X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=c8b94cecf83e3d4710d2186fc8d0b4a551b03d4d;hb=853624fb32058cccc544ae7d13af6ad4b0800b6c;hp=ec8aa81a1c598f4876984ec79d0cc0b9222e482e;hpb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index ec8aa81..c8b94ce 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -22,12 +22,14 @@ package jalview.datamodel; import jalview.analysis.AlignSeq; import jalview.api.DBRefEntryI; +import jalview.util.Comparison; import jalview.util.DBRefUtils; import jalview.util.MapList; import jalview.util.StringUtils; import java.util.ArrayList; import java.util.Arrays; +import java.util.Collections; import java.util.Enumeration; import java.util.List; import java.util.Vector; @@ -59,8 +61,6 @@ public class Sequence extends ASequence implements SequenceI String vamsasId; - DBRefEntryI sourceDBRef; - DBRefEntry[] dbrefs; RNA rna; @@ -233,8 +233,7 @@ 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) @@ -293,7 +292,6 @@ public class Sequence extends ASequence implements SequenceI } } - @Override public void setSequenceFeatures(SequenceFeature[] features) { @@ -307,8 +305,9 @@ public class Sequence extends ASequence implements SequenceI && datasetSequence.getSequenceFeatures() != null && datasetSequence.getSequenceFeatures().length > 0) { - System.err - .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment"); + new Exception( + "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment") + .printStackTrace(); } datasetSequence.setSequenceFeatures(features); } @@ -317,7 +316,7 @@ public class Sequence extends ASequence implements SequenceI @Override public synchronized void addSequenceFeature(SequenceFeature sf) { - if (sequenceFeatures==null && datasetSequence != null) + if (sequenceFeatures == null && datasetSequence != null) { datasetSequence.addSequenceFeature(sf); return; @@ -347,8 +346,9 @@ public class Sequence extends ASequence implements SequenceI { if (sequenceFeatures == null) { - if (datasetSequence!=null) { - datasetSequence.deleteFeature(sf); + if (datasetSequence != null) + { + datasetSequence.deleteFeature(sf); } return; } @@ -412,28 +412,24 @@ public class Sequence extends ASequence implements SequenceI } @Override - public void addPDBId(PDBEntry entry) + 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 +944,17 @@ 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 +971,12 @@ 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 +1004,23 @@ 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 +1093,7 @@ public class Sequence extends ASequence implements SequenceI @Override public SequenceI deriveSequence() { - Sequence seq=null; + Sequence seq = null; if (datasetSequence == null) { if (isValidDatasetSequence()) @@ -1085,7 +1107,7 @@ public class Sequence extends ASequence implements SequenceI else { // Create a new, valid dataset sequence - createDatasetSequence(); + createDatasetSequence(); } } return new Sequence(this); @@ -1095,6 +1117,10 @@ 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 +1131,7 @@ 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 +1155,9 @@ 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.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 +1251,22 @@ public class Sequence extends ASequence implements SequenceI { return false; } - Vector newpdb = new Vector(); - for (int i = 0; i < dbrefs.length; i++) - { - if (DBRefSource.PDB.equals(dbrefs[i].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) + boolean added = false; + for (DBRefEntry dbr : dbrefs) { - Enumeration en = newpdb.elements(); - while (en.hasMoreElements()) + if (DBRefSource.PDB.equals(dbr.getSource())) { - 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 @@ -1413,25 +1415,24 @@ 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 Arrays.asList(new DBRefEntry[0]); + return Collections.emptyList(); } synchronized (dbrefs) { List primaries = new ArrayList(); - DBRefEntry tmp[] = new DBRefEntry[1], res[] = null; + DBRefEntry[] tmp = new DBRefEntry[1]; for (DBRefEntry ref : dbrefs) { - if (!ref.isPrimary()) + if (!ref.isPrimaryCandidate()) { continue; } @@ -1449,7 +1450,13 @@ public class Sequence extends ASequence implements SequenceI DBRefUtils.getCanonicalName(ref.getSource()))) { // PDB dbrefs imply there should be a PDBEntry associated - if (getPDBEntry(ref.getAccessionId()) != null) + // TODO: tighten PDB dbrefs + // formally imply Jalview has actually downloaded and + // parsed the pdb file. That means there should be a cached file + // handle on the PDBEntry, and a real mapping between sequence and + // extracted sequence from PDB file + PDBEntry pdbentry = getPDBEntry(ref.getAccessionId()); + if (pdbentry != null && pdbentry.getFile() != null) { primaries.add(ref); } @@ -1457,7 +1464,7 @@ public class Sequence extends ASequence implements SequenceI } // check standard protein or dna sources tmp[0] = ref; - res = DBRefUtils.selectDbRefs(!isProtein(), tmp); + DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp); if (res != null && res[0] == tmp[0]) { primaries.add(ref);