From 3858d4f26e39b36f8bf1d66b22c9d7030fbd6fc0 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Mon, 7 May 2018 17:38:29 +0100 Subject: [PATCH] JAL-2321 use StructureImportSettings singleton settings when JmolParser.parse() called from constructor --- src/jalview/ext/jmol/JmolParser.java | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index 975846d..2a510a2 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -188,7 +188,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener } lastID = tmpatom.resNumIns.trim(); } - xferSettings(); + if (isParseImmediately()) + { + // configure parsing settings from the static singleton + xferSettings(); + } makeResidueList(); makeCaBondList(); @@ -205,7 +209,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener prot.add(chainseq); } - if (StructureImportSettings.isProcessSecondaryStructure()) + // look at local setting for adding secondary tructure + if (predictSecondaryStructure) { createAnnotation(chainseq, chain, ms.at); } -- 1.7.10.2