X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=7a1b1008d34592e7352a4ee011098d0d588f9103;hb=df0734bbe3c42eb4e1d2e6471040888c85801ba5;hp=cf5054de0079923f0762d6e38cb9f40d05beb5cc;hpb=3173d5515901341a2ae3211bd8e4400e966add35;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index cf5054d..cd986c0 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -1,47 +1,281 @@ /* - * 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.structure; -import java.io.*; -import java.util.*; +import jalview.analysis.AlignSeq; +import jalview.api.StructureSelectionManagerProvider; +import jalview.commands.CommandI; +import jalview.commands.EditCommand; +import jalview.commands.OrderCommand; +import jalview.datamodel.AlignedCodonFrame; +import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.Annotation; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceI; +import jalview.ext.jmol.JmolParser; +import jalview.gui.IProgressIndicator; +import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; +import jalview.io.StructureFile; +import jalview.util.MappingUtils; +import jalview.util.MessageManager; +import jalview.ws.sifts.SiftsClient; +import jalview.ws.sifts.SiftsException; +import jalview.ws.sifts.SiftsSettings; -import MCview.*; -import jalview.analysis.*; -import jalview.datamodel.*; +import java.io.PrintStream; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.Collections; +import java.util.Enumeration; +import java.util.HashMap; +import java.util.IdentityHashMap; +import java.util.List; +import java.util.Map; +import java.util.Vector; + +import MCview.Atom; +import MCview.PDBChain; +import MCview.PDBfile; public class StructureSelectionManager { - static StructureSelectionManager instance; - StructureMapping[] mappings; - Hashtable mappingData = new Hashtable(); + public final static String NEWLINE = System.lineSeparator(); + + static IdentityHashMap instances; + + private List mappings = new ArrayList<>(); + + private boolean processSecondaryStructure = false; + + private boolean secStructServices = false; + + private boolean addTempFacAnnot = false; + + /* + * Set of any registered mappings between (dataset) sequences. + */ + private List seqmappings = new ArrayList<>(); + + private List commandListeners = new ArrayList<>(); + + private List sel_listeners = new ArrayList<>(); - public static StructureSelectionManager getStructureSelectionManager() + /** + * @return true if will try to use external services for processing secondary + * structure + */ + public boolean isSecStructServices() { - if (instance == null) + return secStructServices; + } + + /** + * control use of external services for processing secondary structure + * + * @param secStructServices + */ + public void setSecStructServices(boolean secStructServices) + { + this.secStructServices = secStructServices; + } + + /** + * flag controlling addition of any kind of structural annotation + * + * @return true if temperature factor annotation will be added + */ + public boolean isAddTempFacAnnot() + { + return addTempFacAnnot; + } + + /** + * set flag controlling addition of structural annotation + * + * @param addTempFacAnnot + */ + public void setAddTempFacAnnot(boolean addTempFacAnnot) + { + this.addTempFacAnnot = addTempFacAnnot; + } + + /** + * + * @return if true, the structure manager will attempt to add secondary + * structure lines for unannotated sequences + */ + + public boolean isProcessSecondaryStructure() + { + return processSecondaryStructure; + } + + /** + * Control whether structure manager will try to annotate mapped sequences + * with secondary structure from PDB data. + * + * @param enable + */ + public void setProcessSecondaryStructure(boolean enable) + { + processSecondaryStructure = enable; + } + + /** + * debug function - write all mappings to stdout + */ + public void reportMapping() + { + if (mappings.isEmpty()) { - instance = new StructureSelectionManager(); + System.err.println("reportMapping: No PDB/Sequence mappings."); } + else + { + System.err.println( + "reportMapping: There are " + mappings.size() + " mappings."); + int i = 0; + for (StructureMapping sm : mappings) + { + System.err.println("mapping " + i++ + " : " + sm.pdbfile); + } + } + } + + /** + * map between the PDB IDs (or structure identifiers) used by Jalview and the + * absolute filenames for PDB data that corresponds to it + */ + Map pdbIdFileName = new HashMap<>(); + + Map pdbFileNameId = new HashMap<>(); + + public void registerPDBFile(String idForFile, String absoluteFile) + { + pdbIdFileName.put(idForFile, absoluteFile); + pdbFileNameId.put(absoluteFile, idForFile); + } + + public String findIdForPDBFile(String idOrFile) + { + String id = pdbFileNameId.get(idOrFile); + return id; + } + + public String findFileForPDBId(String idOrFile) + { + String id = pdbIdFileName.get(idOrFile); + return id; + } + + public boolean isPDBFileRegistered(String idOrFile) + { + return