X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=a8cff264d2e5cd8c65b4ddb4dae0bace3e42691b;hb=6568287d7ca9ab336a83e27b9bfbd548a10cf748;hp=b50e5af92191c7cd2df24696f40a95db15634d7a;hpb=e44876a5a8801c0118b67793ebd57d21079be7b0;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index b50e5af..a8cff26 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.BitSet; import java.util.Collections; import java.util.Enumeration; import java.util.List; @@ -232,8 +234,7 @@ 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 +293,6 @@ public class Sequence extends ASequence implements SequenceI } } - @Override public void setSequenceFeatures(SequenceFeature[] features) { @@ -315,12 +315,11 @@ 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 (sequenceFeatures == null && datasetSequence != null) { - datasetSequence.addSequenceFeature(sf); - return; + return datasetSequence.addSequenceFeature(sf); } if (sequenceFeatures == null) { @@ -331,7 +330,7 @@ public class Sequence extends ASequence implements SequenceI { if (sequenceFeatures[i].equals(sf)) { - return; + return false; } } @@ -340,6 +339,7 @@ public class Sequence extends ASequence implements SequenceI temp[sequenceFeatures.length] = sf; sequenceFeatures = temp; + return true; } @Override @@ -347,8 +347,9 @@ 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 +413,24 @@ 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; } /** @@ -823,6 +820,40 @@ public class Sequence extends ASequence implements SequenceI } @Override + public BitSet getInsertionsAsBits() + { + BitSet map = new BitSet(); + int lastj = -1, j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) + { + if (jalview.util.Comparison.isGap(sequence[j])) + { + if (lastj == -1) + { + lastj = j; + } + } + else + { + if (lastj != -1) + { + map.set(lastj, j - 1); + lastj = -1; + } + } + j++; + } + if (lastj != -1) + { + map.set(lastj, j - 1); + lastj = -1; + } + return map; + } + + @Override public void deleteChars(int i, int j) { int newstart = start, newend = end; @@ -948,7 +979,17 @@ 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 +1006,12 @@ 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 +1039,23 @@ 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 +1128,7 @@ public class Sequence extends ASequence implements SequenceI @Override public SequenceI deriveSequence() { - Sequence seq=null; + Sequence seq = null; if (datasetSequence == null) { if (isValidDatasetSequence()) @@ -1085,7 +1142,7 @@ public class Sequence extends ASequence implements SequenceI else { // Create a new, valid dataset sequence - createDatasetSequence(); + createDatasetSequence(); } } return new Sequence(this); @@ -1095,6 +1152,10 @@ 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 +1166,7 @@ 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 +1190,9 @@ 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 +1286,22 @@ 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 @@ -1413,15 +1450,14 @@ 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(); } @@ -1431,7 +1467,7 @@ public class Sequence extends ASequence implements SequenceI DBRefEntry[] tmp = new DBRefEntry[1]; for (DBRefEntry ref : dbrefs) { - if (!ref.isPrimary()) + if (!ref.isPrimaryCandidate()) { continue; }