X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=0128b9c8b66016653dcf72531da682381eca0aba;hb=d9c7868a610eff29a8eddb160b6dc78a94a72470;hp=7df3eaf5c7c1dd18cc0be284cab4cf8634bf9991;hpb=0ff5a953c6b319333779bc27c9bcae5814530f66;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 7df3eaf..21f7830 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,106 +1,162 @@ /* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2006 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 -*/ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 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. + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.datamodel; -import java.awt.*; +import jalview.analysis.AlignSeq; +import jalview.api.DBRefEntryI; +import jalview.util.Comparison; +import jalview.util.DBRefUtils; +import jalview.util.MapList; +import jalview.util.StringUtils; -import java.util.*; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Enumeration; +import java.util.List; +import java.util.Vector; +import fr.orsay.lri.varna.models.rna.RNA; /** - * DOCUMENT ME! - * + * + * Implements the SequenceI interface for a char[] based sequence object. + * * @author $author$ * @version $Revision$ */ -public class Sequence implements SequenceI +public class Sequence extends ASequence implements SequenceI { SequenceI datasetSequence; + String name; - private String sequence; + + private char[] sequence; + String description; + int start; + int end; - Vector pdbIds; + + 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; + RNA rna; - /** DOCUMENT ME!! */ - public SequenceFeature[] sequenceFeatures; + /** + * This annotation is displayed below the alignment but the positions are tied + * to the residues of this sequence + * + * TODO: change to List<> + */ + Vector annotation; - /** This array holds hidden sequences - * of which this sequence is the representitive member of a group + /** + * The index of the sequence in a MSA */ - SequenceGroup hiddenSequences; + int index = -1; + + /** array of sequence features - may not be null for a valid sequence object */ + public SequenceFeature[] sequenceFeatures; /** * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! + * + * @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; - this.start = start; - this.end = end; + initSeqAndName(name, sequence.toCharArray(), start, end); + } - parseId(); + public Sequence(String name, char[] sequence, int start, int 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(); } com.stevesoft.pat.Regex limitrx = new com.stevesoft.pat.Regex( - "[/][0-9]{1,}[-][0-9]{1,}$"); - com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex( - "[0-9]{1,}$"); + "[/][0-9]{1,}[-][0-9]{1,}$"); + + com.stevesoft.pat.Regex endrx = new com.stevesoft.pat.Regex("[0-9]{1,}$"); void parseId() { - // Does sequence have the /start-end signiature? + if (name == null) + { + System.err + .println("POSSIBLE IMPLEMENTATION ERROR: null sequence name passed to constructor."); + name = ""; + } + // Does sequence have the /start-end signature? if (limitrx.search(name)) { name = limitrx.left(); endrx.search(limitrx.stringMatched()); setStart(Integer.parseInt(limitrx.stringMatched().substring(1, - endrx.matchedFrom() - 1))); + endrx.matchedFrom() - 1))); setEnd(Integer.parseInt(endrx.stringMatched())); } } 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; - char ch; - for (int j = 0; j < sequence.length(); j++) + for (int j = 0; j < sequence.length; j++) { - ch = sequence.charAt(j); - if (!jalview.util.Comparison.isGap( (ch))) + if (!jalview.util.Comparison.isGap(sequence[j])) { endRes++; } @@ -110,16 +166,21 @@ public class Sequence implements SequenceI endRes += start - 1; } - this.end = endRes; + if (end < endRes) + { + end = endRes; + } } } /** * Creates a new Sequence object. - * - * @param name DOCUMENT ME! - * @param sequence DOCUMENT ME! + * + * @param name + * DOCUMENT ME! + * @param sequence + * DOCUMENT ME! */ public Sequence(String name, String sequence) { @@ -127,27 +188,139 @@ public class Sequence implements SequenceI } /** - * Creates a new Sequence object. - * - * @param