pdbFileNameId.containsKey(idOrFile) + || pdbIdFileName.containsKey(idOrFile); + } + private static StructureSelectionManager nullProvider = null; + + public static StructureSelectionManager getStructureSelectionManager( + StructureSelectionManagerProvider context) + { + if (context == null) + { + if (nullProvider == null) + { + if (instances != null) + { + throw new Error(MessageManager.getString( + "error.implementation_error_structure_selection_manager_null"), + new NullPointerException(MessageManager + .getString("exception.ssm_context_is_null"))); + } + else + { + nullProvider = new StructureSelectionManager(); + } + return nullProvider; + } + } + if (instances == null) + { + instances = new java.util.IdentityHashMap<>(); + } + StructureSelectionManager instance = instances.get(context); + if (instance == null) + { + if (nullProvider != null) + { + instance = nullProvider; + } + else + { + instance = new StructureSelectionManager(); + } + instances.put(context, instance); + } return instance; } + /** + * flag controlling whether SeqMappings are relayed from received sequence + * mouse over events to other sequences + */ + boolean relaySeqMappings = true; + + /** + * Enable or disable relay of seqMapping events to other sequences. You might + * want to do this if there are many sequence mappings and the host computer + * is slow + * + * @param relay + */ + public void setRelaySeqMappings(boolean relay) + { + relaySeqMappings = relay; + } + + /** + * get the state of the relay seqMappings flag. + * + * @return true if sequence mouse overs are being relayed to other mapped + * sequences + */ + public boolean isRelaySeqMappingsEnabled() + { + return relaySeqMappings; + } + Vector listeners = new Vector(); + + /** + * register a listener for alignment sequence mouseover events + * + * @param svl + */ public void addStructureViewerListener(Object svl) { if (!listeners.contains(svl)) @@ -50,162 +284,541 @@ public class StructureSelectionManager } } + /** + * Returns the filename the PDB id is already mapped to if known, or null if + * it is not mapped + * + * @param pdbid + * @return + */ public String alreadyMappedToFile(String pdbid) { - if (mappings != null) + for (StructureMapping sm : mappings) { - for (int i = 0; i < mappings.length; i++) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { - if (mappings[i].getPdbId().equals(pdbid)) - { - return mappings[i].pdbfile; - } + return sm.pdbfile; } } return null; } - /* - There will be better ways of doing this in the future, for now we'll use - the tried and tested MCview pdb mapping + /** + * Import structure data and register a structure mapping for broadcasting + * colouring, mouseovers and selection events (convenience wrapper). + * + * @param sequence + * - one or more sequences to be mapped to pdbFile + * @param targetChains + * - optional chain specification for mapping each sequence to pdb + * (may be nill, individual elements may be nill) + * @param pdbFile + * - structure data resource + * @param protocol + * - how to resolve data from resource + * @return null or the structure data parsed as a pdb file */ - synchronized public MCview.PDBfile setMapping( - SequenceI[] sequence, - String[] targetChains, - String pdbFile, - String protocol) + synchronized public StructureFile setMapping(SequenceI[] sequence, + String[] targetChains, String pdbFile, DataSourceType protocol, + IProgressIndicator progress) { - MCview.PDBfile pdb = null; + return computeMapping(true, sequence, targetChains, pdbFile, protocol, + progress); + } + + /** + * Import a single structure file and register sequence structure mappings for + * broadcasting colouring, mouseovers and selection events (convenience + * wrapper). + * + * @param forStructureView + * when true, record the mapping for use in mouseOvers + * @param sequence + * - one or more sequences to be mapped to pdbFile + * @param targetChains + * - optional chain specification for mapping each sequence to pdb + * (may be nill, individual elements may be nill) + * @param pdbFile + * - structure data resource + * @param protocol + * - how to resolve data from resource + * @return null or the structure data parsed as a pdb file + */ + synchronized public StructureFile setMapping(boolean forStructureView, + SequenceI[] sequenceArray, String[] targetChainIds, + String pdbFile, DataSourceType sourceType) + { + return computeMapping(forStructureView, sequenceArray, targetChainIds, + pdbFile, sourceType, null); + } + + /** + * create sequence structure mappings between each sequence and the given + * pdbFile (retrieved via the given protocol). Either constructs a mapping + * using NW alignment or derives one from any available SIFTS mapping data. + * + * @param forStructureView + * when true, record the mapping for use in mouseOvers + * + * @param sequenceArray + * - one or more sequences to be mapped to pdbFile + * @param targetChainIds + * - optional chain specification for mapping each sequence