X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=f5558559b37e5f6dbeb3dac62d4e06ed490d3681;hb=db80eb8e1acf352e72a33e1e3825d40f7c6e4046;hp=15d1378fce1d97673e2bdb67baaf3cb330eac2cf;hpb=2b4cc5fb6217217761b4a8bd2529e51b4775a57d;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 15d1378..f555855 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -34,6 +34,7 @@ import java.util.Arrays; import java.util.BitSet; import java.util.Collections; import java.util.Enumeration; +import java.util.Iterator; import java.util.List; import java.util.ListIterator; import java.util.Vector; @@ -42,10 +43,7 @@ import fr.orsay.lri.varna.models.rna.RNA; /** * - * Implements the SequenceI interface for a char[] based sequence object. - * - * @author $author$ - * @version $Revision$ + * Implements the SequenceI interface for a char[] based sequence object */ public class Sequence extends ASequence implements SequenceI { @@ -408,7 +406,7 @@ public class Sequence extends ASequence implements SequenceI { if (pdbIds == null) { - pdbIds = new Vector(); + pdbIds = new Vector<>(); pdbIds.add(entry); return true; } @@ -444,7 +442,7 @@ public class Sequence extends ASequence implements SequenceI @Override public Vector getAllPDBEntries() { - return pdbIds == null ? new Vector() : pdbIds; + return pdbIds == null ? new Vector<>() : pdbIds; } /** @@ -657,10 +655,10 @@ public class Sequence extends ASequence implements SequenceI } /** - * DOCUMENT ME! + * Sets the sequence description, and also parses out any special formats of + * interest * * @param desc - * DOCUMENT ME! */ @Override public void setDescription(String desc) @@ -668,10 +666,67 @@ public class Sequence extends ASequence implements SequenceI this.description = desc; } + @Override + public void setGeneLoci(String speciesId, String assemblyId, + String chromosomeId, MapList map) + { + addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME + + ":" + chromosomeId, new Mapping(map))); + } + /** - * DOCUMENT ME! + * Returns the gene loci mapping for the sequence (may be null) * - * @return DOCUMENT ME! + * @return + */ + @Override + public GeneLociI getGeneLoci() + { + DBRefEntry[] refs = getDBRefs(); + if (refs != null) + { + for (final DBRefEntry ref : refs) + { + if (ref.isChromosome()) + { + return new GeneLociI() + { + @Override + public String getSpeciesId() + { + return ref.getSource(); + } + + @Override + public String getAssemblyId() + { + return ref.getVersion(); + } + + @Override + public String getChromosomeId() + { + // strip off "chromosome:" prefix to chrId + return ref.getAccessionId().substring( + DBRefEntry.CHROMOSOME.length() + 1); + } + + @Override + public MapList getMap() + { + return ref.getMap().getMap(); + } + }; + } + } + } + return null; + } + + /** + * Answers the description + * + * @return */ @Override public String getDescription() @@ -739,6 +794,7 @@ public class Sequence extends ASequence implements SequenceI * preserve end residue column provided cursor was valid */ int endColumn = isValidCursor(cursor) ? cursor.lastColumnPosition : 0; + if (residuePos == this.end) { endColumn = column; @@ -757,7 +813,7 @@ public class Sequence extends ASequence implements SequenceI * @param curs * @return */ - protected int findIndex(int pos, SequenceCursor curs) + protected int findIndex(final int pos, SequenceCursor curs) { if (!isValidCursor(curs)) { @@ -775,18 +831,22 @@ public class Sequence extends ASequence implements SequenceI /* * move left or right to find pos from hint.position */ - int col = curs.columnPosition - 1; // convert from base 1 to 0-based array - // index + int col = curs.columnPosition - 1; // convert from base 1 to base 0 int newPos = curs.residuePosition; int delta = newPos > pos ? -1 : 1; while (newPos != pos) { col += delta; // shift one column left or right - if (col < 0 || col == sequence.length) + if (col < 0) { break; } + if (col == sequence.length) + { + col--; // return last column if we failed to reach pos + break; + } if (!Comparison.isGap(sequence[col])) { newPos += delta; @@ -794,7 +854,14 @@ public class Sequence extends ASequence implements SequenceI } col++; // convert back to base 1 - updateCursor(pos, col, curs.firstColumnPosition); + + /* + * only update cursor if we found the target position + */ + if (newPos == pos) + { + updateCursor(pos, col, curs.firstColumnPosition); + } return col; } @@ -1071,6 +1138,27 @@ public class Sequence extends ASequence implements SequenceI return map; } + /** + * Build a bitset corresponding to sequence gaps + * + * @return a BitSet where set values correspond to gaps in the sequence + */ + @Override + public BitSet gapBitset() + { + BitSet gaps = new BitSet(sequence.length); + int j = 0; + while (j < sequence.length) + { + if (jalview.util.Comparison.isGap(sequence[j])) + { + gaps.set(j); + } + j++; + } + return gaps; + } + @Override public int[] findPositionMap() { @@ -1094,7 +1182,7 @@ public class Sequence extends ASequence implements SequenceI @Override public List getInsertions() { - ArrayList map = new ArrayList(); + ArrayList map = new ArrayList<>(); int lastj = -1, j = 0; int pos = start; int seqlen = sequence.length; @@ -1172,12 +1260,13 @@ public class Sequence extends ASequence implements SequenceI boolean createNewDs = false; // TODO: take a (second look) at the dataset creation validation method for // the very large sequence case + int startIndex = findIndex(start) - 1; int endIndex = findIndex(end) - 1; int startDeleteColumn = -1; // for dataset sequence deletions int deleteCount = 0; - for (int s = i; s < j; s++) + for (int s = i; s < j && s < sequence.length; s++) { if (Comparison.isGap(sequence[s])) { @@ -1405,7 +1494,7 @@ public class Sequence extends ASequence implements SequenceI { if (this.annotation == null) { - this.annotation = new Vector(); + this.annotation = new Vector<>(); } if (!this.annotation.contains(annotation)) { @@ -1572,7 +1661,7 @@ public class Sequence extends ASequence implements SequenceI return null; } - Vector subset = new Vector(); + Vector subset = new Vector<>(); Enumeration e = annotation.elements(); while (e.hasMoreElements()) { @@ -1706,7 +1795,7 @@ public class Sequence extends ASequence implements SequenceI public List getAlignmentAnnotations(String calcId, String label) { - List result = new ArrayList(); + List result = new ArrayList<>(); if (this.annotation != null) { for (AlignmentAnnotation ann : annotation) @@ -1762,7 +1851,7 @@ public class Sequence extends ASequence implements SequenceI } synchronized (dbrefs) { - List primaries = new ArrayList(); + List primaries = new ArrayList<>(); DBRefEntry[] tmp = new DBRefEntry[1]; for (DBRefEntry ref : dbrefs) { @@ -1822,6 +1911,15 @@ public class Sequence extends ASequence implements SequenceI List result = getFeatures().findFeatures(startPos, endPos, types); + if (datasetSequence != null) + { + result = datasetSequence.getFeatures().findFeatures(startPos, endPos, + types); + } + else + { + result = sequenceFeatureStore.findFeatures(startPos, endPos, types); + } /* * if end column is gapped, endPos may be to the right, @@ -1904,4 +2002,73 @@ public class Sequence extends ASequence implements SequenceI return count; } + + @Override + public String getSequenceStringFromIterator(Iterator it) + { + StringBuilder newSequence = new StringBuilder(); + while (it.hasNext()) + { + int[] block = it.next(); + if (it.hasNext()) + { + newSequence.append(getSequence(block[0], block[1] + 1)); + } + else + { + newSequence.append(getSequence(block[0], block[1])); + } + } + + return newSequence.toString(); + } + + @Override + public int firstResidueOutsideIterator(Iterator regions) + { + int start = 0; + + if (!regions.hasNext()) + { + return findIndex(getStart()) - 1; + } + + // Simply walk along the sequence whilst watching for region + // boundaries + int hideStart = getLength(); + int hideEnd = -1; + boolean foundStart = false; + + // step through the non-gapped positions of the sequence + for (int i = getStart(); i <= getEnd() && (!foundStart); i++) + { + // get alignment position of this residue in the sequence + int p = findIndex(i) - 1; + + // update region start/end + while (hideEnd < p && regions.hasNext()) + { + int[] region = regions.next(); + hideStart = region[0]; + hideEnd = region[1]; + } + if (hideEnd < p) + { + hideStart = getLength(); + } + // update boundary for sequence + if (p < hideStart) + { + start = p; + foundStart = true; + } + } + + if (foundStart) + { + return start; + } + // otherwise, sequence was completely hidden + return 0; + } }