X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=9cec37052ad74f30342b293e7087e3a876fe0317;hb=24759045defbd5bb87bb699c6ba363f171464d7f;hp=722edf21259bf2076967cd4906072f78d57fd7e6;hpb=45d4eb5f2d3772ac51e2512d49fb0a3a958f2260;p=jalview.git diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java index 722edf2..9cec370 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 ($$Version-Rel$$) + * 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.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; /** * @@ -43,33 +51,42 @@ 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; + Vector annotation; - /** array of seuqence features - may not be null for a valid sequence object */ + /** + * The index of the sequence in a MSA + */ + 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 - * 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) { @@ -117,7 +134,8 @@ 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 +150,10 @@ public class Sequence implements SequenceI endRes += start - 1; } - this.end = endRes; + if (end < endRes) + { + end = endRes; + } } } @@ -141,9 +162,9 @@ 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 +177,7 @@ public class Sequence implements SequenceI * reference. * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public Sequence(SequenceI seq) { @@ -169,9 +190,9 @@ 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) { @@ -185,15 +206,16 @@ 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(); @@ -234,7 +256,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param v - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequenceFeatures(SequenceFeature[] features) { @@ -305,32 +327,57 @@ 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) { @@ -367,7 +414,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param name - * DOCUMENT ME! + * DOCUMENT ME! */ public void setName(String name) { @@ -389,7 +436,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param start - * DOCUMENT ME! + * DOCUMENT ME! */ public void setStart(int start) { @@ -410,7 +457,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param end - * DOCUMENT ME! + * DOCUMENT ME! */ public void setEnd(int end) { @@ -441,7 +488,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ public void setSequence(String seq) { @@ -472,7 +519,9 @@ 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 +540,7 @@ 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 +572,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param i - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -552,7 +592,7 @@ public class Sequence implements SequenceI * DOCUMENT ME! * * @param desc - * DOCUMENT ME! + * DOCUMENT ME! */ public void setDescription(String desc) { @@ -569,20 +609,17 @@ 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 +640,7 @@ 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; @@ -657,33 +687,77 @@ 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) + { + 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 +768,11 @@ 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 +782,11 @@ 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 +797,7 @@ 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 +818,7 @@ 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]; @@ -775,31 +848,42 @@ 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) @@ -832,40 +916,43 @@ 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; - } + return annotation == null ? null : annotation + .toArray(new AlignmentAnnotation[annotation.size()]); + } - AlignmentAnnotation[] ret = new AlignmentAnnotation[annotation.size()]; - for (int r = 0; r < ret.length; r++) - { - ret[r] = (AlignmentAnnotation) annotation.elementAt(r); - } - 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.addElement(annotation); + if (!this.annotation.contains(annotation)) + { + this.annotation.addElement(annotation); + } annotation.setSequenceRef(this); } @@ -875,7 +962,9 @@ public class Sequence implements SequenceI { this.annotation.removeElement(annotation); if (this.annotation.size() == 0) + { this.annotation = null; + } } } @@ -899,11 +988,7 @@ public class Sequence implements SequenceI return true; } - /* - * (non-Javadoc) - * - * @see jalview.datamodel.SequenceI#deriveSequence() - */ + @Override public SequenceI deriveSequence() { SequenceI seq = new Sequence(this); @@ -954,6 +1039,17 @@ public class Sequence implements SequenceI datasetSequence.setPDBId(getPDBId()); 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; } @@ -961,8 +1057,9 @@ 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) { @@ -975,16 +1072,14 @@ 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 +1112,7 @@ public class Sequence implements SequenceI return anns; } + @Override public boolean updatePDBIds() { if (datasetSequence != null) @@ -1070,12 +1166,7 @@ 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) @@ -1139,4 +1230,55 @@ 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; + } + }