Package org.wymiwyg.rdf.molecules.impl

Examples of org.wymiwyg.rdf.molecules.impl.SimpleTerminalMolecule.markFinalized()

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      @Override
      protected TerminalMolecule asMolecule(Graph graphFromModel) {
        SimpleTerminalMolecule result = new SimpleTerminalMolecule();
        result.addAll(deNaturalize(graphFromModel));
        result.markFinalized();
        return result;
      }

    }.readComponent(new ComponentDirectory(moleculeRef.getURIRef()));
  }
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                      .replaceNode(
                          molecule,
                          orig,
                          current,
                          new SimpleTerminalMolecule());
                  replacement.markFinalized();
                  tMolecules.add(replacement);
                } catch (SourceNodeNotFoundException e) {
                  tMolecules.add(molecule);
                }
              }
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    for (Iterator<TerminalMolecule> iter = terminalMolecules.iterator(); iter.hasNext();) {
      TerminalMolecule current = iter.next();
      try {
        SimpleTerminalMolecule newMolecule = new SimpleTerminalMolecule();
        newMolecule.addAll(GraphUtil.replaceNode(current, replacingNodes, newNode));
        newMolecule.markFinalized();
        iter.remove();
        newTerminalMolecules.add(newMolecule);
      } catch (SourceNodeNotFoundException e) {
        //nothing, did not remove
      }
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  private TerminalMolecule getTerminalMoleculeFromPathNode(
      PathNode dirPathNode, String name) throws IOException {

    SimpleTerminalMolecule molecule = new SimpleTerminalMolecule();
    molecule.addAll(getTriplesFromPathNode(dirPathNode, name));
    molecule.markFinalized();
    return molecule;
  }

  private Graph getTriplesFromPathNode(PathNode dirPathNode, String name)
      throws IOException {
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          try {
            SimpleTerminalMolecule replacement = new SimpleTerminalMolecule();
            new GraphUtil<TerminalMolecule>()
                .replaceNode(terminalMolecule, orig, current,
                    replacement);
            replacement.markFinalized();
            newTerminalMolecules.add(replacement);
            nodeReplaced = true;
          } catch (SourceNodeNotFoundException e) {
            newTerminalMolecules.add(terminalMolecule);
            log.debug("source not found");
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