From 2a193973a99a80b2b2d13af673ea64863cdbb6c2 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 13 Feb 2018 15:34:22 +0000 Subject: [PATCH] =?utf8?q?JAL-2780=20JAL-2781=20only=20create=20a=20mapping=20?= =?utf8?q?entry=20or=20write=20a=20character=20to=20the=20=E2=80=98mapped=20?= =?utf8?q?sequence=E2=80=99=20for=20observed=20residues=20regardless=20of=20?= =?utf8?q?to/from=20coordinate=20frames?= MIME-Version: 1.0 Content-Type: text/plain; charset=utf8 Content-Transfer-Encoding: 8bit --- src/jalview/ws/sifts/SiftsClient.java | 15 ++++++--------- 1 file changed, 6 insertions(+), 9 deletions(-) diff --git a/src/jalview/ws/sifts/SiftsClient.java b/src/jalview/ws/sifts/SiftsClient.java index c9c4618..5050c34 100644 --- a/src/jalview/ws/sifts/SiftsClient.java +++ b/src/jalview/ws/sifts/SiftsClient.java @@ -706,21 +706,18 @@ public class SiftsClient implements SiftsClientI : getLeadingIntegerValue(pdbRefDb.getDbResNum(), UNASSIGNED); - if (isResidueObserved(residue) - || seqCoordSys == CoordinateSys.UNIPROT) + if (isObserved) { char resCharCode = ResidueProperties .getSingleCharacterCode(ResidueProperties .getCanonicalAminoAcid(residue.getDbResName())); resNumMap.put(currSeqIndex, String.valueOf(resCharCode)); + + int[] mappingcols = new int[] { Integer.valueOf(resNum), + UNASSIGNED, isObserved ? firstPDBResNum : UNASSIGNED }; + + mapping.put(currSeqIndex - nonObservedShiftIndex, mappingcols); } - // TODO: mapping should have SeqCoordSysNum => int[] {PDBeNum, - // PDBRESNUM, ATOMNUM } - mapping.put(currSeqIndex - nonObservedShiftIndex, - new int[] - { Integer.valueOf(resNum), UNASSIGNED, - isObserved ? firstPDBResNum - : UNASSIGNED }); } } } -- 1.7.10.2