X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=9e81d8188df0e7c3f4047e13d3ac47b283e75209;hb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;hp=96a2fa17b5b6c3253130b8df9552b83cfc0a2ad8;hpb=bba9e58f08fc55c0f789f8354d1444e5c5e1b0e6;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 96a2fa1..9e81d81 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -38,8 +38,6 @@ import java.util.List; import java.util.ListIterator; import java.util.Vector; -import com.stevesoft.pat.Regex; - import fr.orsay.lri.varna.models.rna.RNA; /** @@ -51,11 +49,6 @@ import fr.orsay.lri.varna.models.rna.RNA; */ public class Sequence extends ASequence implements SequenceI { - private static final Regex limitrx = new Regex( - "[/][0-9]{1,}[-][0-9]{1,}$"); - - private static final Regex endrx = new Regex("[0-9]{1,}$"); - SequenceI datasetSequence; String name; @@ -84,12 +77,7 @@ public class Sequence extends ASequence implements SequenceI */ Vector annotation; - /** - * The index of the sequence in a MSA - */ - int index = -1; - - private SequenceFeatures sequenceFeatureStore; + private SequenceFeaturesI sequenceFeatureStore; /* * A cursor holding the approximate current view position to the sequence, @@ -151,25 +139,49 @@ public class Sequence extends ASequence implements SequenceI checkValidRange(); } + /** + * If 'name' ends in /i-j, where i >= j > 0 are integers, extracts i and j as + * start and end respectively and removes the suffix from the name + */ void parseId() { 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? - if (limitrx.search(name)) + int slashPos = name.lastIndexOf('/'); + if (slashPos > -1 && slashPos < name.length() - 1) { - name = limitrx.left(); - endrx.search(limitrx.stringMatched()); - setStart(Integer.parseInt(limitrx.stringMatched().substring(1, - endrx.matchedFrom() - 1))); - setEnd(Integer.parseInt(endrx.stringMatched())); + String suffix = name.substring(slashPos + 1); + String[] range = suffix.split("-"); + if (range.length == 2) + { + try + { + int from = Integer.valueOf(range[0]); + int to = Integer.valueOf(range[1]); + if (from > 0 && to >= from) + { + name = name.substring(0, slashPos); + setStart(from); + setEnd(to); + checkValidRange(); + } + } catch (NumberFormatException e) + { + // leave name unchanged if suffix is invalid + } + } } } + /** + * Ensures that 'end' is not before the end of the sequence, that is, + * (end-start+1) is at least as long as the count of ungapped positions. Note + * that end is permitted to be beyond the end of the sequence data. + */ void checkValidRange() { // Note: JAL-774 : @@ -178,7 +190,7 @@ public class Sequence extends ASequence implements SequenceI int endRes = 0; for (int j = 0; j < sequence.length; j++) { - if (!jalview.util.Comparison.isGap(sequence[j])) + if (!Comparison.isGap(sequence[j])) { endRes++; } @@ -453,15 +465,15 @@ public class Sequence extends ASequence implements SequenceI } /** - * DOCUMENT ME! + * Sets the sequence name. If the name ends in /start-end, then the start-end + * values are parsed out and set, and the suffix is removed from the name. * - * @param name - * DOCUMENT ME! + * @param theName */ @Override - public void setName(String name) + public void setName(String theName) { - this.name = name; + this.name = theName; this.parseId(); } @@ -645,10 +657,10 @@ 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) @@ -656,10 +668,67 @@ 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() @@ -1364,8 +1433,9 @@ 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 @@ -1477,8 +1547,9 @@ 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; @@ -1620,7 +1691,7 @@ public class Sequence extends ASequence implements SequenceI List sfs = entry.getSequenceFeatures(); for (SequenceFeature feature : sfs) { - SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature) + SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature) : new SequenceFeature[] { new SequenceFeature(feature) }; if (sf != null) { @@ -1663,30 +1734,6 @@ public class Sequence extends ASequence implements SequenceI } } - /** - * @return The index (zero-based) on this sequence in the MSA. It returns - * {@code -1} if this information is not available. - */ - @Override - public int getIndex() - { - return index; - } - - /** - * Defines the position of this sequence in the MSA. Use the value {@code -1} - * if this information is undefined. - * - * @param The - * position for this sequence. This value is zero-based (zero for - * this first sequence) - */ - @Override - public void setIndex(int value) - { - index = value; - } - @Override public void setRNA(RNA r) { @@ -1777,8 +1824,8 @@ 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 @@ -1821,12 +1868,13 @@ public class Sequence extends ASequence implements SequenceI endPos, types); /* - * if the start or end column is gapped, startPos or endPos may be to the - * left or right, and we may have included adjacent or enclosing features; - * remove any that are not enclosing features + * if end column is gapped, endPos may be to the right, + * and we may have included adjacent or enclosing features; + * remove any that are not enclosing, non-contact features */ - if (endPos > this.end || Comparison.isGap(sequence[fromColumn - 1]) - || Comparison.isGap(sequence[toColumn - 1])) + boolean endColumnIsGapped = toColumn > 0 && toColumn <= sequence.length + && Comparison.isGap(sequence[toColumn - 1]); + if (endPos > this.end || endColumnIsGapped) { ListIterator it = result.listIterator(); while (it.hasNext()) @@ -1847,6 +1895,13 @@ public class Sequence extends ASequence implements SequenceI { it.remove(); } + else if (featureEndColumn > toColumn && sf.isContactFeature()) + { + /* + * remove an enclosing feature if it is a contact feature + */ + it.remove(); + } } } }