*/
package jalview.structure;
+
import jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
import jalview.bin.ApplicationSingletonProvider;
import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
import java.util.HashMap;
import java.util.IdentityHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Vector;
{
public final static String NEWLINE = System.lineSeparator();
+
private List<StructureMapping> mappings = new ArrayList<>();
private boolean processSecondaryStructure = false;
private List<CommandListener> commandListeners = new ArrayList<>();
private List<SelectionListener> sel_listeners = new ArrayList<>();
-
/*
* instances of this class scoped by some context class
*/
}
return instance;
}
+/** Null provider in 2.11.2
+
+
+ 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;
+ }
+*/
/**
* @return true if will try to use external services for processing secondary
} catch (SiftsException e)
{
isMapUsingSIFTs = false;
- Cache.log.error("SIFTS mapping failed", e);
- Cache.log.error("Falling back on Needleman & Wunsch alignment");
+ Console.error("SIFTS mapping failed", e);
+ Console.error("Falling back on Needleman & Wunsch alignment");
siftsClient = null;
}
pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");
+ maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));
maxChain.transferResidueAnnotation(siftsMapping, null);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
} catch (SiftsException e)
{
// fall back to NW alignment
- Cache.log.error(e.getMessage());
+ Console.error(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.transferRESNUMFeatures(seq, "IEA:Jalview",
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is
+ // this
+ // "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
siftsClient);
foundSiftsMappings.add(siftsMapping);
chain.makeExactMapping(siftsMapping, seq);
- chain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
+ chain.transferRESNUMFeatures(seq, "IEA: SIFTS",
+ pdb.getId().toLowerCase(Locale.ROOT));// FIXME: is this
// "IEA:SIFTS" ?
chain.transferResidueAnnotation(siftsMapping, null);
} catch (SiftsException e)
StructureMapping nwMapping = getNWMappings(seq, pdbFile,
maxChainId, maxChain, pdb, maxAlignseq);
seqToStrucMapping.add(nwMapping);
- maxChain.transferRESNUMFeatures(seq, null); // FIXME: is this
- // "IEA:Jalview" ?
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is this
+ // "IEA:Jalview" ?
maxChain.transferResidueAnnotation(nwMapping, sqmpping);
ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0));
}
{
ds = ds.getDatasetSequence();
}
+ ;
if (ds.getAnnotation() != null)
{
for (AlignmentAnnotation ala : ds.getAnnotation())
maxChain.makeExactMapping(maxAlignseq, seq);
jalview.datamodel.Mapping sqmpping = maxAlignseq
.getMappingFromS1(false);
- maxChain.transferRESNUMFeatures(seq, null);
+ maxChain.transferRESNUMFeatures(seq, null,
+ pdb.getId().toLowerCase(Locale.ROOT));
HashMap<Integer, int[]> mapping = new HashMap<>();
int resNum = -10000;
if (s != null)
{
result = s;
+ }
}
}
- }
return result;
}
{
slis.viewPosition(startRes, endRes, startSeq, endSeq, source);
}
-
+ ;
}
}
}
*
* @param provider
*/
-
public static void release(StructureSelectionManagerProvider provider)
{
getInstance().selectionManagers.remove(provider);
}
-
+
public void registerPDBEntry(PDBEntry pdbentry)
{
if (pdbentry.getFile() != null