X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=9cec37052ad74f30342b293e7087e3a876fe0317;hb=bc27e1b604af729b363da1f29bdd5774ca79f4e4;hp=338aa627c01c85833414953a851dcdf883199a84;hpb=ab43013b7e357b84b4abade0dba949668dfb2a0e;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 338aa62..9cec370 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -21,6 +21,7 @@ package jalview.datamodel; import jalview.analysis.AlignSeq; +import jalview.util.StringUtils; import java.util.ArrayList; import java.util.Enumeration; @@ -50,7 +51,7 @@ public class Sequence implements SequenceI int end; - Vector pdbIds; + Vector pdbIds; String vamsasId; @@ -326,27 +327,52 @@ public class Sequence implements SequenceI } /** - * DOCUMENT ME! + * Returns the sequence features (if any), looking first on the sequence, then + * on its dataset sequence, and so on until a non-null value is found (or + * none). This supports retrieval of sequence features stored on the sequence + * (as in the applet) or on the dataset sequence (as in the Desktop version). * - * @return DOCUMENT ME! + * @return */ public SequenceFeature[] getSequenceFeatures() { - return sequenceFeatures; + SequenceFeature[] features = sequenceFeatures; + + SequenceI seq = this; + int count = 0; // failsafe against loop in sequence.datasetsequence... + while (features == null && seq.getDatasetSequence() != null + && count++ < 10) + { + seq = seq.getDatasetSequence(); + features = ((Sequence) seq).sequenceFeatures; + } + return features; } public void addPDBId(PDBEntry entry) { if (pdbIds == null) { - pdbIds = new Vector(); + pdbIds = new Vector(); + } + if (pdbIds.contains(entry)) + { + updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry); } - if (!pdbIds.contains(entry)) + else { pdbIds.addElement(entry); } } + private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry) + { + if (newEntry.getFile() != null) + { + oldEntry.setFile(newEntry.getFile()); + } + } + /** * DOCUMENT ME! * @@ -661,11 +687,7 @@ public class Sequence implements SequenceI return map; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#findPositionMap() - */ + @Override public int[] findPositionMap() { int map[] = new int[sequence.length]; @@ -685,11 +707,43 @@ public class Sequence implements SequenceI return map; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deleteChars(int, int) - */ + @Override + public List getInsertions() + { + ArrayList map = new ArrayList(); + 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.add(new int[] + { lastj, j - 1 }); + lastj = -1; + } + } + j++; + } + if (lastj != -1) + { + map.add(new int[] + { lastj, j - 1 }); + lastj = -1; + } + return map; + } + + @Override public void deleteChars(int i, int j) { int newstart = start, newend = end; @@ -698,24 +752,12 @@ public class Sequence implements SequenceI return; } - char[] tmp; - - if (j >= sequence.length) - { - tmp = new char[i]; - System.arraycopy(sequence, 0, tmp, 0, i); - j = sequence.length; - } - else - { - tmp = new char[sequence.length - j + i]; - System.arraycopy(sequence, 0, tmp, 0, i); - System.arraycopy(sequence, j, tmp, i, sequence.length - j); - } + char[] tmp = StringUtils.deleteChars(sequence, i, j); boolean createNewDs = false; - // TODO: take a look at the new dataset creation validation method below - - // this could become time comsuming for large sequences - consider making it - // more efficient + // TODO: take a (second look) at the dataset creation validation method for + // the very large sequence case + int eindex = -1, sindex = -1; + boolean ecalc = false, scalc = false; for (int s = i; s < j; s++) { if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23) @@ -726,7 +768,11 @@ public class Sequence implements SequenceI } else { - int sindex = findIndex(start) - 1; + if (!scalc) + { + sindex = findIndex(start) - 1; + scalc = true; + } if (sindex == s) { // delete characters including start of sequence @@ -736,7 +782,11 @@ public class Sequence implements SequenceI else { // delete characters after start. - int eindex = findIndex(end) - 1; + if (!ecalc) + { + eindex = findIndex(end) - 1; + ecalc = true; + } if (eindex < j) { // delete characters at end of sequence @@ -768,16 +818,7 @@ public class Sequence implements SequenceI sequence = tmp; } - /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! - * @param c - * DOCUMENT ME! - * @param chop - * DOCUMENT ME! - */ + @Override public void insertCharAt(int i, int length, char c) { char[] tmp = new char[sequence.length + length]; @@ -807,26 +848,31 @@ public class Sequence implements SequenceI sequence = tmp; } + @Override public void insertCharAt(int i, char c) { insertCharAt(i, 1, c); } + @Override public String getVamsasId() { return vamsasId; } + @Override public void setVamsasId(String id) { vamsasId = id; } + @Override public void setDBRef(DBRefEntry[] dbref) { dbrefs = dbref; } + @Override public DBRefEntry[] getDBRef() { if (dbrefs == null && datasetSequence != null @@ -837,6 +883,7 @@ public class Sequence implements SequenceI return dbrefs; } + @Override public void addDBRef(DBRefEntry entry) { if (dbrefs == null) @@ -869,40 +916,33 @@ public class Sequence implements SequenceI dbrefs = temp; } + @Override public void setDatasetSequence(SequenceI seq) { datasetSequence = seq; } + @Override public SequenceI getDatasetSequence() { return datasetSequence; } - /** - * Returns a new array containing this sequence's annotations, or null. - */ + @Override public AlignmentAnnotation[] getAnnotation() { return annotation == null ? null : annotation .toArray(new AlignmentAnnotation[annotation.size()]); } - /** - * Returns true if this sequence has the given annotation (by object - * identity). - */ + @Override public boolean hasAnnotation(AlignmentAnnotation ann) { return annotation == null ? false : annotation.contains(ann); } - /** - * Add the given annotation, if not already added, and set its sequence ref to - * be this sequence. Does nothing if this sequence's annotations already - * include this annotation (by identical object reference). - */ + @Override public void addAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation == null) @@ -948,11 +988,7 @@ public class Sequence implements SequenceI return true; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deriveSequence() - */ + @Override public SequenceI deriveSequence() { SequenceI seq = new Sequence(this); @@ -1010,7 +1046,7 @@ public class Sequence implements SequenceI AlignmentAnnotation _aa = new AlignmentAnnotation(aa); _aa.sequenceRef = datasetSequence; _aa.adjustForAlignment(); // uses annotation's own record of - // sequence-column mapping + // sequence-column mapping datasetSequence.addAlignmentAnnotation(_aa); } } @@ -1043,11 +1079,7 @@ public class Sequence implements SequenceI } } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String) - */ + @Override public AlignmentAnnotation[] getAnnotation(String label) { if (annotation == null || annotation.size() == 0) @@ -1080,6 +1112,7 @@ public class Sequence implements SequenceI return anns; } + @Override public boolean updatePDBIds() { if (datasetSequence != null) @@ -1133,13 +1166,7 @@ public class Sequence implements SequenceI return false; } - /* - * (non-Javadoc) - * - * @see - * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI, - * jalview.datamodel.Mapping) - */ + @Override public void transferAnnotation(SequenceI entry, Mapping mp) { if (datasetSequence != null) @@ -1235,20 +1262,15 @@ public class Sequence implements SequenceI return rna; } - /** - * Returns a (possibly empty) list of any annotations that match on given - * calcId (source) and label (type). Null values do not match. - * - * @param calcId - * @param label - */ @Override public List getAlignmentAnnotations(String calcId, String label) { List result = new ArrayList(); - if (this.annotation != null) { - for (AlignmentAnnotation ann : annotation) { + if (this.annotation != null) + { + for (AlignmentAnnotation ann : annotation) + { if (ann.calcId != null && ann.calcId.equals(calcId) && ann.label != null && ann.label.equals(label)) {