コード例 #1
0
  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();
  }
コード例 #2
0
  /**
   * 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);
  }