From cbed78c74fd2b24bcca79c1d3d8c62ec19c5276f Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Tue, 21 Oct 2014 09:37:24 +0100 Subject: [PATCH] JAL-674 remove any spurious PDBEntrys generated by Jmol/RNAView parsing processes --- src/MCview/PDBfile.java | 22 ++++++++++++++++++++++ 1 file changed, 22 insertions(+) diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 019aba9..a99f172 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -327,6 +327,17 @@ public class PDBfile extends jalview.io.AlignFile {}).invoke(jmf)); cl.getMethod("addAnnotations", new Class[] { Alignment.class }).invoke(jmf, al); + for (SequenceI sq : al.getSequences()) + { + if (sq.getDatasetSequence() != null) + { + sq.getDatasetSequence().getPDBId().clear(); + } + else + { + sq.getPDBId().clear(); + } + } AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false); } } catch (ClassNotFoundException q) @@ -355,6 +366,17 @@ public class PDBfile extends jalview.io.AlignFile new Class[] { FileParse.class }).invoke(annotate3d, new Object[] { new FileParse(getDataName(), type) })); + for (SequenceI sq : al.getSequences()) + { + if (sq.getDatasetSequence() != null) + { + sq.getDatasetSequence().getPDBId().clear(); + } + else + { + sq.getPDBId().clear(); + } + } AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false); } } catch (ClassNotFoundException x) -- 1.7.10.2