X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=b0969b5cdf686aa08a809435e17a65707d2a1bd9;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=34c1cd917f6f0fb252de743de48435710db7bfae;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 34c1cd9..b0969b5 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,488 +1,1175 @@ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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 -* 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. -* -* 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 -*/ -package jalview.datamodel; - -import MCview.*; - -import jalview.analysis.*; - -import java.awt.*; - -import java.util.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class Sequence implements SequenceI -{ - protected String name; - protected String sequence; - protected String description; - protected int start; - protected int end; - protected String displayId; - protected Color color = Color.white; - String pdbId; - - /** DOCUMENT ME!! */ - public Vector sequenceFeatures = new Vector(); - - /** - * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - */ - public Sequence(String name, String sequence, int start, int end) - { - this.name = name; - this.sequence = sequence; - this.start = start; - this.end = end; - - setDisplayId(); - } - - /** - * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - */ - public Sequence(String name, String sequence) - { - this(name, sequence, 1, sequence.length()); - } - - /** - * Creates a new Sequence object. - * - * @param seq DOCUMENT ME! - */ - public Sequence(SequenceI seq) - { - this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); - } - - /** - * DOCUMENT ME! - * - * @param v DOCUMENT ME! - */ - public void setSequenceFeatures(Vector v) - { - sequenceFeatures = v; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Vector getSequenceFeatures() - { - return sequenceFeatures; - } - - /** - * DOCUMENT ME! - * - * @param id DOCUMENT ME! - */ - public void setPDBId(String id) - { - pdbId = id; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getPDBId() - { - return pdbId; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getDisplayId() - { - return displayId; - } - - /** - * DOCUMENT ME! - */ - public void setDisplayId() - { - displayId = name + "/" + start + "-" + end; - } - - /** - * DOCUMENT ME! - * - * @param name DOCUMENT ME! - */ - public void setName(String name) - { - this.name = name; - setDisplayId(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getName() - { - return this.name; - } - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - */ - public void setStart(int start) - { - this.start = start; - setDisplayId(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getStart() - { - return this.start; - } - - /** - * DOCUMENT ME! - * - * @param end DOCUMENT ME! - */ - public void setEnd(int end) - { - this.end = end; - setDisplayId(); - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getEnd() - { - return this.end; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int getLength() - { - return this.sequence.length(); - } - - /** - * DOCUMENT ME! - * - * @param seq DOCUMENT ME! - */ - public void setSequence(String seq) - { - this.sequence = seq; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence() - { - return this.sequence; - } - - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence(int start, int end) - { - // JBPNote - left to user to pad the result here (TODO:Decide on this policy) - if (start >= sequence.length()) - { - return ""; - } - - if (end >= sequence.length()) - { - end = sequence.length(); - } - - return this.sequence.substring(start, end); - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public char getCharAt(int i) - { - if (i < sequence.length()) - { - return sequence.charAt(i); - } - else - { - return ' '; - } - } - - /** - * DOCUMENT ME! - * - * @param desc DOCUMENT ME! - */ - public void setDescription(String desc) - { - this.description = desc; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getDescription() - { - return this.description; - } - - /** - * DOCUMENT ME! - * - * @param pos DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int findIndex(int