X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=f5e6fc7f10bfc4ccfbe6b5f930df8c234e6556aa;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=34f8f6edc75ca1b48ad24d53d79f309b83faa125;hpb=36dceb54710feb97a81f4bd69ad051f316141dc3;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 34f8f6e..f5e6fc7 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -21,8 +21,10 @@ 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; @@ -30,7 +32,6 @@ import java.util.Collections; import java.util.Enumeration; import java.util.HashSet; import java.util.Hashtable; -import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Set; @@ -53,11 +54,7 @@ public class Alignment implements AlignmentI protected char gapCharacter = '-'; - protected int type = NUCLEOTIDE; - - public static final int PROTEIN = 0; - - public static final int NUCLEOTIDE = 1; + private boolean nucleotide = true; public boolean hasRNAStructure = false; @@ -65,6 +62,8 @@ public class Alignment implements AlignmentI HiddenSequences hiddenSequences; + HiddenColumns hiddenCols; + public Hashtable alignmentProperties; private List codonFrameList; @@ -73,16 +72,10 @@ public class Alignment implements AlignmentI { groups = Collections.synchronizedList(new ArrayList()); hiddenSequences = new HiddenSequences(this); - codonFrameList = new ArrayList(); + hiddenCols = new HiddenColumns(); + codonFrameList = new ArrayList<>(); - if (Comparison.isNucleotide(seqs)) - { - type = NUCLEOTIDE; - } - else - { - type = PROTEIN; - } + nucleotide = Comparison.isNucleotide(seqs); sequences = Collections.synchronizedList(new ArrayList()); @@ -110,7 +103,10 @@ public class Alignment implements AlignmentI /* * Share the same dataset sequence mappings (if any). */ - this.setCodonFrames(al.getCodonFrames()); + if (dataset == null && al.getDataset() == null) + { + this.setCodonFrames(al.getCodonFrames()); + } } /** @@ -132,7 +128,7 @@ public class Alignment implements AlignmentI public Alignment(SeqCigar[] alseqs) { SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs, - gapCharacter, new ColumnSelection(), null); + gapCharacter, new HiddenColumns(), null); initAlignment(seqs); } @@ -192,14 +188,7 @@ public class Alignment implements AlignmentI return AlignmentUtils.getSequencesByName(this); } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override public SequenceI getSequenceAt(int i) { @@ -213,8 +202,32 @@ public class Alignment implements AlignmentI return null; } + @Override + public SequenceI getSequenceAtAbsoluteIndex(int i) + { + SequenceI seq = null; + if (getHiddenSequences().getSize() > 0) + { + seq = getHiddenSequences().getHiddenSequence(i); + if (seq == null) + { + // didn't find the sequence in the hidden sequences, get it from the + // alignment + int index = getHiddenSequences().findIndexWithoutHiddenSeqs(i); + seq = getSequenceAt(index); + } + } + else + { + seq = getSequenceAt(i); + } + return seq; + } + /** - * Adds a sequence to the alignment. Recalculates maxLength and size. + * Adds a sequence to the alignment. Recalculates maxLength and size. Note + * this currently does not recalculate whether or not the alignment is + * nucleotide, so mixed alignments may have undefined behaviour. * * @param snew */ @@ -223,18 +236,21 @@ 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) { @@ -253,18 +269,22 @@ 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; } } @@ -280,13 +300,23 @@ 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; @@ -295,41 +325,34 @@ 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(); } } - /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - */ @Override public void deleteSequence(SequenceI s) { - deleteSequence(findIndex(s)); + synchronized (sequences) + { + deleteSequence(findIndex(s)); + } } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - */ @Override public void deleteSequence(int i) { - if (i > -1 && i < getHeight()) + synchronized (sequences) { - synchronized (sequences) + if (i > -1 && i < getHeight()) { sequences.remove(i); hiddenSequences.adjustHeightSequenceDeleted(i); @@ -337,23 +360,36 @@ public class Alignment implements AlignmentI } } + @Override + public void deleteHiddenSequence(int i) + { + synchronized (sequences) + { + if (i > -1 && i < getHeight()) + { + sequences.remove(i); + } + } + } + /* * (non-Javadoc) * * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI) */ @Override - public SequenceGroup findGroup(SequenceI s) + public SequenceGroup findGroup(SequenceI seq, int position) { synchronized (groups) { - for (int i = 0; i < this.groups.size(); i++) + for (SequenceGroup sg : groups) { - SequenceGroup sg = groups.get(i); - - if (sg.getSequences(null).contains(s)) + if (sg.getSequences(null).contains(seq)) { - return sg; + if (position >= sg.getStartRes() && position <= sg.getEndRes()) + { + return sg; + } } } } @@ -369,7 +405,7 @@ public class Alignment implements AlignmentI @Override public SequenceGroup[] findAllGroups(SequenceI s) { - ArrayList temp = new ArrayList(); + ArrayList temp = new ArrayList<>(); synchronized (groups) { @@ -420,7 +456,7 @@ public class Alignment implements AlignmentI return; } } - sg.setContext(this); + sg.setContext(this, true); groups.add(sg); } } @@ -497,7 +533,7 @@ public class Alignment implements AlignmentI } for (SequenceGroup sg : groups) { - sg.setContext(null); + sg.setContext(null, false); } groups.clear(); } @@ -513,7 +549,7 @@ public class Alignment implements AlignmentI { removeAnnotationForGroup(g); groups.remove(g); - g.setContext(null); + g.setContext(null, false); } } } @@ -638,7 +674,7 @@ public class Alignment implements AlignmentI * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults) */ @Override - public int findIndex(SearchResults results) + public int findIndex(SearchResultsI results) { int i = 0; @@ -653,22 +689,19 @@ public class Alignment implements AlignmentI return -1; } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override public int getHeight() { return sequences.size(); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override + public int getAbsoluteHeight() + { + return sequences.size() + getHiddenSequences().getSize(); + } + @Override public int getWidth() { @@ -754,6 +787,12 @@ public class Alignment implements AlignmentI return true; } + @Override + public boolean isHidden(int alignmentIndex) + { + return (getHiddenSequences().getHiddenSequence(alignmentIndex) != null); + } + /** * Delete all annotations, including auto-calculated if the flag is set true. * Returns true if at least one annotation was deleted, else false. @@ -954,29 +993,9 @@ public class Alignment implements AlignmentI } @Override - public void setNucleotide(boolean b) - { - if (b) - { - type = NUCLEOTIDE; - } - else - { - type = PROTEIN; - } - } - - @Override public boolean isNucleotide() { - if (type == NUCLEOTIDE) - { - return true; - } - else - { - return false; - } + return nucleotide; } @Override @@ -995,6 +1014,10 @@ public class Alignment implements AlignmentI } else if (dataset == null && data != null) { + if (data == this) + { + throw new IllegalArgumentException("Circular dataset reference"); + } if (!(data instanceof Alignment)) { throw new Error( @@ -1027,6 +1050,67 @@ 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(); + } + } + + List toProcess = new ArrayList<>(); + toProcess.add(currentSeq); + while (toProcess.size() > 0) + { + // use a queue ? + SequenceI curDs = toProcess.remove(0); + + if (!seqs.add(curDs)) + { + continue; + } + // 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. */ @@ -1036,22 +1120,32 @@ public class Alignment implements AlignmentI { return; } - SequenceI[] seqs = new SequenceI[getHeight()]; - SequenceI currentSeq; + // try to avoid using SequenceI.equals at this stage, it will be expensive + Set seqs = new LinkedIdentityHashSet<>(); + for (int i = 0; i < getHeight(); i++) { - currentSeq = getSequenceAt(i); - if (currentSeq.getDatasetSequence() != null) - { - seqs[i] = currentSeq.getDatasetSequence(); - } - else + SequenceI currentSeq = getSequenceAt(i); + resolveAndAddDatasetSeq(currentSeq, seqs, true); + } + + // verify all mappings are in dataset + for (AlignedCodonFrame cf : codonFrameList) + { + for (SequenceToSequenceMapping ssm : cf.getMappings()) { - seqs[i] = currentSeq.createDatasetSequence(); + if (!seqs.contains(ssm.getFromSeq())) + { + resolveAndAddDatasetSeq(ssm.getFromSeq(), seqs, false); + } + if (!seqs.contains(ssm.getMapping().getTo())) + { + resolveAndAddDatasetSeq(ssm.getMapping().getTo(), seqs, false); + } } } - - dataset = new Alignment(seqs); + // 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; @@ -1233,6 +1327,12 @@ public class Alignment implements AlignmentI } @Override + public HiddenColumns getHiddenColumns() + { + return hiddenCols; + } + + @Override public CigarArray getCompactAlignment() { synchronized (sequences) @@ -1293,22 +1393,6 @@ public class Alignment implements AlignmentI } } - /** - * adds a set of mappings (while ignoring any duplicates) - */ - @Override - public void addCodonFrames(Iterable codons) - { - if (codons != null) - { - Iterator it = codons.iterator(); - while (it.hasNext()) - { - addCodonFrame(it.next()); - } - } - } - /* * (non-Javadoc) * @@ -1322,7 +1406,7 @@ public class Alignment implements AlignmentI { return null; } - List cframes = new ArrayList(); + List cframes = new ArrayList<>(); for (AlignedCodonFrame acf : getCodonFrames()) { if (acf.involvesSequence(seq)) @@ -1387,11 +1471,7 @@ public class Alignment implements AlignmentI @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(); @@ -1402,6 +1482,8 @@ 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) @@ -1417,9 +1499,13 @@ 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++) @@ -1427,6 +1513,7 @@ public class Alignment implements AlignmentI addAnnotation(alan[a]); } + // use add method getCodonFrames().addAll(toappend.getCodonFrames()); List sg = toappend.getGroups(); @@ -1506,7 +1593,6 @@ public class Alignment implements AlignmentI String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef) { - assert (name != null); if (annotations != null) { for (AlignmentAnnotation annot : getAlignmentAnnotation()) @@ -1538,33 +1624,35 @@ public class Alignment implements AlignmentI @Override public Iterable findAnnotation(String calcId) { - ArrayList aa = new ArrayList(); - for (AlignmentAnnotation a : getAlignmentAnnotation()) + List aa = new ArrayList<>(); + AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation(); + if (alignmentAnnotation != null) { - if (a.getCalcId() == calcId - || (a.getCalcId() != null && calcId != null && a.getCalcId() - .equals(calcId))) + for (AlignmentAnnotation a : alignmentAnnotation) { - aa.add(a); + if (a.getCalcId() == calcId + || (a.getCalcId() != null && calcId != null && a + .getCalcId().equals(calcId))) + { + aa.add(a); + } } } return aa; } - /** - * Returns an iterable collection of any annotations that match on given - * sequence ref, calcId and label (ignoring null values). - */ @Override public Iterable findAnnotations(SequenceI seq, String calcId, String label) { - ArrayList aa = new ArrayList(); + ArrayList aa = new ArrayList<>(); for (AlignmentAnnotation ann : getAlignmentAnnotation()) { - if (ann.getCalcId() != null && ann.getCalcId().equals(calcId) - && ann.sequenceRef != null && ann.sequenceRef == seq - && ann.label != null && ann.label.equals(label)) + if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId() + .equals(calcId))) + && (seq == null || (ann.sequenceRef != null && ann.sequenceRef == seq)) + && (label == null || (ann.label != null && ann.label + .equals(label)))) { aa.add(ann); } @@ -1717,9 +1805,11 @@ public class Alignment implements AlignmentI * 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 @@ -1730,12 +1820,17 @@ public class Alignment implements AlignmentI boolean preserveUnmappedGaps) { // TODO should this method signature be the one in the interface? + // 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); } + else if (thatIsProtein && thisIsNucleotide) + { + return AlignmentUtils.alignCdsAsProtein(this, al); + } return AlignmentUtils.alignAs(this, al); } @@ -1746,7 +1841,7 @@ public class Alignment implements AlignmentI @Override public String toString() { - return new FastaFile().print(getSequencesArray()); + return new FastaFile().print(getSequencesArray(), true); } /** @@ -1755,7 +1850,7 @@ public class Alignment implements AlignmentI @Override public Set getSequenceNames() { - Set names = new HashSet(); + Set names = new HashSet<>(); for (SequenceI seq : getSequences()) { names.add(seq.getName()); @@ -1855,4 +1950,10 @@ public class Alignment implements AlignmentI } return new int[] { startPos, endPos }; } + + @Override + public void setHiddenColumns(HiddenColumns cols) + { + hiddenCols = cols; + } }