import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
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> structureSelections;
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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.
+ *
+ * @param context
+ * @return
+ */
+ StructureSelectionManager getInstanceForContext(
+ StructureSelectionManagerProvider context)
+ {
+ StructureSelectionManager instance = structureSelections.get(context);
+ if (instance == null)
+ {
+ instance = new StructureSelectionManager();
+ structureSelections.put(context, instance);
+ }
+ return instance;
+ }
+
+ /**
+ * Removes the instance associated with this provider
+ *
+ * @param provider
+ */
+
+ public static void release(StructureSelectionManagerProvider provider)
+ {
+ getInstance().structureSelections.remove(provider);
+ }
+
+ /**
+ * Private constructor as all 'singleton' instances are managed here or by
+ * ApplicationSingletonProvider
+ */
+ private StructureSelectionManager()
+ {
+ structureSelections = new IdentityHashMap<>();
+ }
+
/**
* @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
* broadcasting colouring, mouseovers and selection events (convenience
* wrapper).
*
+ *
+ *
* @param forStructureView
- * when true, record the mapping for use in mouseOvers
+ * 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
* mapping operation
* @return null or the structure data parsed as a pdb file
*/
- synchronized public StructureFile computeMapping(
+ synchronized private StructureFile computeMapping(
boolean forStructureView, SequenceI[] sequenceArray,
String[] targetChainIds, String pdbFile, DataSourceType sourceType,
IProgressIndicator progress)
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)
{
ex.printStackTrace();
return null;
}
-
+ /*
+ * sifts client - non null if SIFTS mappings are to be used
+ */
+ SiftsClient siftsClient = null;
try
{
if (isMapUsingSIFTs)
{
isMapUsingSIFTs = false;
e.printStackTrace();
+ siftsClient = null;
}
String targetChainId;
try
{
siftsMapping = getStructureMapping(seq, pdbFile, targetChainId,
- pdb, maxChain, sqmpping, maxAlignseq);
+ pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
try
{
siftsMapping = getStructureMapping(seq,
- pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq);
+ pdbFile, chain.id, pdb, chain, sqmpping, maxAlignseq,
+ siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
{
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())
{
}
if (forStructureView)
{
- mappings.addAll(seqToStrucMapping);
+ for (StructureMapping sm : seqToStrucMapping)
+ {
+ addStructureMapping(sm); // not addAll!
+ }
}
if (progress != null)
{
{
ds = ds.getDatasetSequence();
}
- ;
if (ds.getAnnotation() != null)
{
for (AlignmentAnnotation ala : ds.getAnnotation())
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);
}
/**
- * 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()
{
- 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();
- }
+ mappings.clear();
+ seqmappings.clear();
+ sel_listeners.clear();
+ listeners.clear();
+ commandListeners.clear();
+ view_listeners.clear();
+ pdbFileNameId.clear();
+ pdbIdFileName.clear();
}
public void addSelectionListener(SelectionListener selecter)
{
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
git://source.jalview.org / jalview.git / blobdiff