public String viewMultiLine(String pdbId, String chainId) {
SequenceCollection coll = SequenceCollectionProvider.get(pdbId);
Sequence s = coll.getChainByPDBID(chainId);
s.ensureAnnotated();
ViewParameters params = new ViewParameters();
Collection<AnnotationName> annos = params.getAnnotations();
List<AnnotationName> newAnnos = new ArrayList<AnnotationName>();
for (AnnotationName anno : annos) {
newAnnos.add(anno);
}
newAnnos.add(AnnotationRegistry.getAnnotationByName(AnnotationConstants.siteRecord));
params.setAnnotations(newAnnos);
PageView pv = new PageView(0, params);
// params.setDesiredSequenceRns(ResidueNumberScheme.ATOM);
// register the anntation mapper for th emulti line view
// Annotation2MultiLineDrawer a2h = new Annotation2MultiLineDrawer();
ChainView view = new ChainView(s, params);
pv.addChain(view.getChain());
return pv.getAnnotationJson();
}
/**
* provide a default view using BioJava.. could be done using some proper configuration
* managment...
*/
public void initBioJavaView() {
// first the Residue Provider
ResidueInfoFactory refactory = new BioJavaResidueInfoFactory();
ResidueProvider.setResidueInfoFactory(refactory);
// next the SequenceCollection Provider
SequenceCollectionFactory sfactory = new BioJavaSequenceCollectionFactory();
SequenceCollectionProvider.setSequenceCollectionFactory(sfactory);
BioJavaPubMedFactory pfactory = new BioJavaPubMedFactory();
PubMedProvider.setPubMedFactory(pfactory);
}