From: jprocter Date: Tue, 4 Dec 2012 10:48:53 +0000 (+0000) Subject: JAL-674 commented out annotate3d calling code for Jmol external processing routine X-Git-Tag: Jalview_2_9~263 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2fdd3b15c68d12fcf0c56e2ee70d3ff593f82249;p=jalview.git JAL-674 commented out annotate3d calling code for Jmol external processing routine --- 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");