- public static boolean isCalcIdForFile(String calcId, String pdbFile)
- {
- return (calcId != null && calcId.startsWith("JalviewPDB:" + pdbFile
- + ":JalviewPDB:"));
- }
- private void markCalcIds()
- {
- for (SequenceI sq : seqs)
- {
- for (AlignmentAnnotation aa : sq.getAnnotation())
- {
- String oldId = aa.getCalcId();
- if (oldId == null)
- {
- oldId = "";
- }
- aa.setCalcId("JalviewPDB:" + getDataName() + ":JalviewPDB:" + oldId);
- }
- }
- }
- private void processPdbFileWithJmol(ArrayList<SequenceI> prot)
- throws Exception
- {
- 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);
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, prot, al, AlignSeq.PEP, false);
- }
- } catch (ClassNotFoundException q)
- {
- }
- }
-
- private void processPdbFileWithAnnotate3d(ArrayList<SequenceI> rna)
- throws Exception
- {
- // System.out.println("this is a PDB format and RNA sequence");
- // 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) }));
- AlignSeq.replaceMatchingSeqsWith(seqs, annotations, rna, al, AlignSeq.DNA, false);
- }
- } catch (ClassNotFoundException x)
- {
- // ignore classnotfounds - occurs in applet
- }
- ;
- }
-