X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=33f30cf5b9c3de2ab7e1f67c88c1e3220cffc3a8;hb=7c19c72efd3433b14f845c265747010d9dc596cc;hp=2f64759767b686e1786bf86d5695e99a799aa9b3;hpb=0d9271962a4c5e720ec8284d579bda635b59b231;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 2f64759..33f30cf 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -24,6 +24,7 @@ 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; @@ -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; @@ -75,14 +72,7 @@ public class Alignment implements AlignmentI hiddenSequences = new HiddenSequences(this); codonFrameList = new ArrayList(); - if (Comparison.isNucleotide(seqs)) - { - type = NUCLEOTIDE; - } - else - { - type = PROTEIN; - } + nucleotide = Comparison.isNucleotide(seqs); sequences = Collections.synchronizedList(new ArrayList()); @@ -195,14 +185,7 @@ public class Alignment implements AlignmentI return AlignmentUtils.getSequencesByName(this); } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ + @Override public SequenceI getSequenceAt(int i) { @@ -216,8 +199,32 @@ 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 */ @@ -290,13 +297,23 @@ 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; @@ -305,14 +322,16 @@ 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(); } } @@ -353,17 +372,18 @@ public class Alignment implements AlignmentI * @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; + } } } } @@ -648,7 +668,7 @@ 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; @@ -663,22 +683,19 @@ 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() { @@ -764,6 +781,12 @@ 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. @@ -964,29 +987,9 @@ 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 @@ -1042,6 +1045,7 @@ public class Alignment implements AlignmentI private void resolveAndAddDatasetSeq(SequenceI currentSeq, Set seqs, boolean createDatasetSequence) { + SequenceI alignedSeq = currentSeq; if (currentSeq.getDatasetSequence() != null) { currentSeq = currentSeq.getDatasetSequence(); @@ -1076,12 +1080,19 @@ public class Alignment implements AlignmentI { 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 + " is not a dataset sequence."); - // TODO: if this happens, could also rewrite the reference to - // point to new dataset sequence + 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 @@ -1103,7 +1114,7 @@ public class Alignment implements AlignmentI return; } // try to avoid using SequenceI.equals at this stage, it will be expensive - Set seqs = new jalview.util.LinkedIdentityHashSet(); + Set seqs = new LinkedIdentityHashSet(); for (int i = 0; i < getHeight(); i++) { @@ -1569,7 +1580,6 @@ public class Alignment implements AlignmentI String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef) { - assert (name != null); if (annotations != null) { for (AlignmentAnnotation annot : getAlignmentAnnotation()) @@ -1601,14 +1611,18 @@ 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; @@ -1816,7 +1830,7 @@ public class Alignment implements AlignmentI @Override public String toString() { - return new FastaFile().print(getSequencesArray()); + return new FastaFile().print(getSequencesArray(), true); } /**