X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=88f430803a14178d7bec70baedef7b9647d8e813;hb=134291d04042b3d7252598a9f73753f40da08a18;hp=722edf21259bf2076967cd4906072f78d57fd7e6;hpb=45d4eb5f2d3772ac51e2512d49fb0a3a958f2260;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 722edf2..88f4308 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,26 +1,36 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.datamodel; -import java.util.*; +import jalview.analysis.AlignSeq; +import jalview.api.DBRefEntryI; +import jalview.util.StringUtils; + +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Enumeration; +import java.util.List; +import java.util.Vector; -import jalview.analysis.*; +import fr.orsay.lri.varna.models.rna.RNA; /** * @@ -29,7 +39,7 @@ import jalview.analysis.*; * @author $author$ * @version $Revision$ */ -public class Sequence implements SequenceI +public class Sequence extends ASequence implements SequenceI { SequenceI datasetSequence; @@ -43,50 +53,71 @@ public class Sequence implements SequenceI int end; - Vector pdbIds; + Vector pdbIds; String vamsasId; + DBRefEntryI sourceDBRef; + DBRefEntry[] dbrefs; + RNA rna; + /** * This annotation is displayed below the alignment but the positions are tied * to the residues of this sequence + * + * TODO: change to List<> + */ + Vector annotation; + + /** + * The index of the sequence in a MSA */ - Vector annotation; + int index = -1; - /** array of seuqence features - may not be null for a valid sequence object */ + /** array of sequence features - may not be null for a valid sequence object */ public SequenceFeature[] sequenceFeatures; /** * Creates a new Sequence object. * * @param name - * display name string + * display name string * @param sequence - * string to form a possibly gapped sequence out of + * string to form a possibly gapped sequence out of * @param start - * first position of non-gap residue in the sequence + * first position of non-gap residue in the sequence * @param end - * last position of ungapped residues (nearly always only used - * for display purposes) + * last position of ungapped residues (nearly always only used for + * display purposes) */ 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(); } @@ -104,7 +135,7 @@ 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(); @@ -117,7 +148,8 @@ public class Sequence implements SequenceI void checkValidRange() { - if (end < 1) + // Note: JAL-774 : + // http://issues.jalview.org/browse/JAL-774?focusedCommentId=11239&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-11239 { int endRes = 0; for (int j = 0; j < sequence.length; j++) @@ -132,7 +164,10 @@ public class Sequence implements SequenceI endRes += start - 1; } - this.end = endRes; + if (end < endRes) + { + end = endRes; + } } } @@ -141,9 +176,9 @@ public class Sequence implements SequenceI * Creates a new Sequence object. * * @param name - * DOCUMENT ME! + * DOCUMENT ME! * @param sequence - * DOCUMENT ME! + * DOCUMENT ME! */ public Sequence(String name, String sequence) { @@ -151,12 +186,13 @@ public class Sequence implements SequenceI } /** - * Creates a new Sequence object with new features, DBRefEntries, - * AlignmentAnnotations, and PDBIds but inherits any existing dataset sequence - * reference. + * Creates a new Sequence object with new AlignmentAnnotations but inherits + * any existing dataset sequence reference. If non exists, everything is + * copied. * * @param seq - * DOCUMENT ME! + * if seq is a dataset sequence, behaves like a plain old copy + * constructor */ public Sequence(SequenceI seq) { @@ -169,31 +205,59 @@ public class Sequence implements SequenceI * annotation that is present in the given annotation array. * * @param seq - * the sequence to be copied + * the sequence to be copied * @param alAnnotation - * an array of annotation including some associated with seq + * an array of annotation including some associated with seq */ public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation) { - this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); + initSeqFrom(seq, alAnnotation); + + } + + /** + * does the heavy lifting when cloning a dataset sequence, or coping data from + * dataset to a new derived sequence. + * + * @param seq + * - source of attributes. + * @param alAnnotation + * - alignment annotation present on seq that should be copied onto + * this sequence + */ + protected void initSeqFrom(SequenceI seq, + AlignmentAnnotation[] alAnnotation) + { + { + char[] oseq = seq.getSequence(); + initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length), + seq.getStart(), + seq.getEnd()); + } description = seq.getDescription(); - if (seq.getSequenceFeatures() != null) + sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry( + seq.getSourceDBRef()); + if (seq != datasetSequence) { - SequenceFeature[] sf = seq.getSequenceFeatures(); - for (int i = 0; i < sf.length; i++) - { - addSequenceFeature(new SequenceFeature(sf[i])); - } + setDatasetSequence(seq.getDatasetSequence()); } - if (seq.getDBRef() != null) + if (datasetSequence == null && seq.getDBRefs() != null) { - DBRefEntry[] dbr = seq.getDBRef(); + // only copy DBRefs and seqfeatures if we really are a dataset sequence + DBRefEntry[] dbr = seq.getDBRefs(); for (int i = 0; i < dbr.length; i++) { addDBRef(new DBRefEntry(dbr[i])); } + if (seq.getSequenceFeatures() != null) + { + SequenceFeature[] sf = seq.getSequenceFeatures(); + for (int i = 0; i < sf.length; i++) + { + addSequenceFeature(new SequenceFeature(sf[i])); + } + } } - setDatasetSequence(seq.getDatasetSequence()); if (seq.getAnnotation() != null) { AlignmentAnnotation[] sqann = seq.getAnnotation(); @@ -219,30 +283,46 @@ public class Sequence implements SequenceI } } } - if (seq.getPDBId() != null) + if (seq.getAllPDBEntries() != null) { - Vector ids = seq.getPDBId(); - Enumeration e = ids.elements(); - while (e.hasMoreElements()) + Vector ids = seq.getAllPDBEntries(); + for (PDBEntry pdb : ids) { - this.addPDBId(new PDBEntry((PDBEntry) e.nextElement())); + this.addPDBId(new PDBEntry(pdb)); } } } - /** - * DOCUMENT ME! - * - * @param v - * DOCUMENT ME! - */ + + @Override public void setSequenceFeatures(SequenceFeature[] features) { - sequenceFeatures = features; + if (datasetSequence == null) + { + sequenceFeatures = features; + } + else + { + if (datasetSequence.getSequenceFeatures() != features + && datasetSequence.getSequenceFeatures() != null + && datasetSequence.getSequenceFeatures().length > 0) + { + new Exception( + "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment") + .printStackTrace(); + } + datasetSequence.setSequenceFeatures(features); + } } + @Override public synchronized void addSequenceFeature(SequenceFeature sf) { + if (sequenceFeatures==null && datasetSequence != null) + { + datasetSequence.addSequenceFeature(sf); + return; + } if (sequenceFeatures == null) { sequenceFeatures = new SequenceFeature[0]; @@ -263,10 +343,14 @@ public class Sequence implements SequenceI sequenceFeatures = temp; } + @Override public void deleteFeature(SequenceFeature sf) { if (sequenceFeatures == null) { + if (datasetSequence!=null) { + datasetSequence.deleteFeature(sf); + } return; } @@ -305,34 +389,62 @@ 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 */ + @Override 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; } + @Override 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! + * DOCUMENT ME! */ - public void setPDBId(Vector id) + @Override + public void setPDBId(Vector id) { pdbIds = id; } @@ -342,9 +454,10 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ - public Vector getPDBId() + @Override + public Vector getAllPDBEntries() { - return pdbIds; + return pdbIds == null ? new Vector() : pdbIds; } /** @@ -352,6 +465,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDisplayId(boolean jvsuffix) { StringBuffer result = new StringBuffer(name); @@ -367,8 +481,9 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void setName(String name) { this.name = name; @@ -380,6 +495,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getName() { return this.name; @@ -389,8 +505,9 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param start - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void setStart(int start) { this.start = start; @@ -401,6 +518,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getStart() { return this.start; @@ -410,8 +528,9 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param end - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void setEnd(int end) { this.end = end; @@ -422,6 +541,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getEnd() { return this.end; @@ -432,6 +552,7 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public int getLength() { return this.sequence.length; @@ -441,24 +562,28 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void setSequence(String seq) { this.sequence = seq.toCharArray(); checkValidRange(); } + @Override public String getSequenceAsString() { return new String(sequence); } + @Override public String getSequenceAsString(int start, int end) { return new String(getSequence(start, end)); } + @Override public char[] getSequence() { return sequence; @@ -469,10 +594,13 @@ public class Sequence implements SequenceI * * @see jalview.datamodel.SequenceI#getSequence(int, int) */ + @Override public char[] getSequence(int start, int end) { if (start < 0) + { start = 0; + } // JBPNote - left to user to pad the result here (TODO:Decide on this // policy) if (start >= sequence.length) @@ -491,16 +619,7 @@ 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) @@ -529,16 +648,15 @@ public class Sequence implements SequenceI } /** - * DOCUMENT ME! - * - * @param i - * DOCUMENT ME! + * Returns the character of the aligned sequence at the given position (base + * zero), or space if the position is not within the sequence's bounds * - * @return DOCUMENT ME! + * @return */ + @Override public char getCharAt(int i) { - if (i < sequence.length) + if (i >= 0 && i < sequence.length) { return sequence[i]; } @@ -552,8 +670,9 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param desc - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void setDescription(String desc) { this.description = desc; @@ -564,25 +683,24 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ + @Override public String getDescription() { return this.description; } - /** - * Return the alignment position for a sequence position - * - * @param pos - * lying from start to end + /* + * (non-Javadoc) * - * @return aligned position of residue pos + * @see jalview.datamodel.SequenceI#findIndex(int) */ + @Override public int findIndex(int pos) { // returns the alignment position for a residue int j = start; int i = 0; - + // Rely on end being at least as long as the length of the sequence. while ((i < sequence.length) && (j <= end) && (j <= pos)) { if (!jalview.util.Comparison.isGap(sequence[i])) @@ -603,14 +721,7 @@ 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; @@ -636,6 +747,7 @@ public class Sequence implements SequenceI * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no * residues in SequenceI object */ + @Override public int[] gapMap() { String seq = jalview.analysis.AlignSeq.extractGaps( @@ -657,33 +769,75 @@ 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 int[] findPositionMap() { - int newstart = start, newend = end; - if (i >= sequence.length) + int map[] = new int[sequence.length]; + int j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) { - return; - } + map[j] = pos; + if (!jalview.util.Comparison.isGap(sequence[j])) + { + pos++; + } - char[] tmp; + j++; + } + return map; + } - if (j >= sequence.length) + @Override + public List getInsertions() + { + ArrayList map = new ArrayList(); + int lastj = -1, j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) { - tmp = new char[i]; - System.arraycopy(sequence, 0, tmp, 0, i); + 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++; } - else + if (lastj != -1) { - tmp = new char[sequence.length - j + i]; - System.arraycopy(sequence, 0, tmp, 0, i); - System.arraycopy(sequence, j, tmp, i, sequence.length - j); + map.add(new int[] { lastj, j - 1 }); + lastj = -1; + } + return map; + } + + @Override + public void deleteChars(int i, int j) + { + int newstart = start, newend = end; + if (i >= sequence.length || i < 0) + { + return; } + + char[] tmp = StringUtils.deleteChars(sequence, i, j); boolean createNewDs = false; + // 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) @@ -694,7 +848,11 @@ 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 @@ -704,7 +862,11 @@ 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 @@ -715,7 +877,7 @@ public class Sequence implements SequenceI { createNewDs = true; newend--; // decrease end position by one for the deleted residue - // and search further + // and search further } } } @@ -736,16 +898,7 @@ 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]; @@ -775,107 +928,124 @@ 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; } - public void setDBRef(DBRefEntry[] dbref) + @Override + public void setDBRefs(DBRefEntry[] dbref) { dbrefs = dbref; } - public DBRefEntry[] getDBRef() + @Override + public DBRefEntry[] getDBRefs() { + if (dbrefs == null && datasetSequence != null + && this != datasetSequence) + { + return datasetSequence.getDBRefs(); + } return dbrefs; } + @Override public void addDBRef(DBRefEntry entry) { + // TODO add to dataset sequence instead if there is one? if (dbrefs == null) { dbrefs = new DBRefEntry[0]; } - int i, iSize = dbrefs.length; - - for (i = 0; i < iSize; i++) + for (DBRefEntryI dbr : dbrefs) { - if (dbrefs[i].equalRef(entry)) + if (dbr.updateFrom(entry)) { - if (entry.getMap() != null) - { - if (dbrefs[i].getMap() == null) - { - // overwrite with 'superior' entry that contains a mapping. - dbrefs[i] = entry; - } - } + /* + * found a dbref that either matched, or could be + * updated from, the new entry - no need to add it + */ return; } } - DBRefEntry[] temp = new DBRefEntry[iSize + 1]; - System.arraycopy(dbrefs, 0, temp, 0, iSize); + /* + * extend the array to make room for one more + */ + // TODO use an ArrayList instead + int j = dbrefs.length; + DBRefEntry[] temp = new DBRefEntry[j + 1]; + System.arraycopy(dbrefs, 0, temp, 0, j); temp[temp.length - 1] = entry; dbrefs = temp; } + @Override public void setDatasetSequence(SequenceI seq) { + // TODO check for circular reference before setting? 