pos) - { - // returns the alignment position for a residue - int j = start; - int i = 0; - - while ((i < sequence.length()) && (j <= end) && (j <= pos)) - { - char c = sequence.charAt(i); - - if (!jalview.util.Comparison.isGap((c))) - { - j++; - } - - i++; - } - - if ((j == end) && (j < pos)) - { - return end + 1; - } - else - { - return i; - } - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int findPosition(int i) - { - // Returns the sequence position for an alignment position - int j = 0; - int pos = start; - - while ((j < i) && (j < sequence.length())) - { - char c = sequence.charAt(j); - - if (!jalview.util.Comparison.isGap((c))) - { - pos++; - } - - j++; - } - - return pos; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public int[] gapMap() - { - // Returns an int array giving the position of each residue in the sequence in the alignment - String seq = jalview.analysis.AlignSeq.extractGaps("-. ", sequence); - int[] map = new int[seq.length()]; - int j = 0; - int p = 0; - - while (j < sequence.length()) - { - if (!jalview.util.Comparison.isGap(sequence.charAt(j))) - { - map[p++] = j; - } - - j++; - } - - return map; - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - public void deleteCharAt(int i) - { - if (i >= sequence.length()) - { - return; - } - - sequence = sequence.substring(0, i) + sequence.substring(i + 1); - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param j DOCUMENT ME! - */ - public void deleteChars(int i, int j) - { - if (i >= sequence.length()) - { - return; - } - - if (j >= sequence.length()) - { - sequence = sequence.substring(0, i); - } - else - { - sequence = sequence.substring(0, i) + sequence.substring(j); - } - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param c DOCUMENT ME! - */ - public void insertCharAt(int i, char c) - { - insertCharAt(i, c, true); - } - - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param c DOCUMENT ME! - * @param chop DOCUMENT ME! - */ - public void insertCharAt(int i, char c, boolean chop) - { - String tmp = new String(sequence); - - if (i < sequence.length()) - { - sequence = tmp.substring(0, i) + String.valueOf(c) + - tmp.substring(i); - } - else - { - // JBPNote : padding char at end of sequence. We'll not get away with this when we insert residues, I bet! - char[] ch = new char[(1 + i) - sequence.length()]; - - for (int j = 0, k = ch.length; j < k; j++) - ch[j] = c; - - sequence = tmp + String.valueOf(ch); - } - } - - /** - * DOCUMENT ME! - * - * @param c DOCUMENT ME! - */ - public void setColor(Color c) - { - this.color = c; - } - - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public Color getColor() - { - return color; - } -} +/* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * 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. + * + * 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 Jalview. If not, see . + */ +package jalview.datamodel; + +import java.util.*; + +import jalview.analysis.*; + +/** + * + * Implements the SequenceI interface for a char[] based sequence object. + * + * @author $author$ + * @version $Revision$ + */ +public class Sequence implements SequenceI +{ + SequenceI datasetSequence; + + String name; + + private char[] sequence; + + String description; + + int start; + + int end; + + Vector pdbIds; + + String vamsasId; + + DBRefEntry[] dbrefs; + + /** + * This annotation is displayed below the alignment but the positions are tied + * to the residues of this sequence + */ + Vector annotation; + + /** array of seuqence features - may not be null for a valid sequence object */ + public SequenceFeature[] sequenceFeatures; + + /** + * Creates a new Sequence object. + * + * @param name + * display name string + * @param sequence + * string to form a possibly gapped sequence out of + * @param start + * first position of non-gap residue in the sequence + * @param end + * 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(); + } + + public Sequence(String name, char[] sequence, int start, int end) + { + this.name = name; + this.sequence = sequence; + this.start = start; + this.end = end; + parseId(); + checkValidRange(); + } + + com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex( + "[/][0-9]{1,}[-][0-9]{1,}$"); + + com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$"); + + void parseId() + { + if (name == null) + { + System.err + .