From 55f5073cca8637a3ccb329f62fda12bd11a41dab Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 11 Feb 2018 10:49:50 +0000 Subject: [PATCH] JAL-2780 JAL-2781 include a Mapping object in StructureMapping to pass to sequence annotation and feature transfer --- src/jalview/ws/sifts/SiftsClient.java | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index 948b23f..289030e 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -92,6 +92,14 @@ public class SiftsClient implements SiftsClientI private CoordinateSys seqCoordSys = CoordinateSys.UNIPROT; + /** + * PDB sequence position to sequence coordinate mapping as derived from SIFTS + * record for the identified SeqCoordSys Used for lift-over from sequence + * derived from PDB (with first extracted PDBRESNUM as 'start' to the sequence + * being annotated with PDB data + */ + private jalview.datamodel.Mapping seqFromPdbMapping; + private static final int BUFFER_SIZE = 4096; public static final int UNASSIGNED = Integer.MIN_VALUE; @@ -442,6 +450,9 @@ public class SiftsClient implements SiftsClientI String mappingOutput = mappingDetails.toString(); StructureMapping siftsMapping = new StructureMapping(seq, pdbFile, pdbId, chain, mapping, mappingOutput); + StructureMapping siftsMapping = new StructureMapping(aseq, pdbFile, + pdbId, chain, mapping, mappingOutput, seqFromPdbMapping); + return siftsMapping; } -- 1.7.10.2