From 138f7c321c983ab59d4e920518fce401aa1061f0 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 10 Oct 2014 16:22:24 +0100 Subject: [PATCH 1/1] JAL-674 parser flag to control secondary structure processing --- src/MCview/PDBfile.java | 17 ++++------------- 1 file changed, 4 insertions(+), 13 deletions(-) diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 7f5c427..bc58c9a 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -42,6 +42,7 @@ public class PDBfile extends jalview.io.AlignFile boolean VisibleChainAnnotation = false; public PDBfile(String inFile, String inType) throws IOException + boolean processSecondaryStructure=true; { super(inFile, inType); } @@ -202,6 +203,8 @@ public class PDBfile extends jalview.io.AlignFile } } } + if (processSecondaryStructure) + { if (rna.size() > 0) try { @@ -225,19 +228,7 @@ public class PDBfile extends jalview.io.AlignFile x.printStackTrace(); } - ; - if (prot.size() > 0) - try - { - processPdbFileWithJmol(prot); - } catch (Exception x) - { - System.err - .println("Exceptions when dealing with RNA in pdb file"); - x.printStackTrace(); - - } - ; + } } catch (OutOfMemoryError er) { System.out.println("OUT OF MEMORY LOADING PDB FILE"); -- 1.7.10.2