X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=8b089a22da302a9fe21a84496fa5e63655ed0f86;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=68bf8f223592ca7f3f28decffc0e4196b825e35b;hpb=195c41c18f6a059b334d063312cd15de6a937ea5;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 68bf8f2..8b089a2 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 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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; @@ -36,7 +37,7 @@ import fr.orsay.lri.varna.models.rna.RNA; * @author $author$ * @version $Revision$ */ -public class Sequence implements SequenceI +public class Sequence extends ASequence implements SequenceI { SequenceI datasetSequence; @@ -50,7 +51,7 @@ public class Sequence implements SequenceI int end; - Vector pdbIds; + Vector pdbIds; String vamsasId; @@ -89,20 +90,30 @@ public class Sequence implements SequenceI */ public Sequence(String name, String sequence, int start, int end) { - this.name = name; - this.sequence = sequence.toCharArray(); - this.start = start; - this.end = end; - parseId(); - checkValidRange(); + initSeqAndName(name, sequence.toCharArray(), start, end); } public Sequence(String name, char[] sequence, int start, int end) { - this.name = name; - this.sequence = sequence; - this.start = start; - this.end = end; + initSeqAndName(name, sequence, start, end); + } + + /** + * Stage 1 constructor - assign name, sequence, and set start and end fields. + * start and end are updated values from name2 if it ends with /start-end + * + * @param name2 + * @param sequence2 + * @param start2 + * @param end2 + */ + protected void initSeqAndName(String name2, char[] sequence2, int start2, + int end2) + { + this.name = name2; + this.sequence = sequence2; + this.start = start2; + this.end = end2; parseId(); checkValidRange(); } @@ -120,7 +131,7 @@ public class Sequence implements SequenceI .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); name = ""; } - // Does sequence have the /start-end signiature? + // Does sequence have the /start-end signature? if (limitrx.search(name)) { name = limitrx.left(); @@ -195,7 +206,15 @@ public class Sequence implements SequenceI */ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation) { - this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); + initSeqFrom(seq, alAnnotation); + + } + + protected void initSeqFrom(SequenceI seq, + AlignmentAnnotation[] alAnnotation) + { + initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(), + seq.getEnd()); description = seq.getDescription(); if (seq.getSequenceFeatures() != null) { @@ -240,9 +259,9 @@ public class Sequence implements SequenceI } } } - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - Vector ids = seq.getPDBId(); + Vector ids = seq.getAllPDBEntries(); Enumeration e = ids.elements(); while (e.hasMoreElements()) { @@ -326,34 +345,60 @@ 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! * * @param id * DOCUMENT ME! */ - public void setPDBId(Vector id) + @Override + public void setPDBId(Vector id) { pdbIds = id; } @@ -363,7 +408,8 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ - public Vector getPDBId() + @Override + public Vector getAllPDBEntries() { return pdbIds; } @@ -514,16 +560,7 @@ public class Sequence implements SequenceI return reply; } - /** - * make a new Sequence object from start to end (including gaps) over this - * seqeunce - * - * @param start - * int - * @param end - * int - * @return SequenceI - */ + @Override public SequenceI getSubSequence(int start, int end) { if (start < 0) @@ -623,14 +660,7 @@ public class Sequence implements SequenceI } } - /** - * Returns the sequence position for an alignment position - * - * @param i - * column index in alignment (from 1) - * - * @return residue number for residue (left of and) nearest ith column - */ + @Override public int findPosition(int i) { int j = 0; @@ -677,11 +707,7 @@ public class Sequence implements SequenceI return map; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#findPositionMap() - */ + @Override public int[] findPositionMap() { int map[] = new int[sequence.length]; @@ -701,37 +727,55 @@ public class Sequence implements SequenceI return map; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deleteChars(int, int) - */ - public void deleteChars(int i, int