X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=271374ff0dc2380c4e8165642514fe6605e0f96d;hb=b1c9b42f08c639868c2509dffacdf29f299c5f0d;hp=4e279d3772e5b91662613b07718199a4f1350792;hpb=28a00b99bbd8f25fd894d5941149f2e1a45ed0f2;p=jalview.git diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 4e279d3..271374f 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -1,40 +1,39 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * + * 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 + * 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 + * + * 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.*; - /** * Data structure to hold and manipulate a multiple sequence alignment */ /** * @author JimP - * + * */ public class Alignment implements AlignmentI { protected Alignment dataset; - protected Vector sequences; + protected List sequences; - protected Vector groups = new Vector(); + protected List groups = java.util.Collections + .synchronizedList(new ArrayList()); protected char gapCharacter = '-'; @@ -44,6 +43,8 @@ public class Alignment implements AlignmentI public static final int NUCLEOTIDE = 1; + public boolean hasRNAStructure = false; + /** DOCUMENT ME!! */ public AlignmentAnnotation[] annotations; @@ -64,18 +65,19 @@ public class Alignment implements AlignmentI type = PROTEIN; } - sequences = new Vector(); + sequences = java.util.Collections + .synchronizedList(new ArrayList()); for (i = 0; i < seqs.length; i++) { - sequences.addElement(seqs[i]); + sequences.add(seqs[i]); } } /** * Make an alignment from an array of Sequences. - * + * * @param sequences */ public Alignment(SequenceI[] seqs) @@ -85,7 +87,7 @@ public class Alignment implements AlignmentI /** * Make a new alignment from an array of SeqCigars - * + * * @param seqs * SeqCigar[] */ @@ -101,7 +103,7 @@ public class Alignment implements AlignmentI * compactAlignment does not contain hidden regions. JBPNote - must also check * that compactAlignment resolves to a set of SeqCigars - or construct them * appropriately. - * + * * @param compactAlignment * CigarArray */ @@ -113,49 +115,62 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public Vector getSequences() + @Override + public List getSequences() + { + return sequences; + } + + @Override + public List getSequences( + Map hiddenReps) { + // TODO: in jalview 2.8 we don't do anything with hiddenreps - fix design to + // work on this. return sequences; } + @Override public SequenceI[] getSequencesArray() { if (sequences == null) return null; - SequenceI[] reply = new SequenceI[sequences.size()]; - for (int i = 0; i < sequences.size(); i++) + synchronized (sequences) { - reply[i] = (SequenceI) sequences.elementAt(i); + return sequences.toArray(new SequenceI[sequences.size()]); } - return reply; } /** * DOCUMENT ME! - * + * * @param i * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public SequenceI getSequenceAt(int i) { - if (i>-1 && i < sequences.size()) + synchronized (sequences) { - return (SequenceI) sequences.elementAt(i); + if (i > -1 && i < sequences.size()) + { + return sequences.get(i); + } } - return null; } /** * Adds a sequence to the alignment. Recalculates maxLength and size. - * + * * @param snew */ + @Override public void addSequence(SequenceI snew) { if (dataset != null) @@ -180,7 +195,10 @@ public class Alignment implements AlignmentI } else { - sequences.addElement(snew); + synchronized (sequences) + { + sequences.add(snew); + } } if (hiddenSequences != null) hiddenSequences.adjustHeightSequenceAdded(); @@ -188,27 +206,32 @@ public class Alignment implements AlignmentI /** * Adds a sequence to the alignment. Recalculates maxLength and size. - * + * * @param snew */ + @Override public void setSequenceAt(int i, SequenceI snew) { SequenceI oldseq = getSequenceAt(i); - deleteSequence(oldseq); - - sequences.setElementAt(snew, i); + deleteSequence(i); + synchronized (sequences) + { + sequences.set(i, snew); + } } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ - public Vector getGroups() + @Override + public List getGroups() { return groups; } + @Override public void finalize() { if (getDataset() != null) @@ -235,10 +258,11 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param s * DOCUMENT ME! */ + @Override public void deleteSequence(SequenceI s) { deleteSequence(findIndex(s)); @@ -246,105 +270,115 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param i * DOCUMENT ME! */ + @Override public void deleteSequence(int i) { if (i > -1 && i < getHeight()) { - sequences.removeElementAt(i); + synchronized (sequences) + { + sequences.remove(i); + } hiddenSequences.adjustHeightSequenceDeleted(i); } } - /** */ + /* + * (non-Javadoc) + * + * @see jalview.datamodel.AlignmentI#findGroup(jalview.datamodel.SequenceI) + */ + @Override public SequenceGroup findGroup(SequenceI s) { - for (int i = 0; i < this.groups.size(); i++) + synchronized (groups) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - - if (sg.getSequences(null).contains(s)) + for (int i = 0; i < this.groups.size(); i++) { - return sg; + SequenceGroup sg = groups.get(i); + + if (sg.getSequences(null).contains(s)) + { + return sg; + } } } - return null; } - /** - * DOCUMENT ME! - * - * @param s - * DOCUMENT ME! - * - * @return DOCUMENT ME! + /* + * (non-Javadoc) + * + * @see + * jalview.datamodel.AlignmentI#findAllGroups(jalview.datamodel.SequenceI) */ + @Override public SequenceGroup[] findAllGroups(SequenceI s) { - Vector temp = new Vector(); + ArrayList temp = new ArrayList(); - int gSize = groups.size(); - for (int i = 0; i < gSize; i++) + synchronized (groups) { - SequenceGroup sg = (SequenceGroup) groups.elementAt(i); - if (sg == null || sg.getSequences(null) == null) + int gSize = groups.size(); + for (int i = 0; i < gSize; i++) { - this.deleteGroup(sg); - gSize--; - continue; - } + SequenceGroup sg = groups.get(i); + if (sg == null || sg.getSequences(null) == null) + { + this.deleteGroup(sg); + gSize--; + continue; + } - if (sg.getSequences(null).contains(s)) - { - temp.addElement(sg); + if (sg.getSequences(null).contains(s)) + { + temp.add(sg); + } } } - SequenceGroup[] ret = new SequenceGroup[temp.size()]; - - for (int i = 0; i < temp.size(); i++) - { - ret[i] = (SequenceGroup) temp.elementAt(i); - } - - return ret; + return temp.toArray(ret); } /** */ + @Override public void addGroup(SequenceGroup sg) { - if (!groups.contains(sg)) + synchronized (groups) { - if (hiddenSequences.getSize() > 0) + if (!groups.contains(sg)) { - int i, iSize = sg.getSize(); - for (i = 0; i < iSize; i++) + if (hiddenSequences.getSize() > 0) { - if (!sequences.contains(sg.getSequenceAt(i))) + int i, iSize = sg.getSize(); + for (i = 0; i < iSize; i++) { - sg.deleteSequence(sg.getSequenceAt(i), false); - iSize--; - i--; + if (!sequences.contains(sg.getSequenceAt(i))) + { + sg.deleteSequence(sg.getSequenceAt(i), false); + iSize--; + i--; + } } - } - if (sg.getSize() < 1) - { - return; + if (sg.getSize() < 1) + { + return; + } } - } - groups.addElement(sg); + groups.add(sg); + } } } /** * remove any annotation that references gp - * + * * @param gp * (if null, removes all group associated annotation) */ @@ -402,26 +436,35 @@ public class Alignment implements AlignmentI } } + @Override public void deleteAllGroups() { - if (annotations != null) + synchronized (groups) { - removeAnnotationForGroup(null); + if (annotations != null) + { + removeAnnotationForGroup(null); + } + groups.clear(); } - groups.removeAllElements(); } /** */ + @Override public void deleteGroup(SequenceGroup g) { - if (groups.contains(g)) + synchronized (groups) { - removeAnnotationForGroup(g); - groups.removeElement(g); + if (groups.contains(g)) + { + removeAnnotationForGroup(g); + groups.remove(g); + } } } /** */ + @Override public SequenceI