- 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);
- 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");
- // 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)
- {
- if (al!=null && al.getHeight()>0)
- {
- ArrayList<SequenceI> matches=new ArrayList<SequenceI>();
- ArrayList<AlignSeq> aligns=new ArrayList<AlignSeq>();
-
- for (SequenceI sq:ochains)
- {
- SequenceI bestm=null;
- AlignSeq bestaseq=null;
- int bestscore=0;
- for (SequenceI msq:al.getSequences())
- {
- AlignSeq aseq = AlignSeq.doGlobalNWAlignment(msq, sq, dnaOrProtein);
- if (bestm==null || aseq.getMaxScore()>bestscore)
- {
- bestscore=aseq.getMaxScore();
- bestaseq= aseq;
- bestm=msq;
- }
- }
- System.out.println("Best Score for "+(matches.size()+1)+" :"+bestscore);
- matches.add(bestm);
- aligns.add(bestaseq);
- al.deleteSequence(bestm);
- }
- for (int p=0,pSize=seqs.size();p<pSize;p++)
- {
- SequenceI sq,sp=seqs.get(p);
- int q;
- if ((q=ochains.indexOf(sp))>-1)
- {
- seqs.set(p, sq=matches.get(q));
- sq.setName(sp.getName());
- sq.setDescription(sp.getDescription());
- sq.transferAnnotation(sp, aligns.get(q).getMappingFromS1(false));
- int inspos=-1;
- for (int ap=0;ap<annotations.size();)
- {
- if (((AlignmentAnnotation)annotations.get(ap)).sequenceRef==sp) {
- if (inspos==-1)
- {
- inspos=ap;
- }
- annotations.remove(ap);
- } else {
- ap++;
- }
- }
- if (sq.getAnnotation()!=null) {
- annotations.addAll(inspos, Arrays.asList(sq.getAnnotation()));
- }
- }
- }
- }
- }