+++ /dev/null
-/*
- * 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.
- *
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.structure;
-
-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.PDBEntry;
-import jalview.datamodel.SearchResults;
-import jalview.datamodel.SequenceI;
-import jalview.gui.IProgressIndicator;
-import jalview.io.AppletFormatAdapter;
-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
-{
- public final static String NEWLINE = System.lineSeparator();
-
- static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
-
- private List<StructureMapping> mappings = new ArrayList<StructureMapping>();
-
- private boolean processSecondaryStructure = false;
-
- private boolean secStructServices = false;
-
- private boolean addTempFacAnnot = false;
-
- private SiftsClient siftsClient = null;
-
- /*
- * Set of any registered mappings between (dataset) sequences.
- */
- private List<AlignedCodonFrame> seqmappings = new ArrayList<AlignedCodonFrame>();
-
- private List<CommandListener> commandListeners = new ArrayList<CommandListener>();
-
- private List<SelectionListener> sel_listeners = new ArrayList<SelectionListener>();
-
- /**
- * @return true if will try to use external services for processing secondary
- * structure
- */
- public boolean isSecStructServices()
- {
- 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())
- {
- 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<String, String> pdbIdFileName = new HashMap<String, String>();
-
- Map<String, String> pdbFileNameId = new HashMap<String, String>();
-
- 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<StructureSelectionManagerProvider, StructureSelectionManager>();
- }
- 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))
- {
- listeners.addElement(svl);
- }
- }
-
- /**
- * Returns the file name for a mapped PDB id (or null if not mapped).
- *
- * @param pdbid
- * @return
- */
- public String alreadyMappedToFile(String pdbid)
- {
- for (StructureMapping sm : mappings)
- {
- if (sm.getPdbId().equals(pdbid))
- {
- return sm.pdbfile;
- }
- }
- return null;
- }
-
- /**
- * 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 StructureFile setMapping(SequenceI[] sequence,
- String[] targetChains, String pdbFile, String protocol,
- IProgressIndicator progress)
- {
- return computeMapping(true, sequence, targetChains, pdbFile, protocol,
- progress);
- }
-
-
- /**
- * create sequence structure mappings between each sequence and the given
- * pdbFile (retrieved via the given protocol).
- *
- * @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 null, individual elements may be null)
- * @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,
- String protocol)
- {
- return computeMapping(forStructureView, sequenceArray, targetChainIds,
- pdbFile, protocol, null);
- }
-
- synchronized public StructureFile computeMapping(
- boolean forStructureView, SequenceI[] sequenceArray,
- String[] targetChainIds, String pdbFile, String 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
- */
- boolean parseSecStr = processSecondaryStructure;
- if (isPDBFileRegistered(pdbFile))
- {
- for (SequenceI sq : sequenceArray)
- {
- 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;
- }
- }
- }
- }
- }
- StructureFile pdb = null;
- boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
- try
- {
-
- if (pdbFile != null && isCIFFile(pdbFile))
- {
- pdb = new jalview.ext.jmol.JmolParser(addTempFacAnnot, parseSecStr,
- secStructServices, pdbFile, protocol);
- }
- else
- {
- pdb = new PDBfile(addTempFacAnnot, parseSecStr, secStructServices,
- pdbFile, protocol);
- }
-
- if (pdb.getId() != null && pdb.getId().trim().length() > 0
- && AppletFormatAdapter.FILE.equals(protocol))
- {
- registerPDBFile(pdb.getId().trim(), pdbFile);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- return null;
- }
-
- try
- {
- if (isMapUsingSIFTs)
- {
- siftsClient = new SiftsClient(pdb);
- }
- } catch (SiftsException e)
- {
- isMapUsingSIFTs = false;
- e.printStackTrace();
- }
-
- String targetChainId;
- for (int s = 0; s < sequenceArray.length; s++)
- {
- boolean infChain = true;
- final SequenceI seq = sequenceArray[s];
- 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 = "";
- }
-
- /*
- * Attempt pairwise alignment of the sequence with each chain in the PDB,
- * and remember the highest scoring chain
- */
- int max = -10;
- AlignSeq maxAlignseq = null;
- String maxChainId = " ";
- PDBChain maxChain = null;
- boolean first = true;
- for (PDBChain chain : pdb.getChains())
- {
