import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
import jalview.io.StructureFile;
import jalview.util.MappingUtils;
import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.ws.sifts.SiftsClient;
import jalview.ws.sifts.SiftsException;
import jalview.ws.sifts.SiftsSettings;
import java.util.Map;
import java.util.Vector;
-import MCview.Atom;
-import MCview.PDBChain;
-import MCview.PDBfile;
+import mc_view.Atom;
+import mc_view.PDBChain;
+import mc_view.PDBfile;
-public class StructureSelectionManager
+public class StructureSelectionManager implements ApplicationSingletonI
{
public final static String NEWLINE = System.lineSeparator();
- static IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> instances;
-
private List<StructureMapping> mappings = new ArrayList<>();
private boolean processSecondaryStructure = false;
private boolean addTempFacAnnot = false;
- private SiftsClient siftsClient = null;
-
/*
* Set of any registered mappings between (dataset) sequences.
*/
private List<SelectionListener> sel_listeners = new ArrayList<>();
+ /*
+ * instances of this class scoped by some context class
+ */
+ private IdentityHashMap<StructureSelectionManagerProvider, StructureSelectionManager> selectionManagers;
+
+ /**
+ * Answers an instance of this class for the current application (Java or JS
+ * 'applet') scope
+ *
+ * @return
+ */
+ private static StructureSelectionManager getInstance()
+ {
+ return (StructureSelectionManager) ApplicationSingletonProvider
+ .getInstance(StructureSelectionManager.class);
+ }
+
+ /**
+ * Private constructor as all 'singleton' instances are managed here or by
+ * ApplicationSingletonProvider
+ */
+ private StructureSelectionManager()
+ {
+ selectionManagers = new IdentityHashMap<>();
+ }
+
+ /**
+ * Answers an instance of this class for the current application (Java or JS
+ * 'applet') scope, and scoped to the specified context
+ *
+ * @param context
+ * @return
+ */
+ public static StructureSelectionManager getStructureSelectionManager(
+ StructureSelectionManagerProvider context)
+ {
+ return getInstance().getInstanceForContext(context);
+ }
+
+ /**
+ * Answers an instance of this class scoped to the given context. The instance
+ * is created on the first request for the context, thereafter the same
+ * instance is returned. Note that the context may be null (this is the case
+ * when running headless without a Desktop).
+ *
+ * @param context
+ * @return
+ */
+ StructureSelectionManager getInstanceForContext(
+ StructureSelectionManagerProvider context)
+ {
+ StructureSelectionManager instance = selectionManagers.get(context);
+ if (instance == null)
+ {
+ instance = new StructureSelectionManager();
+ selectionManagers.put(context, instance);
+ }
+ return instance;
+ }
+
+
/**
* @return true if will try to use external services for processing secondary
* structure
|| 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
return relaySeqMappings;
}
- Vector listeners = new Vector();
+ Vector<Object> listeners = new Vector<>();
/**
* register a listener for alignment sequence mouseover events
}
/**
- * 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
{
for (StructureMapping sm : mappings)
{
- if (sm.getPdbId().equals(pdbid))
+ if (sm.getPdbId().equalsIgnoreCase(pdbid))
{
return sm.pdbfile;
}
* Import structure data and register a structure mapping for broadcasting
* colouring, mouseovers and selection events (convenience wrapper).
*
+ * This is the standard entry point.
+ *
* @param sequence
* - one or more sequences to be mapped to pdbFile
* @param targetChains
}
/**
+ * Import a single structure file and register sequence structure mappings for
+ * broadcasting colouring, mouseovers and selection events (convenience
+ * wrapper).
+ *
+ *
+ *
+ * @param forStructureView
+ * when true (testng only), record the mapping for use in mouseOvers
+ * (testng only)
+ * @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).
+ * 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
* - 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 setMapping(boolean forStructureView,
- SequenceI[] sequenceArray, String[] targetChainIds,
- String pdbFile, DataSourceType sourceType)
- {
- return computeMapping(forStructureView, sequenceArray, targetChainIds,
- pdbFile, sourceType, null);
- }
-
- synchronized public StructureFile computeMapping(
+ synchronized private StructureFile computeMapping(
boolean forStructureView, SequenceI[] sequenceArray,
String[] targetChainIds, String pdbFile, DataSourceType sourceType,
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
+
+ /**
+ * do we extract and transfer annotation from 3D data ?
*/
- 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;
- }
- }
- }
- }
- }
+ // FIXME: possibly should just delete
+
+ boolean parseSecStr = processSecondaryStructure
+ ? isStructureFileProcessed(pdbFile, sequenceArray)
+ : false;
+
StructureFile pdb = null;
boolean isMapUsingSIFTs = SiftsSettings.isMapWithSifts();
try
{
+ // FIXME if sourceType is not null, we've lost data here
sourceType = AppletFormatAdapter.checkProtocol(pdbFile);
- pdb = new JmolParser(pdbFile, sourceType);
-
+ 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();
+ // TODO: JAL-3868 need to know if structure is actually from
+ // PDB (has valid PDB ID and has provenance suggesting it
+ // actually came from PDB)
+ boolean isProtein = false;
+ for (SequenceI s:sequenceArray) {
+ if (s.isProtein()) {
+ isProtein = true;
+ break;
+ }
+ }
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-") && isProtein;
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
-
+ /*
+ * sifts client - non null if SIFTS mappings are to be used
+ */
+ SiftsClient siftsClient = null;
try
{
if (isMapUsingSIFTs)
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- e.printStackTrace();
+ Cache.log.error("SIFTS mapping failed", e);
+ Cache.log.error("Falling back on Needleman & Wunsch alignment");
+ siftsClient = null;
}
String targetChainId;
try
{
siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
- pdb, maxChain, sqmpping, maxAlignseq);
+ pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
- // "IEA:SIFTS" ?
