From df3b92c351aba41e53878b936203e99520c02302 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Sun, 9 Jun 2013 19:34:47 +0100 Subject: [PATCH] JAL-674 avoid runtime dependency on annotate3d webservice in applet --- src/MCview/PDBfile.java | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java index 95dec13..4d9d738 100755 --- a/src/MCview/PDBfile.java +++ b/src/MCview/PDBfile.java @@ -25,7 +25,6 @@ import java.awt.*; import jalview.analysis.AlignSeq; import jalview.datamodel.*; import jalview.io.FileParse; -import jalview.ws.jws1.Annotate3D; public class PDBfile extends jalview.io.AlignFile { @@ -231,10 +230,20 @@ public class PDBfile extends jalview.io.AlignFile } private void processPdbFileWithAnnotate3d(ArrayList rna) throws Exception { // System.out.println("this is a PDB format and RNA sequence"); - Annotate3D an3d = new Annotate3D(); - // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service - AlignmentI al = an3d.getRNAMLFor(new FileParse(getDataName(),type)); - replaceMatchingSeqsWith(rna, al, AlignSeq.DNA); + // note: we use reflection here so that the applet can compile and run without the HTTPClient bits and pieces needed for accessing Annotate3D web service + try { + Class cl = Class.forName("jalview.ws.jws1.Annotate3D"); + if (cl!=null) + { + // TODO: use the PDB ID of the structure if one is available, to save bandwidth and avoid uploading the whole structure to the service + Object annotate3d = cl.getConstructor(new Class[] {}).newInstance(new Object[] {}); + AlignmentI al = ((AlignmentI) cl.getMethod("getRNAMLFor", new Class[] { FileParse.class}).invoke(annotate3d, new Object[] { new FileParse(getDataName(),type)})); + replaceMatchingSeqsWith(rna, al, AlignSeq.DNA); + } + } catch (ClassNotFoundException x) + { + //ignore classnotfounds - occurs in applet + }; } private void replaceMatchingSeqsWith(ArrayList ochains, AlignmentI al, String dnaOrProtein) { -- 1.7.10.2