seq DOCUMENT ME! + * Creates a new Sequence object with new AlignmentAnnotations but inherits + * any existing dataset sequence reference. If non exists, everything is + * copied. + * + * @param seq + * if seq is a dataset sequence, behaves like a plain old copy + * constructor */ public Sequence(SequenceI seq) { - this(seq.getName(), seq.getSequence(), seq.getStart(), seq.getEnd()); + this(seq, seq.getAnnotation()); } /** - * DOCUMENT ME! - * - * @param v DOCUMENT ME! + * Create a new sequence object with new features, DBRefEntries, and PDBIds + * but inherits any existing dataset sequence reference, and duplicate of any + * annotation that is present in the given annotation array. + * + * @param seq + * the sequence to be copied + * @param alAnnotation + * an array of annotation including some associated with seq */ + public Sequence(SequenceI seq, AlignmentAnnotation[] alAnnotation) + { + 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 != datasetSequence) + { + setDatasetSequence(seq.getDatasetSequence()); + } + if (datasetSequence == null && seq.getDBRefs() != null) + { + // 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])); + } + } + } + if (seq.getAnnotation() != null) + { + AlignmentAnnotation[] sqann = seq.getAnnotation(); + for (int i = 0; i < sqann.length; i++) + { + if (sqann[i] == null) + { + continue; + } + boolean found = (alAnnotation == null); + if (!found) + { + for (int apos = 0; !found && apos < alAnnotation.length; apos++) + { + found = (alAnnotation[apos] == sqann[i]); + } + } + if (found) + { + // only copy the given annotation + AlignmentAnnotation newann = new AlignmentAnnotation(sqann[i]); + addAlignmentAnnotation(newann); + } + } + } + if (seq.getAllPDBEntries() != null) + { + Vector ids = seq.getAllPDBEntries(); + for (PDBEntry pdb : ids) + { + this.addPDBId(new PDBEntry(pdb)); + } + } + } + + @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]; @@ -168,12 +341,19 @@ public class Sequence implements SequenceI sequenceFeatures = temp; } + @Override public void deleteFeature(SequenceFeature sf) { - if(sequenceFeatures==null) + if (sequenceFeatures == null) + { + if (datasetSequence != null) + { + datasetSequence.deleteFeature(sf); + } return; + } - int index=0; + int index = 0; for (index = 0; index < sequenceFeatures.length; index++) { if (sequenceFeatures[index].equals(sf)) @@ -182,73 +362,105 @@ public class Sequence implements SequenceI } } - - if(index==sequenceFeatures.length) + if (index == sequenceFeatures.length) + { return; + } int sfLength = sequenceFeatures.length; - if(sfLength<2) + if (sfLength < 2) { sequenceFeatures = null; } else { - SequenceFeature[] temp = new SequenceFeature[sfLength-1]; + SequenceFeature[] temp = new SequenceFeature[sfLength - 1]; System.arraycopy(sequenceFeatures, 0, temp, 0, index); - if(index(); + pdbIds.add(entry); + return true; + } + for (PDBEntry pdbe : pdbIds) + { + if (pdbe.updateFrom(entry)) + { + return false; + } + } pdbIds.addElement(entry); + return true; } /** * DOCUMENT ME! - * - * @param id DOCUMENT ME! + * + * @param id + * DOCUMENT ME! */ - public void setPDBId(Vector id) + @Override + public void setPDBId(Vector id) { pdbIds = id; } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public Vector getPDBId() + @Override + public Vector getAllPDBEntries() { - return pdbIds; + return pdbIds == null ? new Vector() : pdbIds; } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public String getDisplayId(boolean jvsuffix) { StringBuffer result = new StringBuffer(name); @@ -262,9 +474,11 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * - * @param name DOCUMENT ME! + * + * @param name + * DOCUMENT ME! */ + @Override public void setName(String name) { this.name = name; @@ -273,9 +487,10 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public String getName() { return this.name; @@ -283,9 +498,11 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * - * @param start DOCUMENT ME! + * + * @param start + * DOCUMENT ME! */ + @Override public void setStart(int start) { this.start = start; @@ -293,9 +510,10 