From cd84efbd9723bf4a92f2be2e04183612e4ce0a6e Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 13 Dec 2021 14:15:06 +0000 Subject: [PATCH] JAL-3929 preserve lowercase pdbid in group name for transferred features --- src/jalview/structure/StructureSelectionManager.java | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 0ab9baf..b4bd781 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -28,6 +28,7 @@ import java.util.Enumeration; import java.util.HashMap; import java.util.IdentityHashMap; import java.util.List; +import java.util.Locale; import java.util.Map; import java.util.Vector; @@ -548,7 +549,7 @@ public class StructureSelectionManager pdb, maxChain, sqmpping, maxAlignseq, siftsClient); seqToStrucMapping.add(siftsMapping); maxChain.makeExactMapping(siftsMapping, seq); - maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId()); + maxChain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId().toLowerCase(Locale.ROOT)); maxChain.transferResidueAnnotation(siftsMapping, null); ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); @@ -560,7 +561,7 @@ public class StructureSelectionManager targetChainId, maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); maxChain.makeExactMapping(maxAlignseq, seq); - maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId()); // FIXME: is + maxChain.transferRESNUMFeatures(seq, "IEA:Jalview",pdb.getId().toLowerCase(Locale.ROOT)); // FIXME: is // this // "IEA:Jalview" ? maxChain.transferResidueAnnotation(nwMapping, sqmpping); @@ -580,7 +581,7 @@ public class StructureSelectionManager siftsClient); foundSiftsMappings.add(siftsMapping); chain.makeExactMapping(siftsMapping, seq); - chain.transferRESNUMFeatures(seq, "IEA: SIFTS",pdb.getId());// 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) @@ -605,7 +606,7 @@ public class StructureSelectionManager StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); - maxChain.transferRESNUMFeatures(seq, null,pdb.getId()); // FIXME: is this + 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)); @@ -773,7 +774,7 @@ public class StructureSelectionManager maxChain.makeExactMapping(maxAlignseq, seq); jalview.datamodel.Mapping sqmpping = maxAlignseq .getMappingFromS1(false); - maxChain.transferRESNUMFeatures(seq, null, pdb.getId()); + maxChain.transferRESNUMFeatures(seq, null, pdb.getId().toLowerCase(Locale.ROOT)); HashMap mapping = new HashMap<>(); int resNum = -10000; -- 1.7.10.2