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); + name = ""; + } + // Does sequence have the /start-end signiature? + if (limitrx.search(name)) + { + name = limitrx.left(); + endrx.search(limitrx.stringMatched()); + setStart(Integer.parseInt(limitrx.stringMatched().substring(1, + endrx.matchedFrom() - 1))); + setEnd(Integer.parseInt(endrx.stringMatched())); + } + } + + void checkValidRange() + { + // 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++) + { + if (!jalview.util.Comparison.isGap(sequence[j])) + { + endRes++; + } + } + if (endRes > 0) + { + endRes += start - 1; + } + + if (end= sequence.length) + { + return new char[0]; + } + + if (end >= sequence.length) + { + end = sequence.length; + } + + char[] reply = new char[end - start]; + System.arraycopy(sequence, start, reply, 0, end - start); + + return reply; + } + + /** + * make a new Sequence object from start to end (including gaps) over this + * seqeunce + * + * @param start + * int + * @param end + * int + * @return SequenceI + */ + public SequenceI getSubSequence(int start, int end) + { + if (start < 0) + { + start = 0; + } + char[] seq = getSequence(start, end); + if (seq.length == 0) + { + return null; + } + int nstart = findPosition(start); + int nend = findPosition(end) - 1; + // JBPNote - this is an incomplete copy. + SequenceI nseq = new Sequence(this.getName(), seq, nstart, nend); + nseq.setDescription(description); + if (datasetSequence != null) + { + nseq.setDatasetSequence(datasetSequence); + } + else + { + nseq.setDatasetSequence(this); + } + return nseq; + } + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public char getCharAt(int i) + { + if (i < sequence.length) + { + return sequence[i]; + } + else + { + return ' '; + } + } + + /** + * DOCUMENT ME! + * + * @param desc + * DOCUMENT ME! + */ + public void setDescription(String desc) + { + this.description = desc; + } + + /** + * DOCUMENT ME! + * + * @return DOCUMENT ME! + */ + public String getDescription() + { + return this.description; + } + + /** + * Return the alignment position for a sequence position + * + * @param pos + * lying from start to end + * + * @return aligned position of residue pos + */ + 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])) + { + j++; + } + + i++; + } + + if ((j == end) && (j < pos)) + { + return end + 1; + } + else + { + return i; + } + } + + /** + * 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 + */ + public int findPosition(int i) + { + int j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < i) && (j < seqlen)) + { + if (!jalview.util.Comparison.isGap(sequence[j])) + { + pos++; + } + + j++; + } + + return pos; + } + + /** + * Returns an int array where indices correspond to each residue in the + * sequence and the element value gives its position in the alignment + * + * @return int[SequenceI.getEnd()-SequenceI.getStart()+1] or null if no + * residues in SequenceI object + */ + public int[] gapMap() + { + String seq = jalview.analysis.AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, new String(sequence)); + int[] map = new int[seq.length()]; + int j = 0; + int p = 0; + + while (j < sequence.length) + { + if (!jalview.util.Comparison.isGap(sequence[j])) + { + map[p++] = j; + } + + j++; + } + + return map; + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.SequenceI#findPositionMap() + */ + public int[] findPositionMap() + { + int map[] = new int[sequence.length]; + int j = 0; + int pos = start; + int seqlen = sequence.length; + while ((j < seqlen)) + { + map[j] = pos; + if (!jalview.util.Comparison.isGap(sequence[j])) + { + pos++; + } + + j++; + } + return map; + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.SequenceI#deleteChars(int, int) + */ + public void deleteChars(int i, int j) + { + int newstart = start, newend = end; + if (i >= sequence.length) + { + return; + } + + char[] tmp; + + if (j >= sequence.length) + { + tmp = new char[i]; + System.arraycopy(sequence, 0, tmp, 0, i); + } + else + { + tmp = new char[sequence.length - j + i]; + System.arraycopy(sequence, 