From 0fe8f12fea760bfa8f7394edcbd562c6a2a22dfb Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Wed, 12 Nov 2014 12:39:05 +0000 Subject: [PATCH] JAL-674 switch from .transfer to .liftOver for transfer of annotation --- src/MCview/PDBChain.java | 21 +++++++++------------ 1 file changed, 9 insertions(+), 12 deletions(-) diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 5dd38a4..2dd6d37 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -487,22 +487,17 @@ public class PDBChain } } - public AlignmentAnnotation[] transferResidueAnnotation(SequenceI seq, - String status) - { - AlignmentAnnotation[] transferred = null; - - return transferred; - - } - /** * copy any sequence annotation onto the sequence mapped using the provided * StructureMapping * * @param mapping + * - positional mapping between destination sequence and pdb resnum + * @param sqmpping + * - mapping between destination sequence and local chain */ - public void transferResidueAnnotation(StructureMapping mapping) + public void transferResidueAnnotation( + StructureMapping mapping, jalview.datamodel.Mapping sqmpping) { SequenceI sq = mapping.getSequence(); SequenceI dsq = sq; @@ -524,7 +519,8 @@ public class PDBChain if (transfer == null || transfer.size() == 0) { ana.liftOver(sequence, shadowMap); - mapping.transfer(ana); + ana.liftOver(dsq, sqmpping); + dsq.addAlignmentAnnotation(ana); } else { @@ -542,7 +538,8 @@ public class PDBChain ana.getCalcId(), ana.label); if (transfer == null || transfer.size() == 0) { - mapping.transfer(ana); + ana.liftOver(dsq, sqmpping); + // mapping.transfer(ana); } else { -- 1.7.10.2