Package org.biopax.paxtools.model.level2

Examples of org.biopax.paxtools.model.level2.pathway

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    return !biopaxModel.getObjects(org.biopax.paxtools.model.level3.Pathway.class).isEmpty();
  }

  public String createGlobalPathway(String name)
  {
    Pathway p = biopaxModel.addNew(Pathway.class,
      "http://chisiobiopaxeditor/#" + System.currentTimeMillis());

    for (Interaction inter : biopaxModel.getObjects(Interaction.class))
    {
      p.addPathwayComponent(inter);
    }
    p.setDisplayName(makeUniquePathwayName(name));
    return p.getDisplayName();
  }
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    return p.getDisplayName();
  }

  public String createPathway(String name, List<String> intids)
  {
    Pathway p = biopaxModel.addNew(Pathway.class,
      "http://chisiobiopaxeditor/#" + System.currentTimeMillis());

    for (Interaction inter : biopaxModel.getObjects(Interaction.class))
    {
      if (intids.contains(inter.getRDFId()))
      {
        p.addPathwayComponent(inter);
      }
    }
    p.setDisplayName(makeUniquePathwayName(name));
    return p.getDisplayName();
  }
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Related Classes of org.biopax.paxtools.model.level2.pathway

  • org.gvt.action.DeletePathwayAction
  • org.gvt.action.DuplicatePathwayAction
  • org.gvt.action.LocalCommonStreamQueryAction
  • org.gvt.action.SearchCausativePathsAction
  • org.gvt.action.UpdatePathwayAction
  • org.gvt.ChisioMain
  • org.gvt.inspector.CommonStreamQueryParamWithEntitiesDialog
  • org.gvt.inspector.GoIQueryParamWithEntitiesDialog
  • org.gvt.inspector.NeighborhoodQueryParamWithEntitiesDialog
  • org.gvt.inspector.PoIQueryParamWithEntitiesDialog
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