From 1000a9e49d7f7c295348025621e0f8d11817d200 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 10 Oct 2014 16:23:40 +0100 Subject: [PATCH] JAL-674 new constructors to pass flags about annotating sequence with data from PDB file --- src/MCview/PDBfile.java | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index bc58c9a..e99ece0 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -41,15 +41,33 @@ public class PDBfile extends jalview.io.AlignFile */ boolean VisibleChainAnnotation = false; - public PDBfile(String inFile, String inType) throws IOException boolean processSecondaryStructure=true; + + + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure) + { + super(); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + } + + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure, String file, String protocol) throws IOException { - super(inFile, inType); + super(false, file, protocol); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + doParse(); } - public PDBfile(FileParse source) throws IOException + public PDBfile(boolean visibleChainAnnotation, + boolean processSecondaryStructure, FileParse source) throws IOException { - super(source); + super(false, source); + VisibleChainAnnotation = visibleChainAnnotation; + this.processSecondaryStructure = processSecondaryStructure; + doParse(); } public String print() -- 1.7.10.2