- 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 (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;
- }
-
- if (protocol.equals(jalview.io.AppletFormatAdapter.PASTE))
- {
- pdbFile = "INLINE" + pdb.getId();
- }
- ArrayList<StructureMapping> seqToStrucMapping = new ArrayList<StructureMapping>();
- if (isMapUsingSIFTs)
- {
-<<<<<<< Updated upstream
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_sifts"));
-=======
- if (progress!=null) {
- progress.setProgressBar("Obtaining mapping with SIFTS",
- progressSessionId);
- }
->>>>>>> Stashed changes
- 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);
- seqToStrucMapping.add(siftsMapping);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
- maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
- } 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);
- }
- }
- else
- {
- ArrayList<StructureMapping> foundSiftsMappings = new ArrayList<StructureMapping>();
- for (PDBChain chain : pdb.getChains())
- {
- try
- {
- StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile,
- chain.id, pdb, chain, sqmpping, maxAlignseq);
- foundSiftsMappings.add(siftsMapping);
- } catch (SiftsException e)
- {
- System.err.println(e.getMessage());
- }
- }
- if (!foundSiftsMappings.isEmpty())
- {
- seqToStrucMapping.addAll(foundSiftsMappings);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);
- maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
- sqmpping);
- }
- else
- {
- StructureMapping nwMapping = getNWMappings(seq, pdbFile,
- maxChainId, maxChain, pdb, maxAlignseq);
- seqToStrucMapping.add(nwMapping);
- }
- }
- }
- else
- {
-<<<<<<< Updated upstream
- setProgressBar(null);
- setProgressBar(MessageManager
- .getString("status.obtaining_mapping_with_nw_alignment"));
-=======
- if (progress != null)
- {
- progress.setProgressBar("Obtaining mapping with NW alignment",
- progressSessionId);
- }
->>>>>>> Stashed changes
- seqToStrucMapping.add(getNWMappings(seq, pdbFile, maxChainId,
- maxChain, pdb, maxAlignseq));
- }
- if (forStructureView)
- {
- mappings.addAll(seqToStrucMapping);
- }
- if (progress != null)
- {
- progress.setProgressBar(null, progressSessionId);
- }
- }
- return pdb;
- }
-
- private boolean isCIFFile(String filename)
- {
- String fileExt = filename.substring(filename.lastIndexOf(".") + 1,
- filename.length());
- return "cif".equalsIgnoreCase(fileExt);
- }
-
- private StructureMapping getStructureMapping(SequenceI seq,
- String pdbFile, String targetChainId, StructureFile pdb,
- PDBChain maxChain, jalview.datamodel.Mapping sqmpping,
- AlignSeq maxAlignseq) throws SiftsException
- {
- StructureMapping curChainMapping = siftsClient
- .getSiftsStructureMapping(seq, pdbFile, targetChainId);
- try
- {
- PDBChain chain = pdb.findChain(targetChainId);
- if (chain != null)
- {
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
- }
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- return curChainMapping;
- }
-
- 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<Integer, int[]> mapping = new HashMap<Integer, int[]>();
- 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)
- {
- 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;
- }
-
- /*
- * Remove mappings to the closed listener's PDB files, but first check if
- * another listener is still interested
- */
- List<String> pdbs = new ArrayList<String>(Arrays.asList(pdbfiles));
-
- StructureListener sl;
- for (int i = 0; i < listeners.size(); i++)
- {
- if (listeners.elementAt(i) instanceof StructureListener)
- {
- sl = (StructureListener) listeners.elementAt(i);
- for (String pdbfile : sl.getPdbFile())
- {
- pdbs.remove(pdbfile);
- }
- }
- }
-
- /*
- * Rebuild the mappings set, retaining only those which are for 'other' PDB
- * files
- */
- if (pdbs.size() > 0)
- {
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
- for (StructureMapping sm : mappings)
- {
- if (!pdbs.contains(sm.pdbfile))
- {
- tmp.add(sm);
- }
- }
-
- mappings = tmp;
- }
- }
-
- /**
- * 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<AtomSpec> atoms = Collections.singletonList(atomSpec);
- mouseOverStructure(atoms);
- }
-
- /**
- * Propagate mouseover or selection of multiple positions in a structure
- *
- * @param atoms
- */
- public void mouseOverStructure(List<AtomSpec> atoms)
- {
- 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;
- }
-
- SearchResults results = new SearchResults();
- for (AtomSpec atom : atoms)
- {
- SequenceI lastseq = null;
- int lastipos = -1;
- for (StructureMapping sm : mappings)
- {
- if (sm.pdbfile.equals(atom.getPdbFile())
- && sm.pdbchain.equals(atom.getChain()))
- {