findName(String name) { return findName(name, false); @@ -429,9 +472,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findName(java.lang.String, boolean) */ + @Override public SequenceI findName(String token, boolean b) { return findName(null, token, b); @@ -439,10 +483,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findName(SequenceI, java.lang.String, * boolean) */ + @Override public SequenceI findName(SequenceI startAfter, String token, boolean b) { @@ -483,6 +528,7 @@ public class Alignment implements AlignmentI return null; } + @Override public SequenceI[] findSequenceMatch(String name) { Vector matches = new Vector(); @@ -509,9 +555,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SequenceI) */ + @Override public int findIndex(SequenceI s) { int i = 0; @@ -531,10 +578,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#findIndex(jalview.datamodel.SearchResults) */ + @Override public int findIndex(SearchResults results) { int i = 0; @@ -552,9 +600,10 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public int getHeight() { return sequences.size(); @@ -562,9 +611,10 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public int getWidth() { int maxLength = -1; @@ -582,27 +632,30 @@ public class Alignment implements AlignmentI /** * DOCUMENT ME! - * + * * @param gc * DOCUMENT ME! */ + @Override public void setGapCharacter(char gc) { gapCharacter = gc; - - for (int i = 0; i < sequences.size(); i++) + synchronized (sequences) { - Sequence seq = (Sequence) sequences.elementAt(i); - seq.setSequence(seq.getSequenceAsString().replace('.', gc) - .replace('-', gc).replace(' ', gc)); + for (SequenceI seq : sequences) + { + seq.setSequence(seq.getSequenceAsString().replace('.', gc) + .replace('-', gc).replace(' ', gc)); + } } } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ + @Override public char getGapCharacter() { return gapCharacter; @@ -610,9 +663,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#isAligned() */ + @Override public boolean isAligned() { return isAligned(false); @@ -620,9 +674,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#isAligned(boolean) */ + @Override public boolean isAligned(boolean includeHidden) { int width = getWidth(); @@ -646,15 +701,17 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#deleteAnnotation(jalview.datamodel. * AlignmentAnnotation) */ + @Override public boolean deleteAnnotation(AlignmentAnnotation aa) { return deleteAnnotation(aa, true); } - + + @Override public boolean deleteAnnotation(AlignmentAnnotation aa, boolean unhook) { int aSize = 1; @@ -688,7 +745,8 @@ public class Alignment implements AlignmentI if (swap) { annotations = temp; - if (unhook) { + if (unhook) + { unhookAnnotation(aa); } } @@ -697,7 +755,7 @@ public class Alignment implements AlignmentI /** * remove any object references associated with this annotation - * + * * @param aa */ private void unhookAnnotation(AlignmentAnnotation aa) @@ -715,10 +773,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. * AlignmentAnnotation) */ + @Override public void addAnnotation(AlignmentAnnotation aa) { addAnnotation(aa, -1); @@ -726,12 +785,18 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#addAnnotation(jalview.datamodel. * AlignmentAnnotation, int) */ + @Override public void addAnnotation(AlignmentAnnotation aa, int pos) { + if (aa.getRNAStruc() != null) + { + hasRNAStructure = true; + } + int aSize = 1; if (annotations != null) { @@ -767,6 +832,7 @@ public class Alignment implements AlignmentI annotations = temp; } + @Override public void setAnnotationIndex(AlignmentAnnotation aa, int index) { if (aa == null || annotations == null || annotations.length - 1 < index) @@ -799,16 +865,16 @@ public class Alignment implements AlignmentI annotations = temp; } + @Override /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * returns all annotation on the alignment */ public