to pdb + * (may be nill, individual elements may be nill) - JBPNote: JAL-2693 + * - this should be List>, empty lists indicate no + * predefined mappings + * @param pdbFile + * - structure data resource + * @param sourceType + * - how to resolve data from resource + * @param IProgressIndicator + * reference to UI component that maintains a progress bar for the + * mapping operation + * @return null or the structure data parsed as a pdb file + */ + synchronized public StructureFile computeMapping( + boolean forStructureView, SequenceI[] sequenceArray, + String[] targetChainIds, String pdbFile, DataSourceType sourceType, + IProgressIndicator progress) + { + long progressSessionId = System.currentTimeMillis() * 3; + + /** + * do we extract and transfer annotation from 3D data ? + */ + // FIXME: possibly should just delete + + boolean parseSecStr = processSecondaryStructure + ? isStructureFileProcessed(pdbFile, sequenceArray) + : false; + + StructureFile pdb = null; + boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); try { - pdb = new MCview.PDBfile(pdbFile, protocol); - } - catch (Exception ex) + // FIXME if sourceType is not null, we've lost data here + sourceType = AppletFormatAdapter.checkProtocol(pdbFile); + pdb = new JmolParser(false, pdbFile, sourceType); + pdb.addSettings(parseSecStr && processSecondaryStructure, + parseSecStr && addTempFacAnnot, + parseSecStr && secStructServices); + pdb.doParse(); + if (pdb.getId() != null && pdb.getId().trim().length() > 0 + && DataSourceType.FILE == sourceType) + { + registerPDBFile(pdb.getId().trim(), pdbFile); + } + // if PDBId is unavailable then skip SIFTS mapping execution path + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + + } catch (Exception ex) { ex.printStackTrace(); return null; } + /* + * sifts client - non null if SIFTS mappings are to be used + */ + SiftsClient siftsClient = null; + try + { + if (isMapUsingSIFTs) + { + siftsClient = new SiftsClient(pdb); + } + } catch (SiftsException e) + { + isMapUsingSIFTs = false; + e.printStackTrace(); + siftsClient = null; + } - String targetChain; - for (int s = 0; s < sequence.length; s++) + String targetChainId; + for (int s = 0; s < sequenceArray.length; s++) { - if(targetChains!=null && targetChains[s]!=null) - targetChain = targetChains[s]; - else if (sequence[s].getName().indexOf("|") > -1) + boolean infChain = true; + final SequenceI seq = sequenceArray[s]; + SequenceI ds = seq; + while (ds.getDatasetSequence() != null) { - targetChain = sequence[s].getName().substring( - sequence[s].getName().lastIndexOf("|") + 1); + ds = ds.getDatasetSequence(); } - else - targetChain = ""; + if (targetChainIds != null && targetChainIds[s] != null) + { + infChain = false; + targetChainId = targetChainIds[s]; + } + else if (seq.getName().indexOf("|") > -1) + { + targetChainId = seq.getName() + .substring(seq.getName().lastIndexOf("|") + 1); + if (targetChainId.length() > 1) + { + if (targetChainId.trim().length() == 0) + { + targetChainId = " "; + } + else + { + // not a valid chain identifier + targetChainId = ""; + } + } + } + else + { + targetChainId = ""; + } - int max = -10; + /* + * Attempt pairwise alignment of the sequence with each chain in the PDB, + * and remember the highest scoring chain + */ + float max = -10; AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; - - for (int i = 0; i < pdb.chains.size(); i++) + boolean first = true; + for (PDBChain chain : pdb.getChains()) { - AlignSeq as = new AlignSeq(sequence[s], - ( (PDBChain) pdb.chains.elementAt(i)). - sequence, - AlignSeq.PEP); - as.calcScoreMatrix(); - as.traceAlignment(); - PDBChain chain = ( (PDBChain) pdb.chains.elementAt(i)); + if (targetChainId.length() > 0 && !targetChainId.equals(chain.id) + && !infChain) + { + continue; // don't try to map chains don't match. + } + // TODO: correctly determine sequence type for mixed na/peptide + // structures + final String type = chain.isNa ? AlignSeq.DNA : AlignSeq.PEP; + AlignSeq as = AlignSeq.doGlobalNWAlignment(seq, chain.sequence, + type); + // equivalent to: + // AlignSeq as = new AlignSeq(sequence[s], chain.sequence, type); + // as.calcScoreMatrix(); + // as.traceAlignment(); - if (as.maxscore > max - || (as.maxscore == max && chain.id.equals(targetChain))) + if (first || as.maxscore > max + || (as.maxscore == max && chain.id.equals(targetChainId))) { + first = false; maxChain = chain; max = as.maxscore; maxAlignseq = as; maxChainId = chain.id; } } + if (maxChain == null) + { + continue; + } - final StringBuffer mappingDetails = new StringBuffer(); - mappingDetails.append("\n\nPDB Sequence is :\nSequence = " + - maxChain.sequence.getSequenceAsString()); - mappingDetails.append("\nNo of residues = " + - maxChain.residues. - size() + - "\n\n"); - PrintStream ps = new PrintStream(System.out) + if (sourceType == DataSourceType.PASTE) { - public void print(String x) - { - mappingDetails.append(x); + pdbFile = "INLINE" + pdb.getId(); + } + + List seqToStrucMapping = new ArrayList<>(); + if (isMapUsingSIFTs && seq.isProtein()) + { + if (progress!