X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=5008a3e7a32ecc09b62d158e59ac2234cf02e657;hb=bb5fc546aeefa10a30ae93e01446161372d1e36b;hp=59c3fb171029c5d075362d0b7f9ad9d8908e1d02;hpb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 59c3fb1..5008a3e 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -28,6 +28,7 @@ import jalview.util.Comparison; import jalview.util.DBRefUtils; import jalview.util.MapList; import jalview.util.StringUtils; +import jalview.workers.InformationThread; import java.util.ArrayList; import java.util.Arrays; @@ -43,10 +44,7 @@ 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 { @@ -62,6 +60,10 @@ public class Sequence extends ASequence implements SequenceI int end; + HiddenMarkovModel hmm; + + boolean isHMMConsensusSequence = false; + Vector pdbIds; String vamsasId; @@ -338,6 +340,11 @@ public class Sequence extends ASequence implements SequenceI this.addPDBId(new PDBEntry(pdb)); } } + if (seq.getHMM() != null) + { + this.hmm = new HiddenMarkovModel(seq.getHMM(), this); + } + } @Override @@ -445,22 +452,23 @@ public class Sequence extends ASequence implements SequenceI @Override public Vector getAllPDBEntries() { - return pdbIds == null ? new Vector() : pdbIds; + return pdbIds == null ? new Vector<>() : pdbIds; } /** - * DOCUMENT ME! + * Answers the sequence name, with '/start-end' appended if jvsuffix is true * - * @return DOCUMENT ME! + * @return */ @Override public String getDisplayId(boolean jvsuffix) { - StringBuffer result = new StringBuffer(name); - if (jvsuffix) + if (!jvsuffix) { - result.append("/" + start + "-" + end); + return name; } + StringBuilder result = new StringBuilder(name); + result.append("/").append(start).append("-").append(end); return result.toString(); } @@ -673,8 +681,8 @@ public class Sequence extends ASequence implements SequenceI public void setGeneLoci(String speciesId, String assemblyId, String chromosomeId, MapList map) { - addDBRef(new DBRefEntry(speciesId, assemblyId, DBRefEntry.CHROMOSOME - + ":" + chromosomeId, new Mapping(map))); + addDBRef(new GeneLocus(speciesId, assemblyId, chromosomeId, + new Mapping(map))); } /** @@ -690,36 +698,9 @@ public class Sequence extends ASequence implements SequenceI { for (final DBRefEntry ref : refs) { - if (ref.isChromosome()) + if (ref instanceof GeneLociI) { - 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 (GeneLociI) ref; } } } @@ -797,6 +778,7 @@ 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; @@ -815,7 +797,7 @@ 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)) { @@ -833,18 +815,22 @@ 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; @@ -852,7 +838,14 @@ 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; } @@ -1057,9 +1050,10 @@ public class Sequence extends ASequence implements SequenceI * {@inheritDoc} */ @Override - public Range findPositions(int fromColumn, int toColumn) + public ContiguousI findPositions(int fromColumn, int toColumn) { - if (toColumn < fromColumn || fromColumn < 1) + fromColumn = Math.max(fromColumn, 1); + if (toColumn < fromColumn) { return null; } @@ -1251,12 +1245,13 @@ 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])) { @@ -1790,7 +1785,8 @@ public class Sequence extends ASequence implements SequenceI { for (AlignmentAnnotation ann : annotation) { - if (ann.calcId != null && ann.calcId.equals(calcId) + String id = ann.getCalcId(); + if (id != null && id.equals(calcId) && ann.label != null && ann.label.equals(label)) { result.add(ann); @@ -1888,6 +1884,34 @@ public class Sequence extends ASequence implements SequenceI } } + @Override + public HiddenMarkovModel getHMM() + { + return hmm; + } + + @Override + public void setHMM(HiddenMarkovModel hmm) + { + this.hmm = hmm; + } + + @Override + public boolean hasHMMAnnotation() + { + if (this.annotation == null) { + return false; + } + for (AlignmentAnnotation ann : annotation) + { + if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId())) + { + return true; + } + } + return false; + } + /** * {@inheritDoc} */ @@ -1901,6 +1925,15 @@ 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, @@ -2052,4 +2085,10 @@ public class Sequence extends ASequence implements SequenceI // otherwise, sequence was completely hidden return 0; } + + @Override + public boolean hasHMMProfile() + { + return hmm != null; + } }