X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=35ee8c4ef9fafc31d5b7c0e39386fa79ee1deae4;hb=3446323f14bb8a2842cb83f74ed3f41c99b62759;hp=1134857428850bf8e49716f31013e37c56b2c37b;hpb=49428d3a57e4f4863acbdeb3f77049ed95efd6c3;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 1134857..35ee8c4 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -21,6 +21,7 @@ package jalview.datamodel; import jalview.analysis.AlignmentUtils; +import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping; import jalview.io.FastaFile; import jalview.util.Comparison; import jalview.util.MessageManager; @@ -44,7 +45,7 @@ import java.util.Vector; */ public class Alignment implements AlignmentI { - protected Alignment dataset; + private Alignment dataset; protected List sequences; @@ -109,7 +110,10 @@ 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()); + } } /** @@ -222,18 +226,21 @@ 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) { @@ -252,18 +259,22 @@ 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 +290,23 @@ 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 +315,16 @@ 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(); } } @@ -986,7 +1009,7 @@ public class Alignment implements AlignmentI } @Override - public void setDataset(Alignment data) + public void setDataset(AlignmentI data) { if (dataset == null && data == null) { @@ -994,7 +1017,12 @@ public class Alignment implements AlignmentI } 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); @@ -1021,6 +1049,62 @@ 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) + { + 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().getDatasetSequence() != null) + { + throw new Error("Implementation error: Map.getTo() for dbref" + + dbr + " is not a dataset sequence."); + // TODO: if this happens, could also rewrite the reference to + // point to new 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. */ @@ -1030,22 +1114,32 @@ 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 jalview.util.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; @@ -1340,6 +1434,10 @@ public class Alignment implements AlignmentI @Override public List getCodonFrames() { + // 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; } @@ -1361,11 +1459,7 @@ 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(); @@ -1376,6 +1470,8 @@ 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) @@ -1391,9 +1487,13 @@ 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++) @@ -1401,6 +1501,7 @@ public class Alignment implements AlignmentI addAnnotation(alan[a]); } + // use add method getCodonFrames().addAll(toappend.getCodonFrames()); List sg = toappend.getGroups(); @@ -1691,9 +1792,11 @@ 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 @@ -1704,31 +1807,18 @@ public class Alignment implements AlignmentI 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); - - // TODO handle intron regions? Needs a 'holistic' alignment of dna, - // not just sequence by sequence. But how to 'gap' intron regions? - - /* - * 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); } /** @@ -1811,4 +1901,40 @@ public class Alignment implements AlignmentI } 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 }; + } }