X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=af6592bab33ad578c0f5285743a05b77666d968f;hb=6323f1a33650360f131f25cf2797e5600ceee49f;hp=5886ae0eaebcb6392078e094b6c9dbf50c20c70e;hpb=6c43dd36929855a7907380ffb36b4df249d4a557;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 5886ae0..af6592b 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -22,6 +22,9 @@ package jalview.datamodel; import jalview.analysis.AlignSeq; import jalview.api.DBRefEntryI; +import jalview.datamodel.features.SequenceFeatures; +import jalview.datamodel.features.SequenceFeaturesI; +import jalview.util.Comparison; import jalview.util.DBRefUtils; import jalview.util.MapList; import jalview.util.StringUtils; @@ -80,6 +83,8 @@ public class Sequence extends ASequence implements SequenceI /** array of sequence features - may not be null for a valid sequence object */ public SequenceFeature[] sequenceFeatures; + private SequenceFeatures sequenceFeatureStore; + /** * Creates a new Sequence object. * @@ -119,6 +124,7 @@ public class Sequence extends ASequence implements SequenceI this.sequence = sequence2; this.start = start2; this.end = end2; + sequenceFeatureStore = new SequenceFeatures(); parseId(); checkValidRange(); } @@ -232,8 +238,7 @@ public class Sequence extends ASequence implements SequenceI { char[] oseq = seq.getSequence(); initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length), - seq.getStart(), - seq.getEnd()); + seq.getStart(), seq.getEnd()); } description = seq.getDescription(); if (seq != datasetSequence) @@ -292,7 +297,6 @@ public class Sequence extends ASequence implements SequenceI } } - @Override public void setSequenceFeatures(SequenceFeature[] features) { @@ -315,12 +319,18 @@ public class Sequence extends ASequence implements SequenceI } @Override - public synchronized void addSequenceFeature(SequenceFeature sf) + public synchronized boolean addSequenceFeature(SequenceFeature sf) { - if (sequenceFeatures==null && datasetSequence != null) + if (sf.getType() == null) { - datasetSequence.addSequenceFeature(sf); - return; + System.err.println("SequenceFeature type may not be null: " + + sf.toString()); + return false; + } + + if (sequenceFeatures == null && datasetSequence != null) + { + return datasetSequence.addSequenceFeature(sf); } if (sequenceFeatures == null) { @@ -331,7 +341,7 @@ public class Sequence extends ASequence implements SequenceI { if (sequenceFeatures[i].equals(sf)) { - return; + return false; } } @@ -340,6 +350,9 @@ public class Sequence extends ASequence implements SequenceI temp[sequenceFeatures.length] = sf; sequenceFeatures = temp; + + sequenceFeatureStore.add(sf); + return true; } @Override @@ -347,12 +360,21 @@ public class Sequence extends ASequence implements SequenceI { if (sequenceFeatures == null) { - if (datasetSequence!=null) { - datasetSequence.deleteFeature(sf); + if (datasetSequence != null) + { + datasetSequence.deleteFeature(sf); } return; } + /* + * new way + */ + sequenceFeatureStore.delete(sf); + + /* + * old way - to be removed + */ int index = 0; for (index = 0; index < sequenceFeatures.length; index++) { @@ -412,28 +434,31 @@ public class Sequence extends ASequence implements SequenceI } @Override - public void addPDBId(PDBEntry entry) + public SequenceFeaturesI getFeatures() + { + return datasetSequence != null ? datasetSequence.getFeatures() + : sequenceFeatureStore; + } + + @Override + public boolean addPDBId(PDBEntry entry) { if (pdbIds == null) { pdbIds = new Vector(); + pdbIds.add(entry); + return true; } - if (pdbIds.contains(entry)) - { - updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry); - } - else - { - pdbIds.addElement(entry); - } - } - private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry) - { - if (newEntry.getFile() != null) + for (PDBEntry pdbe : pdbIds) { - oldEntry.setFile(newEntry.getFile()); + if (pdbe.updateFrom(entry)) + { + return false; + } } + pdbIds.addElement(entry); + return true; } /** @@ -948,7 +973,17 @@ public class Sequence extends ASequence implements SequenceI @Override public void setDBRefs(DBRefEntry[] dbref) { + if (dbrefs == null && datasetSequence != null + && this != datasetSequence) + { + datasetSequence.setDBRefs(dbref); + return; + } dbrefs = dbref; + if (dbrefs != null) + { + DBRefUtils.ensurePrimaries(this); + } } @Override @@ -965,7 +1000,12 @@ public class Sequence extends ASequence implements SequenceI @Override public void addDBRef(DBRefEntry