X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=010323797a1a950adf074d209e52638718346189;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=2bbc278ba8396491b70feaf11a6e6ccba30cd315;hpb=323209e10678fb37fb1f6ac5321f5032ac8c1ff9;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 2bbc278..0103237 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -22,12 +22,15 @@ 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; import java.util.Vector; @@ -76,7 +79,9 @@ public class Sequence extends ASequence implements SequenceI */ int index = -1; - /** array of sequence features - may not be null for a valid sequence object */ + /** + * array of sequence features - may not be null for a valid sequence object + */ public SequenceFeature[] sequenceFeatures; /** @@ -131,8 +136,8 @@ public class Sequence extends ASequence implements SequenceI { if (name == null) { - System.err - .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); + System.err.println( + "POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); name = ""; } // Does sequence have the /start-end signature? @@ -231,8 +236,7 @@ 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) @@ -291,7 +295,6 @@ public class Sequence extends ASequence implements SequenceI } } - @Override public void setSequenceFeatures(SequenceFeature[] features) { @@ -307,19 +310,18 @@ public class Sequence extends ASequence implements SequenceI { new Exception( "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment") - .printStackTrace(); + .printStackTrace(); } datasetSequence.setSequenceFeatures(features); } } @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) { @@ -330,15 +332,17 @@ public class Sequence extends ASequence implements SequenceI { if (sequenceFeatures[i].equals(sf)) { - return; + return false; } } - SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + 1]; + SequenceFeature[] temp = new SequenceFeature[sequenceFeatures.length + + 1]; System.arraycopy(sequenceFeatures, 0, temp, 0, sequenceFeatures.length); temp[sequenceFeatures.length] = sf; sequenceFeatures = temp; + return true; } @Override @@ -346,8 +350,9 @@ public class Sequence extends ASequence implements SequenceI { if (sequenceFeatures == null) { - if (datasetSequence!=null) { - datasetSequence.deleteFeature(sf); + if (datasetSequence != null) + { + datasetSequence.deleteFeature(sf); } return; } @@ -411,28 +416,24 @@ 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; } /** @@ -822,6 +823,40 @@ 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); + lastj = -1; + } + } + j++; + } + if (lastj != -1) + { + map.set(lastj, j); + lastj = -1; + } + return map; + } + + @Override public void deleteChars(int i, int j) { int newstart = start, newend = end; @@ -947,7 +982,17 @@ 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 @@ -964,7 +1009,12 @@ 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]; @@ -992,12 +1042,23 @@ 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; } @@ -1010,8 +1071,9 @@ public class Sequence extends ASequence implements SequenceI @Override public AlignmentAnnotation[] getAnnotation() { - return annotation == null ? null : annotation - .toArray(new AlignmentAnnotation[annotation.size()]); + return annotation == null ? null + : annotation + .toArray(new AlignmentAnnotation[annotation.size()]); } @Override @@ -1070,7 +1132,7 @@ public class Sequence extends ASequence implements SequenceI @Override public SequenceI deriveSequence() { - Sequence seq=null; + Sequence seq = null; if (datasetSequence == null) { if (isValidDatasetSequence()) @@ -1084,7 +1146,7 @@ public class Sequence extends ASequence implements SequenceI else { // Create a new, valid dataset sequence - createDatasetSequence(); + createDatasetSequence(); } } return new Sequence(this); @@ -1094,6 +1156,10 @@ 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() { @@ -1104,7 +1170,7 @@ 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; }; @@ -1119,8 +1185,9 @@ public class Sequence extends ASequence implements SequenceI { if (datasetSequence == null) { - Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, getSequenceAsString()), + Sequence dsseq = new Sequence(getName(), + AlignSeq.extractGaps(jalview.util.Comparison.GapChars, + getSequenceAsString()), getStart(), getEnd()); datasetSequence = dsseq; @@ -1128,9 +1195,9 @@ 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; @@ -1224,46 +1291,22 @@ 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 @@ -1287,7 +1330,8 @@ public class Sequence extends ASequence implements SequenceI for (int si = 0; si < sfs.length; si++) { SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si]) - : new SequenceFeature[] { new SequenceFeature(sfs[si]) }; + : new SequenceFeature[] + { new SequenceFeature(sfs[si]) }; if (sf != null && sf.length > 0) { for (int sfi = 0; sfi < sf.length; sfi++) @@ -1412,25 +1456,24 @@ 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; } @@ -1444,18 +1487,17 @@ public class Sequence extends ASequence implements SequenceI } } // whilst it looks like it is a primary ref, we also sanity check type - if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals( - DBRefUtils.getCanonicalName(ref.getSource()))) + if (DBRefUtils.getCanonicalName(DBRefSource.PDB) + .equals(DBRefUtils.getCanonicalName(ref.getSource()))) { // PDB dbrefs imply there should be a PDBEntry associated // TODO: tighten PDB dbrefs - // formally imply Jalview has actually downlaoded and + // 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.getType() != null - && pdbentry.getType().equalsIgnoreCase("PDB")) + if (pdbentry != null && pdbentry.getFile() != null) { primaries.add(ref); } @@ -1463,7 +1505,7 @@ 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);