X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureSelectionManager.java;h=59f37d9fdd1c98b068d51f31d8d55ab88d35cc6b;hb=8feb5f87bd94e5d49c9dbc5fd7ec7e866ef80e9d;hp=612b168b5de52e09ab73d8ec8e5ce08682463229;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 612b168..59f37d9 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -31,13 +31,15 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; 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.phyre2.Phyre2Client; import jalview.ws.sifts.SiftsClient; import jalview.ws.sifts.SiftsException; import jalview.ws.sifts.SiftsSettings; @@ -48,6 +50,7 @@ import java.util.Arrays; import java.util.Collections; import java.util.Enumeration; import java.util.HashMap; +import java.util.Hashtable; import java.util.IdentityHashMap; import java.util.List; import java.util.Map; @@ -77,6 +80,7 @@ public class StructureSelectionManager private long progressSessionId; + /* * Set of any registered mappings between (dataset) sequences. */ @@ -86,6 +90,8 @@ public class StructureSelectionManager private List sel_listeners = new ArrayList(); + private Map phyre2ModelTemplates = new Hashtable(); + /** * @return true if will try to use external services for processing secondary * structure @@ -322,11 +328,14 @@ public class StructureSelectionManager * @return null or the structure data parsed as a pdb file */ synchronized public StructureFile setMapping(SequenceI[] sequence, - String[] targetChains, String pdbFile, String protocol) + 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). @@ -338,7 +347,7 @@ public class StructureSelectionManager * - 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) + * (may be null, individual elements may be null) * @param pdbFile * - structure data resource * @param protocol @@ -347,8 +356,18 @@ public class StructureSelectionManager */ synchronized public StructureFile setMapping(boolean forStructureView, SequenceI[] sequenceArray, String[] targetChainIds, - String pdbFile, String protocol) + String pdbFile, DataSourceType protocol) { + return computeMapping(forStructureView, sequenceArray, targetChainIds, + pdbFile, protocol, null); + } + + synchronized public StructureFile computeMapping( + boolean forStructureView, SequenceI[] sequenceArray, + String[] targetChainIds, String pdbFile, DataSourceType protocol, + IProgressIndicator progress) + { + long progressSessionId = System.currentTimeMillis() * 3; /* * There will be better ways of doing this in the future, for now we'll use * the tried and tested MCview pdb mapping @@ -386,10 +405,13 @@ public class StructureSelectionManager pdb = new JmolParser(pdbFile, protocol); if (pdb.getId() != null && pdb.getId().trim().length() > 0 - && AppletFormatAdapter.FILE.equals(protocol)) + && DataSourceType.FILE == protocol) { registerPDBFile(pdb.getId().trim(), pdbFile); } + // if PDBId is unavailable then skip SIFTS mapping execution path + isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable(); + } catch (Exception ex) { ex.printStackTrace(); @@ -432,7 +454,7 @@ public class StructureSelectionManager { if (targetChainId.trim().length() == 0) { - targetChainId = " "; + targetChainId = StructureMapping.NO_CHAIN; } else { @@ -452,7 +474,7 @@ public class StructureSelectionManager */ int max = -10; AlignSeq maxAlignseq = null; - String maxChainId = " "; + String maxChainId = StructureMapping.NO_CHAIN; // space PDBChain maxChain = null; boolean first = true; for (PDBChain chain : pdb.getChains()) @@ -487,17 +509,19 @@ public class StructureSelectionManager continue; } - if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE)) + if (protocol.equals(DataSourceType.PASTE)) { pdbFile = "INLINE" + pdb.getId(); } - - ArrayList seqToStrucMapping = new ArrayList(); - if (isMapUsingSIFTs && seq.isProtein()) + boolean phyre2Template = isPhyre2Template(pdbFile); + List seqToStrucMapping = new ArrayList(); + if (!phyre2Template && isMapUsingSIFTs && seq.isProtein()) { - setProgressBar(null); - setProgressBar(MessageManager - .getString("status.obtaining_mapping_with_sifts")); + 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()) @@ -526,11 +550,14 @@ public class StructureSelectionManager // "IEA:Jalview" ? maxChain.transferResidueAnnotation(nwMapping, sqmpping); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + } catch (Exception e) + { + e.printStackTrace(); } } else { - ArrayList foundSiftsMappings = new ArrayList(); + List foundSiftsMappings = new ArrayList(); for (PDBChain chain : pdb.getChains()) { try @@ -541,6 +568,9 @@ public class StructureSelectionManager } catch (SiftsException e) { System.err.println(e.getMessage()); + } catch (Exception e) + { + e.printStackTrace(); } } if (!foundSiftsMappings.isEmpty()) @@ -565,11 +595,31 @@ public class StructureSelectionManager } } } - else + else if (phyre2Template) { setProgressBar(null); setProgressBar(MessageManager - .getString("status.obtaining_mapping_with_nw_alignment")); + .getString("status.obtaining_mapping_with_phyre2_template_alignment")); + String fastaFile = getPhyre2FastaFileFor(pdbFile); + StructureMapping phyre2ModelMapping = new Phyre2Client(pdb) + .getStructureMapping(seq, pdbFile, fastaFile, + StructureMapping.NO_CHAIN); + seqToStrucMapping.add(phyre2ModelMapping); + maxChain.makeExactMapping(maxAlignseq, seq); + maxChain.transferRESNUMFeatures(seq, null); + jalview.datamodel.Mapping sqmpping = maxAlignseq + .getMappingFromS1(false); + maxChain.transferResidueAnnotation(phyre2ModelMapping, sqmpping); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(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); @@ -585,11 +635,10 @@ public class StructureSelectionManager return pdb; } - private boolean isCIFFile(String filename) + public void registerPhyre2Template(String phyre2Template, + String fastaMappingFile) { - String fileExt = filename.substring(filename.lastIndexOf(".") + 1, - filename.length()); - return "cif".equalsIgnoreCase(fileExt); + phyre2ModelTemplates.put(phyre2Template, fastaMappingFile); } /** @@ -609,10 +658,10 @@ public class StructureSelectionManager private StructureMapping getStructureMapping(SequenceI seq, String pdbFile, String targetChainId, StructureFile pdb, PDBChain maxChain, jalview.datamodel.Mapping sqmpping, - AlignSeq maxAlignseq) throws SiftsException + AlignSeq maxAlignseq) throws Exception { StructureMapping curChainMapping = siftsClient - .getSiftsStructureMapping(seq, pdbFile, targetChainId); + .getStructureMapping(seq, pdbFile, targetChainId); try { PDBChain chain = pdb.findChain(targetChainId); @@ -737,7 +786,7 @@ 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); } @@ -802,7 +851,28 @@ 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; @@ -813,7 +883,7 @@ 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; @@ -827,13 +897,7 @@ public class StructureSelectionManager } } } - for (Object li : listeners) - { - if (li instanceof SequenceListener) - { - ((SequenceListener) li).highlightSequence(results); - } - } + return results; } /** @@ -852,7 +916,7 @@ public class StructureSelectionManager { boolean hasSequenceListeners = handlingVamsasMo || !seqmappings.isEmpty(); - SearchResults results = null; + SearchResultsI results = null; if (seqPos == -1) { seqPos = seq.findPosition(indexpos); @@ -1352,4 +1416,31 @@ public class StructureSelectionManager return seqmappings; } + public boolean isPhyre2Template(String structureFile) + { + if (structureFile == null || phyre2ModelTemplates == null + || phyre2ModelTemplates.isEmpty()) + { + return false; + } + return phyre2ModelTemplates.get(structureFile) != null + && !phyre2ModelTemplates.get(structureFile).isEmpty(); + } + + public String getPhyre2FastaFileFor(String structureFile) + { + return phyre2ModelTemplates.get(structureFile); + } + + + public static StructureSelectionManager getStructureSelectionManager() + { + return instances.values().iterator().next(); + } + + public void addStructureMapping(StructureMapping smapping) + { + mappings.add(smapping); + } + }