entry) { - // TODO add to dataset sequence instead if there is one? + if (datasetSequence != null) + { + datasetSequence.addDBRef(entry); + return; + } + if (dbrefs == null) { dbrefs = new DBRefEntry[0]; @@ -993,12 +1033,23 @@ public class Sequence extends ASequence implements SequenceI temp[temp.length - 1] = entry; dbrefs = temp; + + DBRefUtils.ensurePrimaries(this); } @Override public void setDatasetSequence(SequenceI seq) { - // TODO check for circular reference before setting? + if (seq == this) + { + throw new IllegalArgumentException( + "Implementation Error: self reference passed to SequenceI.setDatasetSequence"); + } + if (seq != null && seq.getDatasetSequence() != null) + { + throw new IllegalArgumentException( + "Implementation error: cascading dataset sequences are not allowed."); + } datasetSequence = seq; } @@ -1071,7 +1122,7 @@ public class Sequence extends ASequence implements SequenceI @Override public SequenceI deriveSequence() { - Sequence seq=null; + Sequence seq = null; if (datasetSequence == null) { if (isValidDatasetSequence()) @@ -1085,7 +1136,7 @@ public class Sequence extends ASequence implements SequenceI else { // Create a new, valid dataset sequence - createDatasetSequence(); + createDatasetSequence(); } } return new Sequence(this); @@ -1095,6 +1146,10 @@ public class Sequence extends ASequence implements SequenceI private long _seqhash = 0; + /** + * Answers false if the sequence is more than 85% nucleotide (ACGTU), else + * true + */ @Override public boolean isProtein() { @@ -1105,7 +1160,7 @@ public class Sequence extends ASequence implements SequenceI if (_seqhash != sequence.hashCode()) { _seqhash = sequence.hashCode(); - _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this }); + _isNa = Comparison.isNucleotide(this); } return !_isNa; }; @@ -1129,9 +1184,11 @@ public class Sequence extends ASequence implements SequenceI dsseq.setDescription(description); // move features and database references onto dataset sequence dsseq.sequenceFeatures = sequenceFeatures; - sequenceFeatures=null; + sequenceFeatures = null; + dsseq.sequenceFeatureStore = sequenceFeatureStore; + sequenceFeatureStore = null; dsseq.dbrefs = dbrefs; - dbrefs=null; + dbrefs = null; // TODO: search and replace any references to this sequence with // references to the dataset sequence in Mappings on dbref dsseq.pdbIds = pdbIds; @@ -1225,46 +1282,22 @@ public class Sequence extends ASequence implements SequenceI { return false; } - Vector newpdb = new Vector(); - for (int i = 0; i < dbrefs.length; i++) + boolean added = false; + for (DBRefEntry dbr : dbrefs) { - if (DBRefSource.PDB.equals(dbrefs[i].getSource())) + if (DBRefSource.PDB.equals(dbr.getSource())) { - PDBEntry pdbe = new PDBEntry(); - pdbe.setId(dbrefs[i].getAccessionId()); - if (pdbIds == null || pdbIds.size() == 0) - { - newpdb.addElement(pdbe); - } - else - { - Enumeration en = pdbIds.elements(); - boolean matched = false; - while (!matched && en.hasMoreElements()) - { - PDBEntry anentry = (PDBEntry) en.nextElement(); - if (anentry.getId().equals(pdbe.getId())) - { - matched = true; - } - } - if (!matched) - { - newpdb.addElement(pdbe); - } - } - } - } - if (newpdb.size() > 0) - { - Enumeration en = newpdb.elements(); - while (en.hasMoreElements()) - { - addPDBId((PDBEntry) en.nextElement()); + /* + * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the + * PDB id is not already present in a 'matching' PDBEntry + * Constructor parses out a chain code if appended to the accession id + * (a fudge used to 'store' the chain code in the DBRef) + */ + PDBEntry pdbe = new PDBEntry(dbr); + added |= addPDBId(pdbe); } - return true; } - return false; + return added; } @Override @@ -1413,15 +1446,14 @@ public class Sequence extends ASequence implements SequenceI return null; } - @Override public List getPrimaryDBRefs() { - if (datasetSequence!=null) + if (datasetSequence != null) { return datasetSequence.getPrimaryDBRefs(); } - if (dbrefs==null || dbrefs.length==0) + if (dbrefs == null || dbrefs.length == 0) { return Collections.emptyList(); } @@ -1474,4 +1506,17 @@ public class Sequence extends ASequence implements SequenceI } } + /** + * {@inheritDoc} + */ + @Override + public List findFeatures(int from, int to, + String... types) + { + if (datasetSequence != null) + { + return datasetSequence.findFeatures(from, to, types); + } + return sequenceFeatureStore.findFeatures(from, to, types); + } }