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public int getStart() { return this.start; @@ -303,9 +521,11 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * - * @param end DOCUMENT ME! + * + * @param end + * DOCUMENT ME! */ + @Override public void setEnd(int end) { this.end = end; @@ -313,9 +533,10 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public int getEnd() { return this.end; @@ -323,93 +544,116 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public int getLength() { - return this.sequence.length(); + return this.sequence.length; } /** * DOCUMENT ME! - * - * @param seq DOCUMENT ME! + * + * @param seq + * DOCUMENT ME! */ + @Override public void setSequence(String seq) { - this.sequence = seq; + this.sequence = seq.toCharArray(); checkValidRange(); } - /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public String getSequence() + @Override + public String getSequenceAsString() { - return this.sequence; + return new String(sequence); } - /** - * DOCUMENT ME! - * - * @param start DOCUMENT ME! - * @param end DOCUMENT ME! - * - * @return DOCUMENT ME! + @Override + public String getSequenceAsString(int start, int end) + { + return new String(getSequence(start, end)); + } + + @Override + public char[] getSequence() + { + return sequence; + } + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.SequenceI#getSequence(int, int) */ - public String getSequence(int start, int end) + @Override + public char[] getSequence(int start, int end) { - // JBPNote - left to user to pad the result here (TODO:Decide on this policy) - if (start >= sequence.length()) + if (start < 0) { - return ""; + start = 0; + } + // JBPNote - left to user to pad the result here (TODO:Decide on this + // policy) + if (start >= sequence.length) + { + return new char[0]; } - if (end >= sequence.length()) + if (end >= sequence.length) { - end = sequence.length(); + end = sequence.length; } - return this.sequence.substring(start, end); + 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 - */ + @Override public SequenceI getSubSequence(int start, int end) { if (start < 0) + { start = 0; - String seq = getSequence(start, end); - if (seq == "") + } + 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); - nseq.setDatasetSequence(getDatasetSequence()); + if (datasetSequence != null) + { + nseq.setDatasetSequence(datasetSequence); + } + else + { + nseq.setDatasetSequence(this); + } return nseq; } /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * - * @return 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 */ + @Override public char getCharAt(int i) { - if (i < sequence.length()) + if (i >= 0 && i < sequence.length) { - return sequence.charAt(i); + return sequence[i]; } else { @@ -419,9 +663,11 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * - * @param desc DOCUMENT ME! + * + * @param desc + * DOCUMENT ME! */ + @Override public void setDescription(String desc) { this.description = desc; @@ -429,30 +675,30 @@ public class Sequence implements SequenceI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public String getDescription() { return this.description; } - /** - * DOCUMENT ME! - * - * @param pos DOCUMENT ME! - * - * @return DOCUMENT ME! + /* + * (non-Javadoc) + * + * @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; - - while ( (i < sequence.length()) && (j <= end) && (j <= pos)) + // 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.charAt(i))) + if (!jalview.util.Comparison.isGap(sequence[i])) { j++; } @@ -460,7 +706,7 @@ public class Sequence implements SequenceI i++; } - if ( (j == end) && (j < pos)) + if ((j == end) && (j < pos)) { return end + 1; } @@ -470,21 +716,15 @@ 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; int pos = start; - int seqlen = sequence.length(); - while ( (j < i) && (j < seqlen)) + int seqlen = sequence.length; + while ((j < i) && (j < seqlen)) { - if (!jalview.util.Comparison.isGap( (sequence.charAt(j)))) + if (!jalview.util.Comparison.isGap(sequence[j])) { pos++; } @@ -496,21 +736,24 @@ public class Sequence implements SequenceI } /** - * 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 + * 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 */ + @Override public int[] gapMap() { - String seq = jalview.analysis.AlignSeq.extractGaps(jalview.util.Comparison. - GapChars, sequence); + 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()) + while (j < sequence.length) { - if (!jalview.util.Comparison.isGap(sequence.charAt(j))) + if (!jalview.util.Comparison.isGap(sequence[j])) { map[p++] = j; } @@ -521,175 +764,715 @@ public class Sequence implements SequenceI return map; } - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - */ - public void deleteCharAt(int i) + @Override + public int[] findPositionMap() { - 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++; + } + + j++; } + return map; + } - sequence = sequence.substring(0, i) + sequence.substring(i + 1); + @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; } - /** - * DOCUMENT ME! - * - * @param i DOCUMENT ME! - * @param j DOCUMENT ME! - */ + @Override public void deleteChars(int i, int j) { - if (i >= sequence.length()) + int newstart = start, newend = end; + if (i >= sequence.length || i < 0) { return; } - if (j >= sequence.length()) + 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++) { - sequence = sequence.substring(0, i); + if (jalview.schemes.ResidueProperties.aaIndex[sequence[s]] != 23) + { + if (createNewDs) + { + newend--; + } + else + { + if (!scalc) + { + sindex = findIndex(start) - 1; + scalc = true; + } + 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. + if (!ecalc) + { + eindex = findIndex(end) - 1; + ecalc = true; + } + 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 + } + } + } + } } - else + // deletion occured in the middle of the sequence + if (createNewDs && this.datasetSequence != null) { - sequence = sequence.substring(0, i) + sequence.substring(j); + // 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! - */ + @Override public void insertCharAt(int i, int length, char c) { - StringBuffer tmp; + char[] tmp = new char[sequence.length + length]; - if (i >= sequence.length()) + if (i >= sequence.length) { - tmp = new StringBuffer(sequence); + System.arraycopy(sequence, 0, tmp, 0, sequence.length); + i = sequence.length; } else - tmp = new StringBuffer(sequence.substring(0, i)); + { + System.arraycopy(sequence, 0, tmp, 0, i); + } + int index = i; while (length > 0) { - tmp.append(c); + tmp[index++] = c; length--; } - if (i < sequence.length()) + if (i < sequence.length) { - tmp.append(sequence.substring(i)); + System.arraycopy(sequence, i, tmp, index, sequence.length - i); } - sequence = tmp.toString(); + 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) { + if (dbrefs == null && datasetSequence != null + && this != datasetSequence) + { + datasetSequence.setDBRefs(dbref); + return; + } dbrefs = dbref; + if (dbrefs != null) + { + DBRefUtils.ensurePrimaries(this); + } } - 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) { + if (datasetSequence != null) + { + datasetSequence.addDBRef(entry); + return; + } + if (dbrefs == null) + { dbrefs = new DBRefEntry[0]; + } - int i, iSize = dbrefs.length; - - for(i=0; i(); + } + if (!this.annotation.contains(annotation)) + { + this.annotation.addElement(annotation); + } + annotation.setSequenceRef(this); + } - this.annotation.addElement(annotation); + @Override + 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; } - public SequenceGroup getHiddenSequences() + @Override + public SequenceI deriveSequence() { - return hiddenSequences; + 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 + createDatasetSequence(); + } + } + return new Sequence(this); } - public void addHiddenSequence(SequenceI seq) + private boolean _isNa; + + private long _seqhash = 0; + + /** + * Answers false if the sequence is more than 85% nucleotide (ACGTU), else + * true + */ + @Override + public boolean isProtein() { - if (hiddenSequences == null) + if (datasetSequence != null) + { + return datasetSequence.isProtein(); + } + if (_seqhash != sequence.hashCode()) { - hiddenSequences = new SequenceGroup(); + _seqhash = sequence.hashCode(); + _isNa = Comparison.isNucleotide(this); } - hiddenSequences.addSequence(seq, false); + return !