X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=cd986c0550cecca569f19e213f22cd26e3aacbbc;hb=df0734bbe3c42eb4e1d2e6471040888c85801ba5;hp=0253a7edb39263c1a13303574c2189b9f5196425;hpb=43b415c68805f3dec44a6ddc666d52220483c120;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 0253a7e..cd986c0 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -20,23 +20,6 @@ */ package jalview.structure; -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.LinkedHashSet; -import java.util.List; -import java.util.Map; -import java.util.Set; -import java.util.Vector; - -import MCview.Atom; -import MCview.PDBChain; -import MCview.PDBfile; - import jalview.analysis.AlignSeq; import jalview.api.StructureSelectionManagerProvider; import jalview.commands.CommandI; @@ -46,12 +29,36 @@ 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 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 { @@ -59,7 +66,7 @@ public class StructureSelectionManager static IdentityHashMap instances; - private List mappings = new ArrayList(); + private List mappings = new ArrayList<>(); private boolean processSecondaryStructure = false; @@ -70,17 +77,11 @@ public class StructureSelectionManager /* * Set of any registered mappings between (dataset) sequences. */ - Set seqmappings = new LinkedHashSet(); + private List seqmappings = new ArrayList<>(); - /* - * Reference counters for the above mappings. Remove mappings when ref count - * goes to zero. - */ - Map seqMappingRefCounts = new HashMap(); + private List commandListeners = new ArrayList<>(); - private List commandListeners = new ArrayList(); - - private List sel_listeners = new ArrayList(); + private List sel_listeners = new ArrayList<>(); /** * @return true if will try to use external services for processing secondary @@ -154,8 +155,8 @@ public class StructureSelectionManager } else { - System.err.println("reportMapping: There are " + mappings.size() - + " mappings."); + System.err.println( + "reportMapping: There are " + mappings.size() + " mappings."); int i = 0; for (StructureMapping sm : mappings) { @@ -168,9 +169,9 @@ public class StructureSelectionManager * 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 pdbIdFileName = new HashMap<>(); - Map pdbFileNameId = new HashMap(); + Map pdbFileNameId = new HashMap<>(); public void registerPDBFile(String idForFile, String absoluteFile) { @@ -207,9 +208,8 @@ public class StructureSelectionManager { if (instances != null) { - throw new Error( - MessageManager - .getString("error.implementation_error_structure_selection_manager_null"), + throw new Error(MessageManager.getString( + "error.implementation_error_structure_selection_manager_null"), new NullPointerException(MessageManager .getString("exception.ssm_context_is_null"))); } @@ -222,7 +222,7 @@ public class StructureSelectionManager } if (instances == null) { - instances = new java.util.IdentityHashMap(); + instances = new java.util.IdentityHashMap<>(); } StructureSelectionManager instance = instances.get(context); if (instance == null) @@ -285,7 +285,8 @@ public class StructureSelectionManager } /** - * Returns the file name for a mapped PDB id (or null if not mapped). + * Returns the filename the PDB id is already mapped to if known, or null if + * it is not mapped * * @param pdbid * @return @@ -294,7 +295,7 @@ public class StructureSelectionManager { for (StructureMapping sm : mappings) { - if (sm.getPdbId().equals(pdbid)) + if (sm.getPdbId().equalsIgnoreCase(pdbid)) { return sm.pdbfile; } @@ -317,19 +318,21 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public PDBfile setMapping(SequenceI[] sequence, - String[] targetChains, String pdbFile, String protocol) + synchronized public StructureFile setMapping(SequenceI[] sequence, + String[] targetChains, String pdbFile, DataSourceType protocol, + IProgressIndicator progress) { - return setMapping(true, sequence, targetChains, pdbFile, protocol); + return computeMapping(true, sequence, targetChains, pdbFile, protocol, + progress); } /** - * create sequence structure mappings between each sequence and the given - * pdbFile (retrieved via the given protocol). + * 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 @@ -341,100 +344,145 @@ public class StructureSelectionManager * - how to resolve data from resource * @return null or the structure data parsed as a pdb file */ - synchronized public PDBfile setMapping(boolean forStructureView, - SequenceI[] sequence, String[] targetChains, String pdbFile, - String protocol) + synchronized public StructureFile setMapping(boolean forStructureView, + SequenceI[] sequenceArray, String[] targetChainIds, + String pdbFile, DataSourceType sourceType) { - /* - * There will be better ways of doing this in the future, for now we'll use - * the tried and tested MCview pdb mapping + 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 ? */ - boolean parseSecStr = processSecondaryStructure; - if (isPDBFileRegistered(pdbFile)) + // FIXME: possibly should just delete + + boolean parseSecStr = processSecondaryStructure + ? isStructureFileProcessed(pdbFile, sequenceArray) + : false; + + StructureFile pdb = null; + boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts(); + try { - for (SequenceI sq : sequence) + // 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) { - SequenceI ds = sq; - while (ds.getDatasetSequence() != null) - { - 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; - } - } - } + 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; } - PDBfile pdb = null; + /* + * sifts client - non null if SIFTS mappings are to be used + */ + SiftsClient siftsClient = null; try { - pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices, - pdbFile, protocol); - if (pdb.id != null && pdb.id.trim().length() > 0 - && AppletFormatAdapter.FILE.equals(protocol)) + if (isMapUsingSIFTs) { - registerPDBFile(pdb.id.trim(), pdbFile); + siftsClient = new SiftsClient(pdb); } - } catch (Exception ex) + } catch (SiftsException e) { - ex.printStackTrace(); - return null; + 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++) { boolean infChain = true; - final SequenceI seq = sequence[s]; - if (targetChains != null && targetChains[s] != null) + final SequenceI seq = sequenceArray[s]; + SequenceI ds = seq; + while (ds.getDatasetSequence() != null) + { + ds = ds.getDatasetSequence(); + } + + if (targetChainIds != null && targetChainIds[s] != null) { infChain = false; - targetChain = targetChains[s]; + targetChainId = targetChainIds[s]; } else if (seq.getName().indexOf("|") > -1) { - targetChain = seq.getName().substring( - seq.getName().lastIndexOf("|") + 1); - if (targetChain.length() > 1) + targetChainId = seq.getName() + .substring(seq.getName().lastIndexOf("|") + 1); + if (targetChainId.length() > 1) { - if (targetChain.trim().length() == 0) + if (targetChainId.trim().length() == 0) { - targetChain = " "; + targetChainId = " "; } else { // not a valid chain identifier - targetChain = ""; + targetChainId = ""; } } } else { - targetChain = ""; + targetChainId = ""; } /* * Attempt pairwise alignment of the sequence with each chain in the PDB, * and remember the highest scoring chain */ - int max = -10; + float max = -10; AlignSeq maxAlignseq = null; String maxChainId = " "; PDBChain maxChain = null; boolean first = true; - for (PDBChain chain : pdb.chains) + for (PDBChain chain : pdb.getChains()) { - if (targetChain.length() > 0 && !targetChain.equals(chain.id) + if (targetChainId.length() > 0 && !targetChainId.equals(chain.id) && !infChain) { continue; // don't try to map chains don't match. @@ -450,7 +498,7 @@ public class StructureSelectionManager // as.traceAlignment(); if (first || as.maxscore > max - || (as.maxscore == max && chain.id.equals(targetChain))) + || (as.maxscore == max && chain.id.equals(targetChainId))) { first = false; maxChain = chain; @@ -463,83 +511,287 @@ public class StructureSelectionManager { continue; } - final StringBuilder mappingDetails = new StringBuilder(128); - 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) + + if (sourceType == DataSourceType.PASTE) { - @Override - public void print(String 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()) { - mappingDetails.append(x); + 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)); + + } 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)); + } } - - @Override - public void println() + else { - mappingDetails.append(NEWLINE); + 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(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.getEnd() - 1)); - - maxChain.makeExactMapping(maxAlignseq, seq); - jalview.datamodel.Mapping sqmpping = maxAlignseq - .getMappingFromS1(false); - jalview.datamodel.Mapping omap = new jalview.datamodel.Mapping( - sqmpping.getMap().getInverse()); - maxChain.transferRESNUMFeatures(seq, null); - - // allocate enough slots to store the mapping from positions in - // sequence[s] to the associated chain - int[][] mapping = new int[seq.findPosition(seq.getLength()) + 2][2]; - int resNum = -10000; - int index = 0; - - do + } + else { - Atom tmp = maxChain.atoms.elementAt(index); - if (resNum != tmp.resNumber && tmp.alignmentMapping != -1) + if (progress != null) { - resNum = tmp.resNumber; - mapping[tmp.alignmentMapping + 1][0] = tmp.resNumber; - mapping[tmp.alignmentMapping + 1][1] = tmp.atomIndex; + 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; + } - index++; - } while (index < maxChain.atoms.size()); - - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + /** + * 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) { - pdbFile = "INLINE" + pdb.id; + SequenceI ds = sq; + while (ds.getDatasetSequence() != null) + { + 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; + } + } + } } - StructureMapping