- int indexpos = sm.getSeqPos(atom.getPdbResNum());
- if (lastipos != indexpos && lastseq != sm.sequence)
- {
- results.addResult(sm.sequence, indexpos, indexpos);
- lastipos = indexpos;
- lastseq = sm.sequence;
- // construct highlighted sequence list
- for (AlignedCodonFrame acf : seqmappings)
- {
- acf.markMappedRegion(sm.sequence, indexpos, results);
- }
- }
- }
- }
- }
- for (Object li : listeners)
- {
- if (li instanceof SequenceListener)
- {
- ((SequenceListener) li).highlightSequence(results);
- }
- }
- }
-
- /**
- * 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)
- {
- boolean hasSequenceListeners = handlingVamsasMo
- || !seqmappings.isEmpty();
- SearchResults results = null;
- if (seqPos == -1)
- {
- seqPos = seq.findPosition(indexpos);
- }
- for (int i = 0; i < listeners.size(); i++)
- {
- Object listener = listeners.elementAt(i);
- if (listener == source)
- {
- // 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)
- {
- final SequenceListener seqListener = (SequenceListener) listener;
- if (hasSequenceListeners
- && seqListener.getVamsasSource() != source)
- {
- if (relaySeqMappings)
- {
- if (results == null)
- {
- results = MappingUtils.buildSearchResults(seq, seqPos,
- seqmappings);
- }
- if (handlingVamsasMo)
- {
- results.addResult(seq, seqPos, seqPos);
-
- }
- if (!results.isEmpty())
- {
- seqListener.highlightSequence(results);
- }
- }
- }
- }
- 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<AtomSpec> atoms = new ArrayList<AtomSpec>();
- 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;
-
- /**
- * 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<seq.getLength(); index++) {
- * if(jalview.util.Comparison.isGap(seq.getCharAt(index))) continue;
- *
- * atomNo = mappings[j].getAtomNum(seq.findPosition(index)); col =
- * java.awt.Color.white; if (atomNo > 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)
- {
- StructureListener sl;
- for (int i = 0; i < listeners.size(); i++)
- {
- if (listeners.elementAt(i) instanceof StructureListener)
- {
- sl = (StructureListener) listeners.elementAt(i);
- sl.updateColours(source);
- }
- }
- }
-
- public StructureMapping[] getMapping(String pdbfile)
- {
- List<StructureMapping> tmp = new ArrayList<StructureMapping>();
- for (StructureMapping sm : mappings)
- {
- if (sm.pdbfile.equals(pdbfile))
- {
- tmp.add(sm);
- }
- }
- return tmp.toArray(new StructureMapping[tmp.size()]);
- }
-
- /**
- * 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<SequenceI> seqs)
- {
- if (pdbfile == null || seqs == null || seqs.isEmpty())
- {
- return "";
- }
-
- 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();
- }
-
- /**
- * Remove the given mapping
- *
- * @param acf
- */
- public void deregisterMapping(AlignedCodonFrame acf)
- {
- if (acf != null)
- {
- 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<AlignedCodonFrame> mappings)
- {
- if (mappings != null)
- {
- for (AlignedCodonFrame acf : mappings)
- {
- registerMapping(acf);
- }
- }
- }
-
- /**
- * 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, SelectionSource source)
- {
- for (SelectionListener slis : sel_listeners)
- {
- if (slis != source)
- {
- slis.selection(selection, colsel, source);
- }
- }
- }
-
- Vector<AlignmentViewPanelListener> view_listeners = new Vector<AlignmentViewPanelListener>();
-
- 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<AlignmentViewPanelListener> 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<AlignedCodonFrame> getSequenceMappings()
- {
- return seqmappings;
- }
-
-}
import jalview.api.FeatureSettingsModelI;
import jalview.bin.Console;
+import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ContactMatrixI;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.io.PDBFeatureSettings;
+import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
File pae, int index, String seqId)
{
- FileInputStream pae_input = null;
+ addAlphaFoldPAE(pdbAlignment, pae, index, seqId, false, false);
+ }
+
+ public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
+ File pae, int index, String structIdOrFile, boolean isStructId)
+ {
+ addAlphaFoldPAE(pdbAlignment, pae, index, structIdOrFile, true,
+ isStructId);
+ }
+
+ public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+ int index, String id, boolean isStruct, boolean isStructId)
+ {
+ FileInputStream paeInput = null;
try
{
- pae_input = new FileInputStream(pae);
+ paeInput = new FileInputStream(pae);
} catch (FileNotFoundException e)
{
Console.error(
"Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
}
- try
+ if (isStruct)
{
- if (!importPaeJSONAsContactMatrix(pdbAlignment, pae_input, index,