=null) { + progress.setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_sifts"), + progressSessionId); } + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + if (targetChainId != null && !targetChainId.trim().isEmpty()) + { + StructureMapping siftsMapping; + try + { + siftsMapping = getStructureMapping(seq, pdbFile, targetChainId, + pdb, maxChain, sqmpping, maxAlignseq, siftsClient); + seqToStrucMapping.add(siftsMapping); + maxChain.makeExactMapping(siftsMapping, seq); + maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this + // "IEA:SIFTS" ? + maxChain.transferResidueAnnotation(siftsMapping, null); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); - public void println() + } catch (SiftsException e) + { + // fall back to NW alignment + System.err.println(e.getMessage()); + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + targetChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is + // this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } + } + else { - mappingDetails.append("\n"); + List foundSiftsMappings = new ArrayList<>(); + for (PDBChain chain : pdb.getChains()) + { + StructureMapping siftsMapping = null; + try + { + siftsMapping = getStructureMapping(seq, + pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq, + siftsClient); + foundSiftsMappings.add(siftsMapping); + chain.makeExactMapping(siftsMapping, seq); + chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this + // "IEA:SIFTS" ? + chain.transferResidueAnnotation(siftsMapping, null); + } catch (SiftsException e) + { + System.err.println(e.getMessage()); + } + catch (Exception e) + { + System.err + .println( + "Unexpected exception during SIFTS mapping - falling back to NW for this sequence/structure pair"); + System.err.println(e.getMessage()); + } + } + if (!foundSiftsMappings.isEmpty()) + { + seqToStrucMapping.addAll(foundSiftsMappings); + ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0)); + } + else + { + StructureMapping nwMapping = getNWMappings(seq, pdbFile, + maxChainId, maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this + // "IEA:Jalview" ? + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } } - }; - - maxAlignseq.printAlignment(ps); - - mappingDetails.append("\nPDB start/end " + maxAlignseq.seq2start + " " + - maxAlignseq.seq2end); - mappingDetails.append("\nSEQ start/end " - + (maxAlignseq.seq1start + sequence[s].getStart() - 1) + - " " - + (maxAlignseq.seq1end + sequence[s].getEnd() - 1)); - - maxChain.makeExactMapping(maxAlignseq, sequence[s]); - - maxChain.transferRESNUMFeatures(sequence[s], null); - - int[][] mapping = new int[sequence[s].getEnd() + 2][2]; - int resNum = -10000; - int index = 0; - + } + else + { + if (progress != null) + { + progress.setProgressBar(MessageManager + .getString("status.obtaining_mapping_with_nw_alignment"), + progressSessionId); + } + StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, + maxChain, pdb, maxAlignseq); + seqToStrucMapping.add(nwMapping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } + if (forStructureView) + { + for (StructureMapping sm : seqToStrucMapping) + { + addStructureMapping(sm); // not addAll! + } + } + if (progress != null) + { + progress.setProgressBar(null, progressSessionId); + } + } + return pdb; + } - do + /** + * check if we need to extract secondary structure from given pdbFile and + * transfer to sequences + * + * @param pdbFile + * @param sequenceArray + * @return + */ + private boolean isStructureFileProcessed(String pdbFile, + SequenceI[] sequenceArray) + { + boolean parseSecStr = true; + if (isPDBFileRegistered(pdbFile)) + { + for (SequenceI sq : sequenceArray) { - Atom tmp = (Atom) maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + SequenceI ds = sq; + while (ds.getDatasetSequence() != null) { - resNum = tmp.resNumber; - mapping[tmp.alignmentMapping+1][0] = tmp.resNumber; - mapping[tmp.alignmentMapping+1][1] = tmp.atomIndex; + ds = ds.getDatasetSequence(); } + ; + if (ds.getAnnotation() != null) + { + for (AlignmentAnnotation ala : ds.getAnnotation()) + { + // false if any annotation present from this structure + // JBPNote this fails for jmol/chimera view because the *file* is + // passed, not the structure data ID - + if (PDBfile.isCalcIdForFile(ala, findIdForPDBFile(pdbFile))) + { + parseSecStr = false; + } + } + } + } + } + return parseSecStr; + } - index++; + public void addStructureMapping(StructureMapping sm) + { + if (!mappings.contains(sm)) + { + mappings.add(sm); + } + } + + /** + * retrieve a mapping for seq from SIFTs using associated DBRefEntry for + * uniprot or PDB + * + * @param seq + * @param pdbFile + * @param targetChainId + * @param pdb + * @param maxChain + * @param sqmpping + * @param maxAlignseq + * @param siftsClient + * client for retrieval of SIFTS mappings for this structure + * @return + * @throws SiftsException + */ + private StructureMapping getStructureMapping(SequenceI seq, + String pdbFile, String targetChainId, StructureFile pdb, + PDBChain maxChain, jalview.datamodel.Mapping sqmpping, + AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException + { + StructureMapping curChainMapping = siftsClient + .getSiftsStructureMapping(seq, pdbFile, targetChainId); + try + { + PDBChain chain = pdb.findChain(targetChainId); + if (chain != null) + { + chain.transferResidueAnnotation(curChainMapping, null); } - while(index < maxChain.atoms.size()); + } catch (Exception e) + { + e.printStackTrace(); + } + return curChainMapping; + } - if (mappings == null) + private StructureMapping getNWMappings(SequenceI seq, String pdbFile, + String maxChainId, PDBChain maxChain, StructureFile pdb, + AlignSeq maxAlignseq) + { + final StringBuilder mappingDetails = new StringBuilder(128); + mappingDetails.append(NEWLINE) + .append("Sequence \u27f7 Structure mapping details"); + mappingDetails.append(NEWLINE); + mappingDetails + .append("Method: inferred with Needleman & Wunsch alignment"); + mappingDetails.append(NEWLINE).append("PDB Sequence is :") + .append(NEWLINE).append("Sequence = ") + .append(maxChain.sequence.getSequenceAsString()); + mappingDetails.append(NEWLINE).append("No of residues = ") + .append(maxChain.residues.size()).append(NEWLINE) + .append(NEWLINE); + PrintStream ps = new PrintStream(System.out) + { + @Override + public void print(String x) { - mappings = new StructureMapping[1]; + mappingDetails.append(x); } - else + + @Override + public void println() { - StructureMapping[] tmp = new StructureMapping[mappings.length + 1]; - System.arraycopy(mappings, 0, tmp, 0, mappings.length); - mappings = tmp; + mappingDetails.append(NEWLINE); } + }; - if(protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) - pdbFile = "INLINE"+pdb.id; + maxAlignseq.printAlignment(ps); - mappings[mappings.length - 1] - = new StructureMapping(sequence[s], pdbFile, pdb.id, maxChainId, - mapping, mappingDetails.toString()); - maxChain.transferResidueAnnotation(mappings[mappings.length-1]); - } - ///////// + mappingDetails.append(NEWLINE).append("PDB start/end "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2start)) + .append(" "); + mappingDetails.append(String.valueOf(maxAlignseq.seq2end)); + mappingDetails.append(NEWLINE).append("SEQ start/end "); + mappingDetails + .append(String + .valueOf(maxAlignseq.seq1start + (seq.getStart() - 1))) + .append(" "); + mappingDetails.append( + String.valueOf(maxAlignseq.seq1end + (seq.getStart() - 1))); + mappingDetails.append(NEWLINE); + maxChain.makeExactMapping(maxAlignseq, seq); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + maxChain.transferRESNUMFeatures(seq, null); - return pdb; + HashMap mapping = new HashMap<>(); + int resNum = -10000; + int index = 0; + char insCode = ' '; + + do + { + Atom tmp = maxChain.atoms.elementAt(index); + if ((resNum != tmp.resNumber || insCode != tmp.insCode) + && tmp.alignmentMapping != -1) + { + resNum = tmp.resNumber; + insCode = tmp.insCode; + if (tmp.alignmentMapping >= -1) + { + mapping.put(tmp.alignmentMapping + 1, + new int[] + { tmp.resNumber, tmp.atomIndex }); + } + } + + index++; + } while (index < maxChain.atoms.size()); + + StructureMapping nwMapping = new StructureMapping(seq, pdbFile, + pdb.getId(), maxChainId, mapping, mappingDetails.toString()); + maxChain.transferResidueAnnotation(nwMapping, sqmpping); + return nwMapping; } - public void removeStructureViewerListener(Object svl, String pdbfile) + public void removeStructureViewerListener(Object svl, String[] pdbfiles) { listeners.removeElement(svl); + if (svl instanceof SequenceListener) + { + for (int i = 0; i < listeners.size(); i++) + { + if (listeners.elementAt(i) instanceof StructureListener) + { + ((StructureListener) listeners.elementAt(i)) + .releaseReferences(svl); + } + } + } + + if (pdbfiles == null) + { + return; + } - boolean removeMapping = true; + /* + * Remove mappings to the closed listener's PDB files, but first check if + * another listener is still interested + */ + List pdbs = new ArrayList<>(Arrays.asList(pdbfiles)); StructureListener sl; for (int i = 0; i < listeners.size(); i++) @@ -213,148 +826,305 @@ public class StructureSelectionManager if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - if (sl.getPdbFile().equals(pdbfile)) + for (String pdbfile : sl.getStructureFiles()) { - removeMapping = false; - break; + pdbs.remove(pdbfile); } } } - if (removeMapping && mappings!