newMapping = new StructureMapping(seq, pdbFile, - pdb.id, maxChainId, mapping, mappingDetails.toString()); - if (forStructureView) + } + return parseSecStr; + } + + 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) { - mappings.add(newMapping); + chain.transferResidueAnnotation(curChainMapping, null); } - maxChain.transferResidueAnnotation(newMapping, sqmpping); + } catch (Exception e) + { + e.printStackTrace(); } - // /////// + return curChainMapping; + } - return pdb; + 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) + { + mappingDetails.append(x); + } + + @Override + public void println() + { + mappingDetails.append(NEWLINE); + } + }; + + maxAlignseq.printAlignment(ps); + + 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); + + 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[] pdbfiles) @@ -566,7 +818,7 @@ public class StructureSelectionManager * 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)); + List pdbs = new ArrayList<>(Arrays.asList(pdbfiles)); StructureListener sl; for (int i = 0; i < listeners.size(); i++) @@ -574,7 +826,7 @@ public class StructureSelectionManager if (listeners.elementAt(i) instanceof StructureListener) { sl = (StructureListener) listeners.elementAt(i); - for (String pdbfile : sl.getPdbFile()) + for (String pdbfile : sl.getStructureFiles()) { pdbs.remove(pdbfile); } @@ -587,7 +839,7 @@ public class StructureSelectionManager */ if (pdbs.size() > 0) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (StructureMapping sm : mappings) { if (!pdbs.contains(sm.pdbfile)) @@ -607,7 +859,8 @@ public class StructureSelectionManager * @param chain * @param pdbfile */ - public void mouseOverStructure(int pdbResNum, String chain, String pdbfile) + public void mouseOverStructure(int pdbResNum, String chain, + String pdbfile) { AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0); List atoms = Collections.singletonList(atomSpec); @@ -639,7 +892,29 @@ public class StructureSelectionManager return; } - SearchResults results = new SearchResults(); + SearchResultsI results = findAlignmentPositionsForStructurePositions( + atoms); + for (Object li : listeners) + { + if (li instanceof SequenceListener) + { + ((SequenceListener) li).highlightSequence(results); + } + } + } + + /** + * 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) + { + SearchResultsI results = new SearchResults(); for (AtomSpec atom : atoms) { SequenceI lastseq = null; @@ -650,7 +925,7 @@ public class StructureSelectionManager && sm.pdbchain.equals(atom.getChain())) { int indexpos = sm.getSeqPos(atom.getPdbResNum()); - if (lastipos != indexpos && lastseq != sm.sequence) + if (lastipos != indexpos || lastseq != sm.sequence) { results.addResult(sm.sequence, indexpos, indexpos); lastipos = indexpos; @@ -664,13 +939,7 @@ public class StructureSelectionManager } } } - for (Object li : listeners) - { - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } - } + return results; } /** @@ -680,19 +949,19 @@ public class StructureSelectionManager * the sequence that the mouse over occurred on * @param indexpos * the absolute position being mouseovered in seq (0 to seq.length()) - * @param index + * @param seqPos * the sequence position (if -1, seq.findPosition is called to * resolve the residue number) */ - public void mouseOverSequence(SequenceI seq, int indexpos, int index, + public void mouseOverSequence(SequenceI seq, int indexpos, int seqPos, VamsasSource source) { boolean hasSequenceListeners = handlingVamsasMo || !seqmappings.isEmpty(); - SearchResults results = null; - if (index == -1) + SearchResultsI results = null; + if (seqPos == -1) { - index = seq.findPosition(indexpos); + seqPos = seq.findPosition(indexpos); } for (int i = 0; i < listeners.size(); i++) { @@ -705,7 +974,7 @@ public class StructureSelectionManager } if (listener instanceof StructureListener) { - highlightStructure((StructureListener) listener, seq, index); + highlightStructure((StructureListener) listener, seq, seqPos); } else { @@ -719,15 +988,18 @@ public class StructureSelectionManager { if (results == null) { - results = MappingUtils.buildSearchResults(seq, index, + results = MappingUtils.buildSearchResults(seq, seqPos, seqmappings); } if (handlingVamsasMo) { - results.addResult(seq, index, index); + results.addResult(seq, seqPos, seqPos); } - seqListener.highlightSequence(results); + if (!results.isEmpty()) + { + seqListener.highlightSequence(results); + } } } } @@ -739,7 +1011,7 @@ public class StructureSelectionManager else if (listener instanceof SecondaryStructureListener) { ((SecondaryStructureListener) listener).mouseOverSequence(seq, - indexpos); + indexpos, seqPos); } } } @@ -747,31 +1019,36 @@ public class StructureSelectionManager /** * Send suitable messages to a StructureListener to highlight atoms - * corresponding to