- maxChain.transferResidueAnnotation(siftsMapping, sqmpping);
+ maxChain.makeExactMapping(siftsMapping, seq);
+ maxChain.transferRESNUMFeatures(seq, "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());
+ Cache.log.error(e.getMessage());
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
targetChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
+ maxChain.transferRESNUMFeatures(seq, "IEA:Jalview"); // FIXME: is
+ // this
// "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
List<StructureMapping> foundSiftsMappings = new ArrayList<>();
for (PDBChain chain : pdb.getChains())
{
+ StructureMapping siftsMapping = null;
try
{
- StructureMapping siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ 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);
- maxChain.makeExactMapping(maxAlignseq, seq);
- maxChain.transferRESNUMFeatures(seq, null);// FIXME: is this
- // "IEA:SIFTS" ?
- maxChain.transferResidueAnnotation(foundSiftsMappings.get(0),
- sqmpping);
ds.addPDBId(sqmpping.getTo().getAllPDBEntries().get(0));
}
else
}
if (forStructureView)
{
- mappings.addAll(seqToStrucMapping);
+ for (StructureMapping sm : seqToStrucMapping)
+ {
+ addStructureMapping(sm); // not addAll!
+ }
}
if (progress != null)
{
return pdb;
}
+ /**
+ * 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)
+ {
+ 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;
+ }
+ }
+ }
+ }
+ }
+ return parseSecStr;
+ }
+
public void addStructureMapping(StructureMapping sm)
{
- mappings.add(sm);
+ if (!mappings.contains(sm))
+ {
+ mappings.add(sm);
+ }
}
/**
* @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) throws SiftsException
+ AlignSeq maxAlignseq, SiftsClient siftsClient) throws SiftsException
{
StructureMapping curChainMapping = siftsClient
.getSiftsStructureMapping(seq, pdbFile, targetChainId);
PDBChain chain = pdb.findChain(targetChainId);
if (chain != null)
{
- chain.transferResidueAnnotation(curChainMapping, sqmpping);
+ chain.transferResidueAnnotation(curChainMapping, null);
}
} catch (Exception e)
{
* @param pdbResNum
* @param chain
* @param pdbfile
+ * @return
*/
- public void mouseOverStructure(int pdbResNum, String chain,
+ public String mouseOverStructure(int pdbResNum, String chain,
String pdbfile)
{
AtomSpec atomSpec = new AtomSpec(pdbfile, chain, pdbResNum, 0);
List<AtomSpec> atoms = Collections.singletonList(atomSpec);
- mouseOverStructure(atoms);
+ return mouseOverStructure(atoms);
}
/**
*
* @param atoms
*/
- public void mouseOverStructure(List<AtomSpec> atoms)
+ public String mouseOverStructure(List<AtomSpec> atoms)
{
if (listeners == null)
{
// old or prematurely sent event
- return;
+ return null;
}
boolean hasSequenceListener = false;
for (int i = 0; i < listeners.size(); i++)
}
if (!hasSequenceListener)
{
- return;
+ return null;
}
SearchResultsI results = findAlignmentPositionsForStructurePositions(
atoms);
+ String result = null;
for (Object li : listeners)
{
if (li instanceof SequenceListener)
{
- ((SequenceListener) li).highlightSequence(results);
+ String s = ((SequenceListener) li).highlightSequence(results);
+ if (s != null)
+ {
+ result = s;
}
}
}
+ return result;
+ }
/**
* Constructs a SearchResults object holding regions (if any) in the Jalview
&& 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;
StringBuilder sb = new StringBuilder(64);
for (StructureMapping sm : mappings)
{
- if (sm.pdbfile.equals(pdbfile) && seqs.contains(sm.sequence))
+ if (Platform.pathEquals(sm.pdbfile, pdbfile)
+ && seqs.contains(sm.sequence))
{
sb.append(sm.mappingDetails);
sb.append(NEWLINE);
}
/**
- * Resets this object to its initial state by removing all registered
- * listeners, codon mappings, PDB file mappings
+ * Reset this object to its initial state by removing all registered
+ * listeners, codon mappings, PDB file mappings.
+ *
+ * Called only by Desktop and testng.
+ *
*/
public void resetAll()
{
}
}
- public void addSelectionListener(SelectionListener selecter)
+ public List<SelectionListener> getListeners() {
+ return sel_listeners;
+ }
+
+ public void addSelectionListener(SelectionListener selecter)
{
if (!sel_listeners.contains(selecter))
{
{
slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
}
- ;
+
}
}
}
+
/**
- * release all references associated with this manager provider
+ * Removes the instance associated with this provider
*
- * @param jalviewLite
+ * @param provider
*/
- public static void release(StructureSelectionManagerProvider jalviewLite)
+
+ public static void release(StructureSelectionManagerProvider provider)
{
- // synchronized (instances)
- {
- if (instances == null)
- {
- return;
- }
- StructureSelectionManager mnger = (instances.get(jalviewLite));
- if (mnger != null)
- {
- instances.remove(jalviewLite);
- try
- {
- mnger.finalize();
- } catch (Throwable x)
- {
- }
- }
- }
+ getInstance().selectionManagers.remove(provider);
}
-
+
public void registerPDBEntry(PDBEntry pdbentry)
{
if (pdbentry.getFile() != null
git://source.jalview.org / jalview.git / blobdiff