=null) + /* + * Rebuild the mappings set, retaining only those which are for 'other' PDB + * files + */ + if (pdbs.size() > 0) { - Vector tmp = new Vector(); - for (int i = 0; i < mappings.length; i++) + List tmp = new ArrayList<>(); + for (StructureMapping sm : mappings) { - if (!mappings[i].pdbfile.equals(pdbfile)) + if (!pdbs.contains(sm.pdbfile)) { - tmp.addElement(mappings[i]); + tmp.add(sm); } } - mappings = new StructureMapping[tmp.size()]; - tmp.copyInto(mappings); + mappings = tmp; } } - public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) + /** + * Propagate mouseover of a single position in a structure + * + * @param pdbResNum + * @param chain + * @param pdbfile + */ + public void mouseOverStructure(int pdbResNum, String chain, + String pdbfile) + { + AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0); + List atoms = Collections.singletonList(atomSpec); + mouseOverStructure(atoms); + } + + /** + * Propagate mouseover or selection of multiple positions in a structure + * + * @param atoms + */ + public void mouseOverStructure(List atoms) { - SequenceListener sl; - SearchResults results = new SearchResults(); + if (listeners == null) + { + // old or prematurely sent event + return; + } + boolean hasSequenceListener = false; for (int i = 0; i < listeners.size(); i++) { if (listeners.elementAt(i) instanceof SequenceListener) { + hasSequenceListener = true; + } + } + if (!hasSequenceListener) + { + return; + } - for (int j = 0; j < mappings.length; j++) - { - if (mappings[j].pdbfile.equals(pdbfile) && - mappings[j].pdbchain.equals(chain)) - { - results.addResult(mappings[j].sequence, - mappings[j].getSeqPos(pdbResNum), - mappings[j].getSeqPos(pdbResNum) - ); - } - } - - if(results.getSize()>0) - { - ( (SequenceListener) listeners.elementAt(i)) - .highlightSequence(results); - } - + SearchResultsI results = findAlignmentPositionsForStructurePositions( + atoms); + for (Object li : listeners) + { + if (li instanceof SequenceListener) + { + ((SequenceListener) li).highlightSequence(results); } } } - public void mouseOverSequence(SequenceI seq, int index) + /** + * Constructs a SearchResults object holding regions (if any) in the Jalview + * alignment which have a mapping to the structure viewer positions in the + * supplied list + * + * @param atoms + * @return + */ + public SearchResultsI findAlignmentPositionsForStructurePositions( + List atoms) { - StructureListener sl; - int atomNo = 0; - for (int i = 0; i < listeners.size(); i++) + SearchResultsI results = new SearchResults(); + for (AtomSpec atom : atoms) { - if (listeners.elementAt(i) instanceof StructureListener) + SequenceI lastseq = null; + int lastipos = -1; + for (StructureMapping sm : mappings) { - sl = (StructureListener) listeners.elementAt(i); - - for (int j = 0; j < mappings.length; j++) + if (sm.pdbfile.equals(atom.getPdbFile()) + && sm.pdbchain.equals(atom.getChain())) { - if (mappings[j].sequence == seq) + int indexpos = sm.getSeqPos(atom.getPdbResNum()); + if (lastipos != indexpos || lastseq != sm.sequence) { - atomNo = mappings[j].getAtomNum(index); - - if (atomNo > 0) + results.addResult(sm.sequence, indexpos, indexpos); + lastipos = indexpos; + lastseq = sm.sequence; + // construct highlighted sequence list + for (AlignedCodonFrame acf : seqmappings) { - sl.highlightAtom(atomNo, - mappings[j].getPDBResNum(index), - mappings[j].pdbchain, - mappings[j].pdbfile); + acf.markMappedRegion(sm.sequence, indexpos, results); } } } } } + return results; } - public Annotation[] colourSequenceFromStructure(SequenceI seq, String pdbid) + /** + * highlight regions associated with a position (indexpos) in seq + * + * @param seq + * the sequence that the mouse over occurred on + * @param indexpos + * the absolute position being mouseovered in seq (0 to seq.length()) + * @param seqPos + * the sequence position (if -1, seq.findPosition is called to + * resolve the residue number) + */ + public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos, + VamsasSource source) { - return null; - //THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3, - //UNTIL THE COLOUR BY ANNOTATION IS REWORKED - /* Annotation [] annotations = new Annotation[seq.getLength()]; - - StructureListener sl; - int atomNo = 0; + boolean hasSequenceListeners = handlingVamsasMo + || !seqmappings.isEmpty(); + SearchResultsI results = null; + if (seqPos == -1) + { + seqPos = seq.findPosition(indexpos); + } for (int i = 0; i < listeners.size(); i++) { - if (listeners.elementAt(i) instanceof StructureListener) + Object listener = listeners.elementAt(i); + if (listener == source) { - sl = (StructureListener) listeners.elementAt(i); - - for (int j = 0; j < mappings.length; j++) + // TODO listener (e.g. SeqPanel) is never == source (AlignViewport) + // Temporary fudge with SequenceListener.getVamsasSource() + continue; + } + if (listener instanceof StructureListener) + { + highlightStructure((StructureListener) listener, seq, seqPos); + } + else + { + if (listener instanceof SequenceListener) { - - if (mappings[j].sequence == seq - && mappings[j].getPdbId().equals(pdbid) - && mappings[j].pdbfile.equals(sl.getPdbFile())) + final SequenceListener seqListener = (SequenceListener) listener; + if (hasSequenceListeners + && seqListener.getVamsasSource() != source) { - System.out.println(pdbid+" "+mappings[j].getPdbId() - +" "+mappings[j].pdbfile); - - java.awt.Color