j) + @Override + public List getInsertions() { - int newstart = start, newend = end; - if (i >= sequence.length) + ArrayList map = new ArrayList(); + int lastj = -1, j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) { - return; + 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++; } - - char[] tmp; - - if (j >= sequence.length) + if (lastj != -1) { - tmp = new char[i]; - System.arraycopy(sequence, 0, tmp, 0, i); - j = sequence.length; + map.add(new int[] { lastj, j - 1 }); + lastj = -1; } - else + return map; + } + + @Override + public void deleteChars(int i, int j) + { + int newstart = start, newend = end; + if (i >= sequence.length || i < 0) { - tmp = new char[sequence.length - j + i]; - System.arraycopy(sequence, 0, tmp, 0, i); - System.arraycopy(sequence, j, tmp, i, sequence.length - j); + return; } + + 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) @@ -742,7 +786,11 @@ 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 @@ -752,7 +800,11 @@ 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 @@ -784,16 +836,7 @@ 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]; @@ -823,26 +866,31 @@ 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 @@ -853,6 +901,7 @@ public class Sequence implements SequenceI return dbrefs; } + @Override public void addDBRef(DBRefEntry entry) { if (dbrefs == null) @@ -885,37 +934,37 @@ public class Sequence implements SequenceI dbrefs = temp; } + @Override public void setDatasetSequence(SequenceI seq) { datasetSequence = seq; } + @Override public SequenceI getDatasetSequence() { return datasetSequence; } + @Override public AlignmentAnnotation[] getAnnotation() { - if (annotation == null) - { - return null; - } - - AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()]; - for (int r = 0; r < ret.length; r++) - { - ret[r] = annotation.elementAt(r); - } + return annotation == null ? null : annotation + .toArray(new AlignmentAnnotation[annotation.size()]); + } - return ret; + @Override + public boolean hasAnnotation(AlignmentAnnotation ann) + { + return annotation == null ? false : annotation.contains(ann); } + @Override public void addAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation == null) { - this.annotation = new Vector(); + this.annotation = new Vector(); } if (!this.annotation.contains(annotation)) { @@ -956,11 +1005,7 @@ public class Sequence implements SequenceI return true; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deriveSequence() - */ + @Override public SequenceI deriveSequence() { SequenceI seq = new Sequence(this); @@ -1008,7 +1053,7 @@ public class Sequence implements SequenceI // move database references onto dataset sequence datasetSequence.setDBRef(getDBRef()); setDBRef(null); - datasetSequence.setPDBId(getPDBId()); + datasetSequence.setPDBId(getAllPDBEntries()); setPDBId(null); datasetSequence.updatePDBIds(); if (annotation != null) @@ -1018,7 +1063,7 @@ 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); } } @@ -1051,11 +1096,7 @@ 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) @@ -1088,6 +1129,7 @@ public class Sequence implements SequenceI return anns; } + @Override public boolean updatePDBIds() { if (datasetSequence != null) @@ -1141,13 +1183,7 @@ 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) @@ -1168,8 +1204,7 @@ public class Sequence 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++) @@ -1181,9 +1216,9 @@ public class Sequence implements SequenceI } // transfer PDB entries - if (entry.getPDBId() != null) + if (entry.getAllPDBEntries() != null) { - Enumeration e = entry.getPDBId().elements(); + Enumeration e = entry.getAllPDBEntries().elements(); while (e.hasMoreElements()) { PDBEntry pdb = (PDBEntry) e.nextElement(); @@ -1243,20 +1278,15 @@ 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)) { @@ -1267,4 +1297,28 @@ public class Sequence implements SequenceI return result; } + public String toString() + { + return getDisplayId(false); + } + + @Override + public PDBEntry getPDBEntry(String pdbIdStr) + { + if (getDatasetSequence() == null + || getDatasetSequence().getAllPDBEntries() == null) + { + return null; + } + List entries = getDatasetSequence().getAllPDBEntries(); + for (PDBEntry entry : entries) + { + if (entry.getId().equalsIgnoreCase(pdbIdStr)) + { + return entry; + } + } + return null; + } + }