - * @param seqrep - * the seqrep to set (null means no sequence representative) - */ - public void setSeqrep(SequenceI seqrep) - { - this.seqrep = seqrep; - } + /** + * set the representative sequence for this group. Note - this affects the + * interpretation of the Hidereps attribute. + * + * @param seqrep + * the seqrep to set (null means no sequence representative) + */ + @Override + public void setSeqrep(SequenceI seqrep) + { + this.seqrep = seqrep; + } - /** - * - * @return true if group has a sequence representative - */ - public boolean hasSeqrep() - { - return seqrep != null; - } + /** + * + * @return true if group has a sequence representative + */ + @Override + public boolean hasSeqrep() + { + return seqrep != null; + } @Override public int getEndRes() @@ -1664,48 +1795,39 @@ public class Alignment implements AlignmentI * identically. If this is nucleotide and the other is protein, make 3 gaps * for each gap in the protein sequences. If this is protein and the other is * nucleotide, insert a gap for each 3 gaps (or part thereof) between - * nucleotide bases. Does nothing if alignment of protein from cDNA is - * requested (not yet implemented). + * nucleotide bases. If this is protein and the other is nucleotide, gaps + * protein to match the relative ordering of codons in the nucleotide. * * Parameters control whether gaps in exon (mapped) and intron (unmapped) * regions are preserved. Gaps that connect introns to exons are treated * conservatively, i.e. only preserved if both intron and exon gaps are - * preserved. + * preserved. TODO: check caveats below where the implementation fails * * @param al + * - must have same dataset, and sequences in al must have equivalent + * dataset sequence and start/end bounds under given mapping * @param preserveMappedGaps * if true, gaps within and between mapped codons are preserved * @param preserveUnmappedGaps * if true, gaps within and between unmapped codons are preserved */ -// @Override + // @Override public int alignAs(AlignmentI al, boolean preserveMappedGaps, boolean preserveUnmappedGaps) { // TODO should this method signature be the one in the interface? - int count = 0; + // JBPComment - yes - neither flag is used, so should be deleted. boolean thisIsNucleotide = this.isNucleotide(); boolean thatIsProtein = !al.isNucleotide(); if (!thatIsProtein && !thisIsNucleotide) { return AlignmentUtils.alignProteinAsDna(this, al); } - - char thisGapChar = this.getGapCharacter(); - String gap = thisIsNucleotide && thatIsProtein ? String - .valueOf(new char[] - { thisGapChar, thisGapChar, thisGapChar }) : String - .valueOf(thisGapChar); - - /* - * Get mappings from 'that' alignment's sequences to this. - */ - for (SequenceI alignTo : getSequences()) + else if (thatIsProtein && thisIsNucleotide) { - count += AlignmentUtils.alignSequenceAs(alignTo, al, gap, preserveMappedGaps, - preserveUnmappedGaps) ? 1 : 0; + return AlignmentUtils.alignCdsAsProtein(this, al); } - return count; + return AlignmentUtils.alignAs(this, al); } /** @@ -1731,4 +1853,97 @@ public class Alignment implements AlignmentI } return names; } + + @Override + public boolean hasValidSequence() + { + boolean hasValidSeq = false; + for (SequenceI seq : getSequences()) + { + if ((seq.getEnd() - seq.getStart()) > 0) + { + hasValidSeq = true; + break; + } + } + return hasValidSeq; + } + + /** + * Update any mappings to 'virtual' sequences to compatible real ones, if + * present in the added sequences. Returns a count of mappings updated. + * + * @param seqs + * @return + */ + @Override + public int realiseMappings(List seqs) + { + int count = 0; + for (SequenceI seq : seqs) + { + for (AlignedCodonFrame mapping : getCodonFrames()) + { + count += mapping.realiseWith(seq); + } + } + return count; + } + + /** + * Returns the first AlignedCodonFrame that has a mapping between the given + * dataset sequences + * + * @param mapFrom + * @param mapTo + * @return + */ + @Override + public AlignedCodonFrame getMapping(SequenceI mapFrom, SequenceI mapTo) + { + for (AlignedCodonFrame acf : getCodonFrames()) + { + if (acf.getAaForDnaSeq(mapFrom) == mapTo) + { + return acf; + } + } + return null; + } + + @Override + public int[] getVisibleStartAndEndIndex(List hiddenCols) + { + int[] alignmentStartEnd = new int[] { 0, getWidth() - 1 }; + int startPos = alignmentStartEnd[0]; + int endPos = alignmentStartEnd[1]; + + int[] lowestRange = new int[] { -1, -1 }; + int[] higestRange = new int[] { -1, -1 }; + + for (int[] hiddenCol : hiddenCols) + { + lowestRange = (hiddenCol[0] <= startPos) ? hiddenCol : lowestRange; + higestRange = (hiddenCol[1] >= endPos) ? hiddenCol : higestRange; + } + + if (lowestRange[0] == -1 && lowestRange[1] == -1) + { + startPos = alignmentStartEnd[0]; + } + else + { + startPos = lowestRange[1] + 1; + } + + if (higestRange[0] == -1 && higestRange[1] == -1) + { + endPos = alignmentStartEnd[1]; + } + else + { + endPos = higestRange[0] - 1; + } + return new int[] { startPos, endPos }; + } }