From 2fdd3b15c68d12fcf0c56e2ee70d3ff593f82249 Mon Sep 17 00:00:00 2001 From: jprocter Date: Tue, 4 Dec 2012 10:48:53 +0000 Subject: [PATCH] JAL-674 commented out annotate3d calling code for Jmol external processing routine --- src/MCview/PDBfile.java | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 8a826a1..6a61f6a 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -235,10 +235,8 @@ public class PDBfile extends jalview.io.AlignFile } private void processPdbFileWithJmol(ArrayList prot) throws Exception { -// System.out.println("this is a PDB format and RNA sequence"); - Annotate3D an3d = new Annotate3D(); - AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type)); - replaceMatchingSeqsWith(prot, al, AlignSeq.PEP); + // process prot sequence with Jmol to get annotated alignment. + // replaceMatchingSeqsWith(prot, al, AlignSeq.PEP); } private void processPdbFileWithAnnotate3d(ArrayList rna) throws Exception { // System.out.println("this is a PDB format and RNA sequence"); -- 1.7.10.2