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] = (AlignmentAnnotation) 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)) + { + this.annotation.addElement(annotation); } - - this.annotation.addElement(annotation); annotation.setSequenceRef(this); } + @Override public void removeAlignmentAnnotation(AlignmentAnnotation annotation) { if (this.annotation != null) { this.annotation.removeElement(annotation); if (this.annotation.size() == 0) + { this.annotation = null; + } } } @@ -899,61 +1069,88 @@ public class Sequence implements SequenceI return true; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deriveSequence() - */ + @Override public SequenceI deriveSequence() { - SequenceI seq = new Sequence(this); - if (datasetSequence != null) - { - // duplicate current sequence with same dataset - seq.setDatasetSequence(datasetSequence); - } - else + Sequence seq=null; + if (datasetSequence == null) { if (isValidDatasetSequence()) { // Use this as dataset sequence + seq = new Sequence(getName(), "", 1, -1); seq.setDatasetSequence(this); + seq.initSeqFrom(this, getAnnotation()); + return seq; } else { // Create a new, valid dataset sequence - SequenceI ds = seq; - ds.setSequence(AlignSeq.extractGaps( - jalview.util.Comparison.GapChars, new String(sequence))); - setDatasetSequence(ds); - ds.setSequenceFeatures(getSequenceFeatures()); - seq = this; // and return this sequence as the derived sequence. + createDatasetSequence(); } } - return seq; + return new Sequence(this); } + private boolean _isNa; + + private long _seqhash = 0; + + @Override + public boolean isProtein() + { + if (datasetSequence != null) + { + return datasetSequence.isProtein(); + } + if (_seqhash != sequence.hashCode()) + { + _seqhash = sequence.hashCode(); + _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this }); + } + return !_isNa; + }; + /* * (non-Javadoc) * * @see jalview.datamodel.SequenceI#createDatasetSequence() */ + @Override public SequenceI createDatasetSequence() { if (datasetSequence == null) { - datasetSequence = new Sequence(getName(), AlignSeq.extractGaps( + Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps( jalview.util.Comparison.GapChars, getSequenceAsString()), getStart(), getEnd()); - datasetSequence.setSequenceFeatures(getSequenceFeatures()); - datasetSequence.setDescription(getDescription()); - setSequenceFeatures(null); - // move database references onto dataset sequence - datasetSequence.setDBRef(getDBRef()); - setDBRef(null); - datasetSequence.setPDBId(getPDBId()); - setPDBId(null); + + datasetSequence = dsseq; + + dsseq.setDescription(description); + // move features and database references onto dataset sequence + dsseq.sequenceFeatures = sequenceFeatures; + sequenceFeatures=null; + dsseq.dbrefs = dbrefs; + dbrefs=null; + // TODO: search and replace any references to this sequence with + // references to the dataset sequence in Mappings on dbref + dsseq.pdbIds = pdbIds; + pdbIds = null; datasetSequence.updatePDBIds(); + if (annotation != null) + { + // annotation is cloned rather than moved, to preserve what's currently + // on the alignment + for (AlignmentAnnotation aa : annotation) + { + AlignmentAnnotation _aa = new AlignmentAnnotation(aa); + _aa.sequenceRef = datasetSequence; + _aa.adjustForAlignment(); // uses annotation's own record of + // sequence-column mapping + datasetSequence.addAlignmentAnnotation(_aa); + } + } } return datasetSequence; } @@ -961,9 +1158,11 @@ public class Sequence implements SequenceI /* * (non-Javadoc) * - * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] - * annotations) + * @see + * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] + * annotations) */ + @Override public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { if (annotation != null) @@ -975,16 +1174,14 @@ public class Sequence implements SequenceI for (int i = 0; i < annotations.length; i++) { if (annotations[i] != null) + { addAlignmentAnnotation(annotations[i]); + } } } } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#getAnnotation(java.lang.String) - */ + @Override public AlignmentAnnotation[] getAnnotation(String label) { if (annotation == null || annotation.size() == 0) @@ -1017,6 +1214,7 @@ public class Sequence implements SequenceI return anns; } + @Override public boolean updatePDBIds() { if (datasetSequence != null) @@ -1070,12 +1268,7 @@ 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) @@ -1096,8 +1289,7 @@ 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++) @@ -1109,9 +1301,9 @@ 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(); @@ -1119,7 +1311,7 @@ public class Sequence implements SequenceI } } // transfer database references - DBRefEntry[] entryRefs = entry.getDBRef(); + DBRefEntry[] entryRefs = entry.getDBRefs(); if (entryRefs != null) { for (int r = 0; r < entryRefs.length; r++) @@ -1139,4 +1331,96 @@ public class Sequence 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) + { + rna = r; + } + + @Override + public RNA getRNA() + { + return rna; + } + + @Override + public List getAlignmentAnnotations(String calcId, + String label) + { + List result = new ArrayList(); + if (this.annotation != null) + { + for (AlignmentAnnotation ann : annotation) + { + if (ann.calcId != null && ann.calcId.equals(calcId) + && ann.label != null && ann.label.equals(label)) + { + result.add(ann); + } + } + } + return result; + } + + @Override + 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; + } + + @Override + public void setSourceDBRef(DBRefEntryI dbRef) + { + this.sourceDBRef = dbRef; + } + + @Override + public DBRefEntryI getSourceDBRef() + { + return this.sourceDBRef; + } + }