0, tmp, 0, i); + System.arraycopy(sequence, j, tmp, i, sequence.length - j); + } + boolean createNewDs = false; + for (int s = i; s < j; s++) + { + if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23) + { + if (createNewDs) + { + newend--; + } + else + { + int sindex = findIndex(start) - 1; + if (sindex == s) + { + // delete characters including start of sequence + newstart = findPosition(j); + break; // don't need to search for any more residue characters. + } + else + { + // delete characters after start. + int eindex = findIndex(end) - 1; + if (eindex < j) + { + // delete characters at end of sequence + newend = findPosition(i - 1); + break; // don't need to search for any more residue characters. + } + else + { + createNewDs = true; + newend--; // decrease end position by one for the deleted residue + // and search further + } + } + } + } + } + // deletion occured in the middle of the sequence + if (createNewDs && this.datasetSequence != null) + { + // construct a new sequence + Sequence ds = new Sequence(datasetSequence); + // TODO: remove any non-inheritable properties ? + // TODO: create a sequence mapping (since there is a relation here ?) + ds.deleteChars(i, j); + datasetSequence = ds; + } + start = newstart; + end = newend; + sequence = tmp; + } + + /** + * DOCUMENT ME! + * + * @param i + * DOCUMENT ME! + * @param c + * DOCUMENT ME! + * @param chop + * DOCUMENT ME! + */ + public void insertCharAt(int i, int length, char c) + { + char[] tmp = new char[sequence.length + length]; + + if (i >= sequence.length) + { + System.arraycopy(sequence, 0, tmp, 0, sequence.length); + i = sequence.length; + } + else + { + System.arraycopy(sequence, 0, tmp, 0, i); + } + + int index = i; + while (length > 0) + { + tmp[index++] = c; + length--; + } + + if (i < sequence.length) + { + System.arraycopy(sequence, i, tmp, index, sequence.length - i); + } + + sequence = tmp; + } + + public void insertCharAt(int i, char c) + { + insertCharAt(i, 1, c); + } + + public String getVamsasId() + { + return vamsasId; + } + + public void setVamsasId(String id) + { + vamsasId = id; + } + + public void setDBRef(DBRefEntry[] dbref) + { + dbrefs = dbref; + } + + public DBRefEntry[] getDBRef() + { + if (dbrefs == null && datasetSequence != null + && this != datasetSequence) + { + return datasetSequence.getDBRef(); + } + return dbrefs; + } + + public void addDBRef(DBRefEntry entry) + { + if (dbrefs == null) + { + dbrefs = new DBRefEntry[0]; + } + + int i, iSize = dbrefs.length; + + for (i = 0; i < iSize; i++) + { + if (dbrefs[i].equalRef(entry)) + { + if (entry.getMap() != null) + { + if (dbrefs[i].getMap() == null) + { + // overwrite with 'superior' entry that contains a mapping. + dbrefs[i] = entry; + } + } + return; + } + } + + DBRefEntry[] temp = new DBRefEntry[iSize + 1]; + System.arraycopy(dbrefs, 0, temp, 0, iSize); + temp[temp.length - 1] = entry; + + dbrefs = temp; + } + + public void setDatasetSequence(SequenceI seq) + { + datasetSequence = seq; + } + + public SequenceI getDatasetSequence() + { + return datasetSequence; + } + + 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 ret; + } + + public void addAlignmentAnnotation(AlignmentAnnotation annotation) + { + if (this.annotation == null) + { + this.annotation = new Vector(); + } + + this.annotation.addElement(annotation); + annotation.setSequenceRef(this); + } + + public void removeAlignmentAnnotation(AlignmentAnnotation annotation) + { + if (this.annotation != null) + { + this.annotation.removeElement(annotation); + if (this.annotation.size() == 0) + this.annotation = null; + } + } + + /** + * test if this is a valid candidate for another sequence's dataset sequence. + * + */ + private boolean isValidDatasetSequence() + { + if (datasetSequence != null) + { + return false; + } + for (int i = 0; i < sequence.length; i++) + { + if (jalview.util.Comparison.isGap(sequence[i])) + { + return false; + } + } + return true; + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.SequenceI#deriveSequence() + */ + public SequenceI deriveSequence() + { + SequenceI seq = new Sequence(this); + if (datasetSequence != null) + { + // duplicate current sequence with same dataset + seq.setDatasetSequence(datasetSequence); + } + else + { + if (isValidDatasetSequence()) + { + // Use this as dataset sequence + seq.setDatasetSequence(this); + } + 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. + } + } + return seq; + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.SequenceI#createDatasetSequence() + */ + public SequenceI createDatasetSequence() + { + if (datasetSequence == null) + { + datasetSequence = 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.updatePDBIds(); + } + return datasetSequence; + } + + /* + * (non-Javadoc) + * + * @see + * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] + * annotations) + */ + public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) + { + if (annotation != null) + { + annotation.removeAllElements(); + } + if (annotations != null) + { + 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) + */ + public AlignmentAnnotation[] getAnnotation(String label) + { + if (annotation == null || annotation.size() == 0) + { + return null; + } + + Vector subset = new Vector(); + Enumeration e = annotation.elements(); + while (e.hasMoreElements()) + { + AlignmentAnnotation ann = (AlignmentAnnotation) e.nextElement(); + if (ann.label != null && ann.label.equals(label)) + { + subset.addElement(ann); + } + } + if (subset.size() == 0) + { + return null; + } + AlignmentAnnotation[] anns = new AlignmentAnnotation[subset.size()]; + int i = 0; + e = subset.elements(); + while (e.hasMoreElements()) + { + anns[i++] = (AlignmentAnnotation) e.nextElement(); + } + subset.removeAllElements(); + return anns; + } + + public boolean updatePDBIds() + { + if (datasetSequence != null) + { + // TODO: could merge DBRefs + return datasetSequence.updatePDBIds(); + } + if (dbrefs == null || dbrefs.length == 0) + { + return false; + } + Vector newpdb = new Vector(); + for (int i = 0; i < dbrefs.length; i++) + { + if (DBRefSource.PDB.equals(dbrefs[i].getSource())) + { + PDBEntry pdbe = new PDBEntry(); + pdbe.setId(dbrefs[i].getAccessionId()); + if (pdbIds == null || pdbIds.size() == 0) + { + newpdb.addElement(pdbe); + } + else + { + Enumeration en = pdbIds.elements(); + boolean matched = false; + while (!matched && en.hasMoreElements()) + { + PDBEntry anentry = (PDBEntry) en.nextElement(); + if (anentry.getId().equals(pdbe.getId())) + { + matched = true; + } + } + if (!matched) + { + newpdb.addElement(pdbe); + } + } + } + } + if (newpdb.size() > 0) + { + Enumeration en = newpdb.elements(); + while (en.hasMoreElements()) + { + addPDBId((PDBEntry) en.nextElement()); + } + return true; + } + return false; + } + + /* + * (non-Javadoc) + * + * @see + * jalview.datamodel.SequenceI#transferAnnotation(jalview.datamodel.SequenceI, + * jalview.datamodel.Mapping) + */ + public void transferAnnotation(SequenceI entry, Mapping mp) + { + if (datasetSequence != null) + { + datasetSequence.transferAnnotation(entry, mp); + return; + } + if (entry.getDatasetSequence() != null) + { + transferAnnotation(entry.getDatasetSequence(), mp); + return; + } + // transfer any new features from entry onto sequence + if (entry.getSequenceFeatures() != null) + { + + SequenceFeature[] sfs = entry.getSequenceFeatures(); + for (int si = 0; si < sfs.length; si++) + { + SequenceFeature sf[] = (mp != null) ? mp.locateFeature(sfs[si]) + : new SequenceFeature[] + { new SequenceFeature(sfs[si]) }; + if (sf != null && sf.length > 0) + { + for (int sfi = 0; sfi < sf.length; sfi++) + { + addSequenceFeature(sf[sfi]); + } + } + } + } + + // transfer PDB entries + if (entry.getPDBId() != null) + { + Enumeration e = entry.getPDBId().elements(); + while (e.hasMoreElements()) + { + PDBEntry pdb = (PDBEntry) e.nextElement(); + addPDBId(pdb); + } + } + // transfer database references + DBRefEntry[] entryRefs = entry.getDBRef(); + if (entryRefs != null) + { + for (int r = 0; r < entryRefs.length; r++) + { + DBRefEntry newref = new DBRefEntry(entryRefs[r]); + if (newref.getMap() != null && mp != null) + { + // remap ref using our local mapping + } + // we also assume all version string setting is done by dbSourceProxy + /* + * if (!newref.getSource().equalsIgnoreCase(dbSource)) { + * newref.setSource(dbSource); } + */ + addDBRef(newref); + } + } + } + +}