X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=010323797a1a950adf074d209e52638718346189;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=6b57ef797b8a530c9411f5a7466d136bdf2b9c52;hpb=b9940c76e03cfc61550c94e5865019f5d6231daf;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 6b57ef7..0103237 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; @@ -77,7 +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; /** @@ -132,8 +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? @@ -232,8 +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) @@ -292,7 +295,6 @@ public class Sequence extends ASequence implements SequenceI } } - @Override public void setSequenceFeatures(SequenceFeature[] features) { @@ -308,19 +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) { @@ -331,15 +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 @@ -347,8 +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; } @@ -819,6 +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; @@ -944,7 +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 @@ -1001,7 +1049,16 @@ public class Sequence extends ASequence implements SequenceI @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; } @@ -1014,8 +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 @@ -1074,7 +1132,7 @@ public class Sequence extends ASequence implements SequenceI @Override public SequenceI deriveSequence() { - Sequence seq=null; + Sequence seq = null; if (datasetSequence == null) { if (isValidDatasetSequence()) @@ -1088,7 +1146,7 @@ public class Sequence extends ASequence implements SequenceI else { // Create a new, valid dataset sequence - createDatasetSequence(); + createDatasetSequence(); } } return new Sequence(this); @@ -1098,6 +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() { @@ -1108,7 +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; }; @@ -1123,8 +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; @@ -1132,9 +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; @@ -1267,7 +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++) @@ -1392,15 +1456,14 @@ 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(); } @@ -1424,8 +1487,8 @@ 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