the given sequence position. + * corresponding to the given sequence position(s) * * @param sl * @param seq - * @param index + * @param positions */ - protected void highlightStructure(StructureListener sl, SequenceI seq, - int index) + public void highlightStructure(StructureListener sl, SequenceI seq, + int... positions) { if (!sl.isListeningFor(seq)) { return; } int atomNo; - List atoms = new ArrayList(); + List atoms = new ArrayList<>(); for (StructureMapping sm : mappings) { - if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence()) + if (sm.sequence == seq || sm.sequence == seq.getDatasetSequence() + || (sm.sequence.getDatasetSequence() != null && sm.sequence + .getDatasetSequence() == seq.getDatasetSequence())) { - atomNo = sm.getAtomNum(index); - - if (atomNo > 0) + for (int index : positions) { - atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, sm - .getPDBResNum(index), atomNo)); + atomNo = sm.getAtomNum(index); + + if (atomNo > 0) + { + atoms.add(new AtomSpec(sm.pdbfile, sm.pdbchain, + sm.getPDBResNum(index), atomNo)); + } } } } @@ -864,7 +1141,7 @@ public class StructureSelectionManager public StructureMapping[] getMapping(String pdbfile) { - List tmp = new ArrayList(); + List tmp = new ArrayList<>(); for (StructureMapping sm : mappings) { if (sm.pdbfile.equals(pdbfile)) @@ -908,80 +1185,89 @@ public class StructureSelectionManager } /** - * Decrement the reference counter for each of the given mappings, and remove - * it entirely if its reference counter reduces to zero. + * Remove the given mapping * - * @param set + * @param acf */ - public void removeMappings(Set set) + public void deregisterMapping(AlignedCodonFrame acf) { - if (set != null) + if (acf != null) { - for (AlignedCodonFrame acf : set) - { - removeMapping(acf); + boolean removed = seqmappings.remove(acf); + if (removed && seqmappings.isEmpty()) + { // debug + System.out.println("All mappings removed"); } } } /** - * Decrement the reference counter for the given mapping, and remove it - * entirely if its reference counter reduces to zero. + * Add each of the given codonFrames to the stored set, if not aready present. * - * @param acf + * @param mappings */ - public void removeMapping(AlignedCodonFrame acf) + public void registerMappings(List mappings) { - if (acf != null && seqmappings.contains(acf)) + if (mappings != null) { - int count = seqMappingRefCounts.get(acf); - count--; - if (count > 0) + for (AlignedCodonFrame acf : mappings) { - seqMappingRefCounts.put(acf, count); - } - else - { - seqmappings.remove(acf); - seqMappingRefCounts.remove(acf); + registerMapping(acf); } } } /** - * Add each of the given codonFrames to the stored set. If not aready present, - * increments its reference count instead. - * - * @param set + * Add the given mapping to the stored set, unless already stored. */ - public void addMappings(Set set) + public void registerMapping(AlignedCodonFrame acf) { - if (set != null) + if (acf != null) { - for (AlignedCodonFrame acf : set) + if (!seqmappings.contains(acf)) { - addMapping(acf); + seqmappings.add(acf); } } } /** - * Add the given mapping to the stored set, or if already stored, increment - * its reference counter. + * Resets this object to its initial state by removing all registered + * listeners, codon mappings, PDB file mappings */ - public void addMapping(AlignedCodonFrame acf) + public void resetAll() { - if (acf != null) + if (mappings != null) { - if (seqmappings.contains(acf)) - { - seqMappingRefCounts.put(acf, seqMappingRefCounts.get(acf) + 1); - } - else - { - seqmappings.add(acf); - seqMappingRefCounts.put(acf, 1); - } + 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(); } } @@ -1003,18 +1289,19 @@ public class StructureSelectionManager public synchronized void sendSelection( jalview.datamodel.SequenceGroup selection, - jalview.datamodel.ColumnSelection colsel, SelectionSource source) + jalview.datamodel.ColumnSelection colsel, HiddenColumns hidden, + SelectionSource source) { for (SelectionListener slis : sel_listeners) { if (slis != source) { - slis.selection(selection, colsel, source); + slis.selection(selection, colsel, hidden, source); } } } - Vector view_listeners = new Vector(); + Vector view_listeners = new Vector<>(); public synchronized void sendViewPosition( jalview.api.AlignmentViewPanel source, int startRes, int endRes, @@ -1126,8 +1413,8 @@ public class StructureSelectionManager { if (command instanceof EditCommand) { - return MappingUtils.mapEditCommand((EditCommand) command, undo, - mapTo, gapChar, seqmappings); + return MappingUtils.mapEditCommand((EditCommand) command, undo, mapTo, + gapChar, seqmappings); } else if (command instanceof OrderCommand) { @@ -1136,4 +1423,10 @@ public class StructureSelectionManager } return null; } + + public List getSequenceMappings() + { + return seqmappings; + } + }