*/
package jalview.structure;
+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 jalview.analysis.AlignSeq;
import jalview.api.StructureSelectionManagerProvider;
+import jalview.bin.Cache;
import jalview.commands.CommandI;
import jalview.commands.EditCommand;
import jalview.commands.OrderCommand;
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 mc_view.Atom;
import mc_view.PDBChain;
import mc_view.PDBfile;
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)
+ isMapUsingSIFTs = isMapUsingSIFTs && pdb.isPPDBIdAvailable() && !pdb.getId().startsWith("AF-");
} catch (Exception ex)
{
} 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;
}
pdb, maxChain, sqmpping, maxAlignseq, siftsClient);
seqToStrucMapping.add(siftsMapping);
maxChain.makeExactMapping(siftsMapping, seq);
- maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS");// FIXME: is this
- // "IEA:SIFTS" ?
+ 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);