R/internal_keep_property_class_list.R

In grishagin/RIGbiopax: Extract and Compare Genes and Pathways from BioPAX

internal_keep_property_class_list<-
  function(keep_list_name=c("property","class")){
    
    #' @keywords internal
    
    if(keep_list_name=="property"){
      keep_list<-
        list(c("term"
               ,"db"
               ,"id"
               ,"positionStatus"
               ,"sequencePosition")
             ,c("term"
                ,"xref"
                ,"evidenceCode"
                ,"featureLocation"
                ,"modificationType"
                ,"sequenceIntervalBegin"
                ,"sequenceIntervalEnd"))
      
    }else if(keep_list_name=="class"){
      keep_list<-
        list(c("Protein"
               ,"SmallMolecule"
               ,"PhysicalEntity"
               ,"RNA"
               ,"DNA")
             ,"Complex"
             # ,c("BiochemicalReaction"
             #    ,"TemplateReaction"
             #    ,"ComplexAssembly"
             #    ,"Transport"
             #    ,"TransportWithBiochemicalReaction"
             #    ,"Degradation")
             # ,c("Catalysis"
             #    ,"TemplateReactionRegulation" 
             #    ,"Control"               
             #    ,"Modulation")
        )
    }
    
    
    return(keep_list)
  }