col; - for(int index=0; index 0) + if (results == null) { - col = sl.getColour(atomNo, - mappings[j].getPDBResNum(index), - mappings[j].pdbchain, - mappings[j].pdbfile); + results = MappingUtils.buildSearchResults(seq, seqPos, + seqmappings); } + if (handlingVamsasMo) + { + results.addResult(seq, seqPos, seqPos); - annotations[index] = new Annotation("X",null,' ',0,col); + } + if (!results.isEmpty()) + { + seqListener.highlightSequence(results); + } } - return annotations; } } + else if (listener instanceof VamsasListener && !handlingVamsasMo) + { + ((VamsasListener) listener).mouseOverSequence(seq, indexpos, + source); + } + else if (listener instanceof SecondaryStructureListener) + { + ((SecondaryStructureListener) listener).mouseOverSequence(seq, + indexpos, seqPos); + } } } + } + + /** + * Send suitable messages to a StructureListener to highlight atoms + * corresponding to the given sequence position(s) + * + * @param sl + * @param seq + * @param positions + */ + public void highlightStructure(StructureListener sl, SequenceI seq, + int... positions) + { + if (!sl.isListeningFor(seq)) + { + return; + } + int atomNo; + List atoms = new ArrayList<>(); + for (StructureMapping sm : mappings) + { + if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence() + || (sm.sequence.getDatasetSequence() != null && sm.sequence + .getDatasetSequence() == seq.getDatasetSequence())) + { + for (int index : positions) + { + atomNo = sm.getAtomNum(index); + + if (atomNo > 0) + { + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, + sm.getPDBResNum(index), atomNo)); + } + } + } + } + sl.highlightAtoms(atoms); + } + + /** + * true if a mouse over event from an external (ie Vamsas) source is being + * handled + */ + boolean handlingVamsasMo = false; + + long lastmsg = 0; - return annotations;*/ + /** + * as mouseOverSequence but only route event to SequenceListeners + * + * @param sequenceI + * @param position + * in an alignment sequence + */ + public void mouseOverVamsasSequence(SequenceI sequenceI, int position, + VamsasSource source) + { + handlingVamsasMo = true; + long msg = sequenceI.hashCode() * (1 + position); + if (lastmsg != msg) + { + lastmsg = msg; + mouseOverSequence(sequenceI, position, -1, source); + } + handlingVamsasMo = false; } + public Annotation[] colourSequenceFromStructure(SequenceI seq, + String pdbid) + { + return null; + // THIS WILL NOT BE AVAILABLE IN JALVIEW 2.3, + // UNTIL THE COLOUR BY ANNOTATION IS REWORKED + /* + * Annotation [] annotations = new Annotation[seq.getLength()]; + * + * StructureListener sl; int atomNo = 0; for (int i = 0; i < + * listeners.size(); i++) { if (listeners.elementAt(i) instanceof + * StructureListener) { sl = (StructureListener) listeners.elementAt(i); + * + * for (int j = 0; j < mappings.length; j++) { + * + * if (mappings[j].sequence == seq && mappings[j].getPdbId().equals(pdbid) + * && mappings[j].pdbfile.equals(sl.getPdbFile())) { + * System.out.println(pdbid+" "+mappings[j].getPdbId() +" + * "+mappings[j].pdbfile); + * + * java.awt.Color col; for(int index=0; index 0) { col = sl.getColour(atomNo, + * mappings[j].getPDBResNum(index), mappings[j].pdbchain, + * mappings[j].pdbfile); } + * + * annotations[index] = new Annotation("X",null,' ',0,col); } return + * annotations; } } } } + * + * return annotations; + */ + } public void structureSelectionChanged() - { } + { + } public void sequenceSelectionChanged() - { } + { + } public void sequenceColoursChanged(Object source) { @@ -371,35 +1141,292 @@ public class StructureSelectionManager public StructureMapping[] getMapping(String pdbfile) { - Vector tmp = new Vector(); - for (int i = 0; i < mappings.length; i++) + List tmp = new ArrayList<>(); + for (StructureMapping sm : mappings) { - if (mappings[i].pdbfile.equals(pdbfile)) + if (sm.pdbfile.equals(pdbfile)) { - tmp.addElement(mappings[i]); + tmp.add(sm); } } + return tmp.toArray(new StructureMapping[tmp.size()]); + } - StructureMapping[] ret = new StructureMapping[tmp.size()]; - for (int i = 0; i < tmp.size(); i++) + /** + * Returns a readable description of all mappings for the given pdbfile to any + * of the given sequences + * + * @param pdbfile + * @param seqs + * @return + */ + public String printMappings(String pdbfile, List seqs) + { + if (pdbfile == null || seqs == null || seqs.isEmpty()) { - ret[i] = (StructureMapping) tmp.elementAt(i); + return ""; } - return ret; + StringBuilder sb = new StringBuilder(64); + for (StructureMapping sm : mappings) + { + if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence)) + { + sb.append(sm.mappingDetails); + sb.append(NEWLINE); + // separator makes it easier to read multiple mappings + sb.append("====================="); + sb.append(NEWLINE); + } + } + sb.append(NEWLINE); + + return sb.toString(); } - public String printMapping(String pdbfile) + /** + * Remove the given mapping + * + * @param acf + */ + public