From 44cbaf5e4c094d90ef1294dd47c75a652e5f2509 Mon Sep 17 00:00:00 2001 From: tcofoegbu Date: Fri, 1 Jul 2016 11:08:43 +0100 Subject: [PATCH] JAL-2135 bugfix for error preventing processing of secondary structure annotation for model produced by Phyre2 --- src/MCview/PDBChain.java | 2 +- src/jalview/ext/jmol/JmolParser.java | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/MCview/PDBChain.java b/src/MCview/PDBChain.java index 073772a..248cf29 100755 --- a/src/MCview/PDBChain.java +++ b/src/MCview/PDBChain.java @@ -82,7 +82,7 @@ public class PDBChain public PDBChain(String pdbid, String id) { - this.pdbid = pdbid.toLowerCase(); + this.pdbid = pdbid == null ? pdbid : pdbid.toLowerCase(); this.id = id; } diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java index 31ed1b7..309e196 100644 --- a/src/jalview/ext/jmol/JmolParser.java +++ b/src/jalview/ext/jmol/JmolParser.java @@ -206,8 +206,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener List significantAtoms = new ArrayList(); for (org.jmol.modelset.Atom atom : ms.at) { - System.out.println("Seq Id : " + atom.getSeqID()); - System.out.println("To String : " + atom.toString()); + // System.out.println("Seq Id : " + atom.getSeqID()); + // System.out.println("To String : " + atom.toString()); if (atom.isHetero()) { continue; -- 1.7.10.2