_isNa; + }; + + /* + * (non-Javadoc) + * + * @see jalview.datamodel.SequenceI#createDatasetSequence() + */ + @Override + public SequenceI createDatasetSequence() + { + if (datasetSequence == null) + { + Sequence dsseq = new Sequence(getName(), AlignSeq.extractGaps( + jalview.util.Comparison.GapChars, getSequenceAsString()), + getStart(), getEnd()); + + 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; } - public void showHiddenSequence(SequenceI seq) + /* + * (non-Javadoc) + * + * @see + * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] + * annotations) + */ + @Override + public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { - hiddenSequences.deleteSequence(seq, false); - if (hiddenSequences.getSize(false) < 1) + if (annotation != null) { - hiddenSequences = null; + annotation.removeAllElements(); + } + if (annotations != null) + { + for (int i = 0; i < annotations.length; i++) + { + if (annotations[i] != null) + { + addAlignmentAnnotation(annotations[i]); + } + } } } -} + @Override + 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; + } + + @Override + public boolean updatePDBIds() + { + if (datasetSequence != null) + { + // TODO: could merge DBRefs + return datasetSequence.updatePDBIds(); + } + if (dbrefs == null || dbrefs.length == 0) + { + return false; + } + boolean added = false; + for (DBRefEntry dbr : dbrefs) + { + if (DBRefSource.PDB.equals(dbr.getSource())) + { + /* + * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the + * PDB id is not already present in a 'matching' PDBEntry + * Constructor parses out a chain code if appended to the accession id + * (a fudge used to 'store' the chain code in the DBRef) + */ + PDBEntry pdbe = new PDBEntry(dbr); + added |= addPDBId(pdbe); + } + } + return added; + } + + @Override + 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.getAllPDBEntries() != null) + { + Enumeration e = entry.getAllPDBEntries().elements(); + while (e.hasMoreElements()) + { + PDBEntry pdb = (PDBEntry) e.nextElement(); + addPDBId(pdb); + } + } + // transfer database references + DBRefEntry[] entryRefs = entry.getDBRefs(); + 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); + } + } + } + + /** + * @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) + { + return getDatasetSequence().getPDBEntry(pdbIdStr); + } + if (pdbIds == null) + { + return null; + } + List entries = getAllPDBEntries(); + for (PDBEntry entry : entries) + { + if (entry.getId().equalsIgnoreCase(pdbIdStr)) + { + return entry; + } + } + return null; + } + + @Override + public List getPrimaryDBRefs() + { + if (datasetSequence != null) + { + return datasetSequence.getPrimaryDBRefs(); + } + if (dbrefs == null || dbrefs.length == 0) + { + return Collections.emptyList(); + } + synchronized (dbrefs) + { + List primaries = new ArrayList(); + DBRefEntry[] tmp = new DBRefEntry[1]; + for (DBRefEntry ref : dbrefs) + { + if (!ref.isPrimaryCandidate()) + { + continue; + } + if (ref.hasMap()) + { + MapList mp = ref.getMap().getMap(); + if (mp.getFromLowest() > start || mp.getFromHighest() < end) + { + // map only involves a subsequence, so cannot be primary + continue; + } + } + // whilst it looks like it is a primary ref, we also sanity check type + if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals( + DBRefUtils.getCanonicalName(ref.getSource()))) + { + // PDB dbrefs imply there should be a PDBEntry associated + // TODO: tighten PDB dbrefs + // formally imply Jalview has actually downloaded and + // parsed the pdb file. That means there should be a cached file + // handle on the PDBEntry, and a real mapping between sequence and + // extracted sequence from PDB file + PDBEntry pdbentry = getPDBEntry(ref.getAccessionId()); + if (pdbentry != null && pdbentry.getFile() != null) + { + primaries.add(ref); + } + continue; + } + // check standard protein or dna sources + tmp[0] = ref; + DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp); + if (res != null && res[0] == tmp[0]) + { + primaries.add(ref); + continue; + } + } + return primaries; + } + } + +}