X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=8b089a22da302a9fe21a84496fa5e63655ed0f86;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=3240f843b243b378d17bfc056bee572d3cc8517d;hpb=e1c9c652059a67ee96f9fc5f6617fd5d604cbdbb;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 3240f84..8b089a2 100755 --- a/src/jalview/datamodel/Sequence.java +++ b/src/jalview/datamodel/Sequence.java @@ -1,26 +1,34 @@ /* - * 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 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. - * - * 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.util.StringUtils; -import jalview.analysis.*; +import java.util.ArrayList; +import java.util.Enumeration; +import java.util.List; +import java.util.Vector; + +import fr.orsay.lri.varna.models.rna.RNA; /** * @@ -29,7 +37,7 @@ import jalview.analysis.*; * @author $author$ * @version $Revision$ */ -public class Sequence implements SequenceI +public class Sequence extends ASequence implements SequenceI { SequenceI datasetSequence; @@ -43,50 +51,69 @@ public class Sequence implements SequenceI int end; - Vector pdbIds; + Vector pdbIds; String vamsasId; 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 +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(); @@ -117,7 +144,8 @@ 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 +160,10 @@ public class Sequence implements SequenceI endRes += start - 1; } - this.end = endRes; + if (end < endRes) + { + end = endRes; + } } } @@ -141,9 +172,9 @@ 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) { @@ -156,7 +187,7 @@ public class Sequence implements SequenceI * reference. * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public Sequence(SequenceI seq) { @@ -169,13 +200,21 @@ 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); + + } + + protected void initSeqFrom(SequenceI seq, + AlignmentAnnotation[] alAnnotation) + { + initSeqAndName(seq.getName(), seq.getSequence(), seq.getStart(), + seq.getEnd()); description = seq.getDescription(); if (seq.getSequenceFeatures() != null) { @@ -185,15 +224,16 @@ public class Sequence implements SequenceI addSequenceFeature(new SequenceFeature(sf[i])); } } - if (seq.getDBRef() != null) + setDatasetSequence(seq.getDatasetSequence()); + if (datasetSequence == null && seq.getDBRef() != null) { + // only copy DBRefs if we really are a dataset sequence DBRefEntry[] dbr = seq.getDBRef(); for (int i = 0; i < dbr.length; i++) { addDBRef(new DBRefEntry(dbr[i])); } } - setDatasetSequence(seq.getDatasetSequence()); if (seq.getAnnotation() != null) { AlignmentAnnotation[] sqann = seq.getAnnotation(); @@ -219,9 +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()) { @@ -234,7 +274,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param v - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequenceFeatures(SequenceFeature[] features) { @@ -305,34 +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)) + if (pdbIds.contains(entry)) + { + updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), 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; } @@ -342,7 +408,8 @@ public class Sequence implements SequenceI * * @return DOCUMENT ME! */ - public Vector getPDBId() + @Override + public Vector getAllPDBEntries() { return pdbIds; } @@ -367,7 +434,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! */ public void setName(String name) { @@ -389,7 +456,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param start - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStart(int start) { @@ -410,7 +477,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param end - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEnd(int end) { @@ -441,7 +508,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequence(String seq) { @@ -472,7 +539,9 @@ public class Sequence implements SequenceI 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 +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) @@ -532,7 +592,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -552,7 +612,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param desc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setDescription(String desc) { @@ -569,20 +629,17 @@ public class Sequence implements SequenceI 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) */ 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 +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; @@ -656,11 +706,8 @@ public class Sequence implements SequenceI return map; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#findPositionMap() - */ + + @Override public int[] findPositionMap() { int map[] = new int[sequence.length]; @@ -679,33 +726,56 @@ 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); + 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 (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) @@ -716,7 +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 @@ -726,7 +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 @@ -737,7 +815,7 @@ public class Sequence implements SequenceI { createNewDs = true; newend--; // decrease end position by one for the deleted residue - // and search further + // and search further } } } @@ -758,16 +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]; @@ -797,31 +866,42 @@ 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 + && this != datasetSequence) + { + return datasetSequence.getDBRef(); + } return dbrefs; } + @Override public void addDBRef(DBRefEntry entry) { if (dbrefs == null) @@ -854,40 +934,42 @@ 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] = (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); } @@ -897,7 +979,9 @@ public class Sequence implements SequenceI { this.annotation.removeElement(annotation); if (this.annotation.size() == 0) + { this.annotation = null; + } } } @@ -921,11 +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); @@ -973,9 +1053,20 @@ 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) + { + 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; } @@ -983,8 +1074,9 @@ public class Sequence implements SequenceI /* * (non-Javadoc) * - * @see jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] - * annotations) + * @see + * jalview.datamodel.SequenceI#setAlignmentAnnotation(AlignmmentAnnotation[] + * annotations) */ public void setAlignmentAnnotation(AlignmentAnnotation[] annotations) { @@ -997,16 +1089,14 @@ 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) @@ -1039,6 +1129,7 @@ public class Sequence implements SequenceI return anns; } + @Override public boolean updatePDBIds() { if (datasetSequence != null) @@ -1092,12 +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) @@ -1118,8 +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++) @@ -1131,9 +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(); @@ -1161,4 +1246,79 @@ 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. + */ + 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) + */ + public void setIndex(int value) + { + index = value; + } + + public void setRNA(RNA r) + { + rna = r; + } + + 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; + } + + 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; + } + }