- seqId))
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
{
- Console.warn("Could not import contact matrix from '"
- + pae.getAbsolutePath() + "'");
- }
- } catch (IOException e1)
- {
- Console.error("Error when importing pAE file '"
- + pae.getAbsolutePath() + "'", e1);
- } catch (ParseException e2)
- {
- Console.error(
- "Error when parsing pAE file '" + pae.getAbsolutePath() + "'",
- e2);
- }
+ String structFile = isStructId ? ssm.findFileForPDBId(id) : id;
+ Console.debug("##### AHA! structFile = " + structFile);
+ Console.debug("##### structFile "
+ + (ssm.isPDBFileRegistered(structFile) ? "IS " : "is NOT ")
+ + "registered.");
- }
+ StructureMapping[] smArray = ssm.getMapping(structFile);
+ Console.debug("##### AHA! smArray obtained with " + smArray.length
+ + " elements");
- public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
- File pae, int index, String structId)
- {
- StructureSelectionManager ssm = StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance);
- if (ssm != null)
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ {
+ Console.warn("Could not import contact matrix from '"
+ + pae.getAbsolutePath() + "' to structure.");
+ }
+ } catch (IOException e1)
+ {
+ Console.error("Error when importing pAE file '"
+ + pae.getAbsolutePath() + "'", e1);
+ } catch (ParseException e2)
+ {
+ Console.error("Error when parsing pAE file '"
+ + pae.getAbsolutePath() + "'", e2);
+ }
+ }
+
+ }
+ else
{
- /*
- ssm.setAddTempFacAnnot(showTemperatureFactor);
- ssm.setProcessSecondaryStructure(showSecondaryStructure);
- */
+ // attach to sequence?!
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
+ index, id))
+ {
+ Console.warn("Could not import contact matrix from '"
+ + pae.getAbsolutePath() + "' to sequence.");
+ }
+ } catch (IOException e1)
+ {
+ Console.error("Error when importing pAE file '"
+ + pae.getAbsolutePath() + "'", e1);
+ } catch (ParseException e2)
+ {
+ Console.error("Error when parsing pAE file '"
+ + pae.getAbsolutePath() + "'", e2);
+ }
}
}
* @throws IOException
* @throws Exception
*/
- public static boolean importPaeJSONAsContactMatrix(
+ public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input)
throws IOException, ParseException
{
- return importPaeJSONAsContactMatrix(pdbAlignment, pae_input, 0, null);
+ return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
+ 0, null);
}
- public static boolean importPaeJSONAsContactMatrix(
+ public static boolean importPaeJSONAsContactMatrixToSequence(
AlignmentI pdbAlignment, InputStream pae_input, int index,
String seqId) throws IOException, ParseException
{
-
- List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
- if (pae_obj == null)
- {
- Console.debug("JSON file did not parse properly.");
- return false;
- }
SequenceI sequence = null;
/* debugging */
SequenceI[] seqs = pdbAlignment.getSequencesArray();
sequence = sequences[0]; // just use the first sequence with this seqId
}
}
+
+ List<Object> pae_obj = (List<Object>) Platform.parseJSON(pae_input);
+ if (pae_obj == null)
+ {
+ Console.debug("JSON file did not parse properly.");
+ return false;
+ }
ContactMatrixI matrix = new PAEContactMatrix(sequence,
(Map<String, Object>) pae_obj.get(0));
return true;
}
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping[] smArray, InputStream paeInput)
+ throws IOException, ParseException
+ {
+ boolean someDone = false;
+ Console.debug("##### smArray.length=" + smArray.length);
+ for (StructureMapping sm : smArray)
+ {
+ Console.debug("##### sm[n]=" + sm.getPdbId());
+ boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
+ paeInput);
+ Console.debug("##### thisDone = " + thisDone);
+ someDone |= thisDone;
+ }
+ return someDone;
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping sm, InputStream paeInput)
+ throws IOException, ParseException
+ {
+
+ List<Object> pae_obj = (List<Object>) Platform.parseJSON(paeInput);
+ if (pae_obj == null)
+ {
+ Console.debug("JSON file did not parse properly.");
+ return false;
+ }
+
+ ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+ (Map<String, Object>) pae_obj.get(0));
+
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ // sm.getSequence().addAlignmentAnnotation(cmannot);
+ sm.transfer(cmannot);
+ // return true;
+
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ List<AlignedCodonFrame> acfList = ssm.getSequenceMappings();
+
+ return true;
+ }
+
/**
* general purpose structure importer - designed to yield alignment useful for
* transfer of annotation to associated sequences
git://source.jalview.org / jalview.git / commitdiff