void deregisterMapping(AlignedCodonFrame acf) { - StringBuffer sb = new StringBuffer(); - for (int i = 0; i < mappings.length; i++) + if (acf != null) { - if (mappings[i].pdbfile.equals(pdbfile)) + boolean removed = seqmappings.remove(acf); + if (removed && seqmappings.isEmpty()) + { // debug + System.out.println("All mappings removed"); + } + } + } + + /** + * Add each of the given codonFrames to the stored set, if not aready present. + * + * @param mappings + */ + public void registerMappings(List mappings) + { + if (mappings != null) + { + for (AlignedCodonFrame acf : mappings) { - sb.append(mappings[i].mappingDetails); + registerMapping(acf); } } + } - return sb.toString(); + /** + * Add the given mapping to the stored set, unless already stored. + */ + public void registerMapping(AlignedCodonFrame acf) + { + if (acf != null) + { + if (!seqmappings.contains(acf)) + { + seqmappings.add(acf); + } + } + } + + /** + * Resets this object to its initial state by removing all registered + * listeners, codon mappings, PDB file mappings + */ + public void resetAll() + { + if (mappings != null) + { + mappings.clear(); + } + if (seqmappings != null) + { + seqmappings.clear(); + } + if (sel_listeners != null) + { + sel_listeners.clear(); + } + if (listeners != null) + { + listeners.clear(); + } + if (commandListeners != null) + { + commandListeners.clear(); + } + if (view_listeners != null) + { + view_listeners.clear(); + } + if (pdbFileNameId != null) + { + pdbFileNameId.clear(); + } + if (pdbIdFileName != null) + { + pdbIdFileName.clear(); + } + } + + public void addSelectionListener(SelectionListener selecter) + { + if (!sel_listeners.contains(selecter)) + { + sel_listeners.add(selecter); + } + } + + public void removeSelectionListener(SelectionListener toremove) + { + if (sel_listeners.contains(toremove)) + { + sel_listeners.remove(toremove); + } } + + public synchronized void sendSelection( + jalview.datamodel.SequenceGroup selection, + jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) + { + for (SelectionListener slis : sel_listeners) + { + if (slis != source) + { + slis.selection(selection, colsel, hidden, source); + } + } + } + + Vector view_listeners = new Vector<>(); + + public synchronized void sendViewPosition( + jalview.api.AlignmentViewPanel source, int startRes, int endRes, + int startSeq, int endSeq) + { + + if (view_listeners != null && view_listeners.size() > 0) + { + Enumeration listeners = view_listeners + .elements(); + while (listeners.hasMoreElements()) + { + AlignmentViewPanelListener slis = listeners.nextElement(); + if (slis != source) + { + slis.viewPosition(startRes, endRes, startSeq, endSeq, source); + } + ; + } + } + } + + /** + * release all references associated with this manager provider + * + * @param jalviewLite + */ + public static void release(StructureSelectionManagerProvider jalviewLite) + { + // synchronized (instances) + { + if (instances == null) + { + return; + } + StructureSelectionManager mnger = (instances.get(jalviewLite)); + if (mnger != null) + { + instances.remove(jalviewLite); + try + { + mnger.finalize(); + } catch (Throwable x) + { + } + } + } + } + + public void registerPDBEntry(PDBEntry pdbentry) + { + if (pdbentry.getFile() != null + && pdbentry.getFile().trim().length() > 0) + { + registerPDBFile(pdbentry.getId(), pdbentry.getFile()); + } + } + + public void addCommandListener(CommandListener cl) + { + if (!commandListeners.contains(cl)) + { + commandListeners.add(cl); + } + } + + public boolean hasCommandListener(CommandListener cl) + { + return this.commandListeners.contains(cl); + } + + public boolean removeCommandListener(CommandListener l) + { + return commandListeners.remove(l); + } + + /** + * Forward a command to any command listeners (except for the command's + * source). + * + * @param command + * the command to be broadcast (in its form after being performed) + * @param undo + * if true, the command was being 'undone' + * @param source + */ + public void commandPerformed(CommandI command, boolean undo, + VamsasSource source) + { + for (CommandListener listener : commandListeners) + { + listener.mirrorCommand(command, undo, this, source); + } + } + + /** + * Returns a new CommandI representing the given command as mapped to the + * given sequences. If no mapping could be made, or the command is not of a + * mappable kind, returns null. + * + * @param command + * @param undo + * @param mapTo + * @param gapChar + * @return + */ + public CommandI mapCommand(CommandI command, boolean undo, + final AlignmentI mapTo, char gapChar) + { + if (command instanceof EditCommand) + { + return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo, + gapChar, seqmappings); + } + else if (command instanceof OrderCommand) + { + return MappingUtils.mapOrderCommand((OrderCommand) command, undo, + mapTo, seqmappings); + } + return null; + } + + public List getSequenceMappings() + { + return seqmappings; + } + }