AlignmentAnnotation[] getAlignmentAnnotation() { return annotations; } + @Override public void setNucleotide(boolean b) { if (b) @@ -821,6 +887,7 @@ public class Alignment implements AlignmentI } } + @Override public boolean isNucleotide() { if (type == NUCLEOTIDE) @@ -833,6 +900,14 @@ public class Alignment implements AlignmentI } } + @Override + public boolean hasRNAStructure() + { + // TODO can it happen that structure is removed from alignment? + return hasRNAStructure; + } + + @Override public void setDataset(Alignment data) { if (dataset == null && data == null) @@ -847,7 +922,7 @@ public class Alignment implements AlignmentI currentSeq = getSequenceAt(i); if (currentSeq.getDatasetSequence() != null) { - seqs[i] = (Sequence) currentSeq.getDatasetSequence(); + seqs[i] = currentSeq.getDatasetSequence(); } else { @@ -877,11 +952,13 @@ public class Alignment implements AlignmentI alignmentRefs++; } + @Override public Alignment getDataset() { return dataset; } + @Override public boolean padGaps() { boolean modified = false; @@ -928,11 +1005,12 @@ public class Alignment implements AlignmentI /** * Justify the sequences to the left or right by deleting and inserting gaps * before the initial residue or after the terminal residue - * + * * @param right * true if alignment padded to right, false to justify to left * @return true if alignment was changed */ + @Override public boolean justify(boolean right) { boolean modified = false; @@ -1030,23 +1108,30 @@ public class Alignment implements AlignmentI return modified; } + @Override public HiddenSequences getHiddenSequences() { return hiddenSequences; } + @Override public CigarArray getCompactAlignment() { - SeqCigar alseqs[] = new SeqCigar[sequences.size()]; - for (int i = 0; i < sequences.size(); i++) + synchronized (sequences) { - alseqs[i] = new SeqCigar((SequenceI) sequences.elementAt(i)); + SeqCigar alseqs[] = new SeqCigar[sequences.size()]; + int i = 0; + for (SequenceI seq : sequences) + { + alseqs[i++] = new SeqCigar(seq); + } + CigarArray cal = new CigarArray(alseqs); + cal.addOperation(CigarArray.M, getWidth()); + return cal; } - CigarArray cal = new CigarArray(alseqs); - cal.addOperation(CigarArray.M, getWidth()); - return cal; } + @Override public void setProperty(Object key, Object value) { if (alignmentProperties == null) @@ -1055,6 +1140,7 @@ public class Alignment implements AlignmentI alignmentProperties.put(key, value); } + @Override public Object getProperty(Object key) { if (alignmentProperties != null) @@ -1063,6 +1149,7 @@ public class Alignment implements AlignmentI return null; } + @Override public Hashtable getProperties() { return alignmentProperties; @@ -1072,11 +1159,12 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#addCodonFrame(jalview.datamodel.AlignedCodonFrame * ) */ + @Override public void addCodonFrame(AlignedCodonFrame codons) { if (codons == null) @@ -1095,9 +1183,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#getCodonFrame(int) */ + @Override public AlignedCodonFrame getCodonFrame(int index) { return codonFrameList[index]; @@ -1105,10 +1194,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see * jalview.datamodel.AlignmentI#getCodonFrame(jalview.datamodel.SequenceI) */ + @Override public AlignedCodonFrame[] getCodonFrame(SequenceI seq) { if (seq == null || codonFrameList == null) @@ -1128,9 +1218,10 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @see jalview.datamodel.AlignmentI#getCodonFrames() */ + @Override public AlignedCodonFrame[] getCodonFrames() { return codonFrameList; @@ -1138,10 +1229,11 @@ public class Alignment implements AlignmentI /* * (non-Javadoc) - * + * * @seejalview.datamodel.AlignmentI#removeCodonFrame(jalview.datamodel. * AlignedCodonFrame) */ + @Override public boolean removeCodonFrame(AlignedCodonFrame codons) { if (codons == null || codonFrameList == null) @@ -1168,8 +1260,13 @@ public class Alignment implements AlignmentI return removed; } + @Override public void append(AlignmentI toappend) { + if (toappend == this) + { + System.err.println("Self append may cause a deadlock."); + } // TODO test this method for a future 2.5 release // currently tested for use in jalview.gui.SequenceFetcher boolean samegap = toappend.getGapCharacter() == getGapCharacter(); @@ -1177,26 +1274,27 @@ public class Alignment implements AlignmentI boolean hashidden = toappend.getHiddenSequences() != null && toappend.getHiddenSequences().hiddenSequences != null; // get all sequences including any hidden ones - Vector sqs = (hashidden) ? toappend.getHiddenSequences() + List sqs = (hashidden) ? toappend.getHiddenSequences() .getFullAlignment().getSequences() : toappend.getSequences(); if (sqs != null) { - Enumeration sq = sqs.elements(); - while (sq.hasMoreElements()) + synchronized (sqs) { - SequenceI addedsq = (SequenceI) sq.nextElement(); - if (!samegap) + for (SequenceI addedsq : sqs) { - char[] oldseq = addedsq.getSequence(); - for (int c = 0; c < oldseq.length; c++) + if (!samegap) { - if (oldseq[c] == oldc) + char[] oldseq = addedsq.getSequence(); + for (int c = 0; c < oldseq.length; c++) { - oldseq[c] = gapCharacter; + if (oldseq[c] == oldc) + { + oldseq[c] = gapCharacter; + } } } + addSequence(addedsq); } - addSequence(addedsq); } } AlignmentAnnotation[] alan = toappend.getAlignmentAnnotation(); @@ -1209,13 +1307,12 @@ public class Alignment implements AlignmentI { this.addCodonFrame(acod[a]); } - Vector sg = toappend.getGroups(); + List sg = toappend.getGroups(); if (sg != null) { - Enumeration el = sg.elements(); - while (el.hasMoreElements()) + for (SequenceGroup _sg : sg) { - addGroup((SequenceGroup) el.nextElement()); + addGroup(_sg); } } if (toappend.getHiddenSequences() != null) @@ -1282,4 +1379,101 @@ public class Alignment implements AlignmentI } } + @Override + public AlignmentAnnotation findOrCreateAnnotation(String name, + String calcId, boolean autoCalc, SequenceI seqRef, SequenceGroup groupRef) + { + assert(name!=null); + for (AlignmentAnnotation annot : getAlignmentAnnotation()) + { + if (annot.autoCalculated == autoCalc + && (name.equals(annot.label)) + && (calcId==null || annot.getCalcId().equals(calcId)) + && annot.sequenceRef == seqRef && annot.groupRef == groupRef) + { + return annot; + } + } + AlignmentAnnotation annot = new AlignmentAnnotation(name, name, + new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH); + annot.hasText = false; + annot.setCalcId(new String(calcId)); + annot.autoCalculated = autoCalc; + if (seqRef != null) + { + annot.setSequenceRef(seqRef); + } + annot.groupRef = groupRef; + addAnnotation(annot); + + return annot; + } + + @Override + public Iterable findAnnotation(String calcId) + { + ArrayList aa = new ArrayList(); + for (AlignmentAnnotation a : getAlignmentAnnotation()) + { + if (a.getCalcId() == calcId + || (a.getCalcId() != null && calcId != null && a.getCalcId() + .equals(calcId))) + { + aa.add(a); + } + } + return aa; + } + + @Override + public void moveSelectedSequencesByOne(SequenceGroup sg, + Map map, boolean up) + { + synchronized (sequences) + { + if (up) + { + + for (int i = 1, iSize = sequences.size(); i < iSize; i++) + { + SequenceI seq = sequences.get(i); + if (!sg.getSequences(map).contains(seq)) + { + continue; + } + + SequenceI temp = sequences.get(i - 1); + if (sg.getSequences(null).contains(temp)) + { + continue; + } + + sequences.set(i, temp); + sequences.set(i - 1, seq); + } + } + else + { + for (int i = sequences.size() - 2; i > -1; i--) + { + SequenceI seq = sequences.get(i); + if (!sg.getSequences(map).contains(seq)) + { + continue; + } + + SequenceI temp = sequences.get(i + 1); + if (sg.getSequences(map).contains(temp)) + { + continue; + } + + sequences.set(i, temp); + sequences.set(i + 1, seq); + } + } + + } + } + }