import jalview.analysis.AlignSeq;
import jalview.datamodel.*;
-import jalview.ext.jmol.PDBFileWithJmol;
import jalview.io.FileParse;
-import jalview.ws.jws1.Annotate3D;
public class PDBfile extends jalview.io.AlignFile
{
}
private void processPdbFileWithJmol(ArrayList<SequenceI> prot) throws Exception
{
- PDBFileWithJmol jmf = new PDBFileWithJmol(new FileParse(getDataName(),type));
- Alignment al = new Alignment(jmf.getSeqsAsArray());
- jmf.addAnnotations(al);
- replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ try {
+ Class cl = Class.forName("jalview.ext.jmol.PDBFileWithJmol");
+ if (cl!=null)
+ {
+ Object jmf = cl.getConstructor(new Class[] {FileParse.class}).newInstance(new Object[] {new FileParse(getDataName(),type)});
+ Alignment al = new Alignment((SequenceI[]) cl.getMethod("getSeqsAsArray", new Class[] {}).invoke(jmf));
+ cl.getMethod("addAnnotations",new Class[] {Alignment.class}).invoke(jmf, al);
+ replaceMatchingSeqsWith(prot, al, AlignSeq.PEP);
+ }
+ } catch (ClassNotFoundException q)
+ {}
}
private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> 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<SequenceI> ochains, AlignmentI al, String dnaOrProtein)
{