\name{KEGGPathway-class}
 \docType{class}
 \alias{KEGGPathway-class}
 \alias{edges,KEGGPathway,ANY-method}
 \alias{edges<-}
 \alias{edges<-,KEGGPathway-method}
 \alias{getName,KEGGPathway-method}
 \alias{getTitle,KEGGPathway-method}
 \alias{nodes<-,KEGGPathway,ANY-method}
 \alias{nodes,KEGGPathway-method}
 \alias{edges,KEGGPathway-method}
 \alias{show,KEGGPathway-method}
 \alias{getTitle,KEGGPathway-method}
 
 \title{Class "KEGGPathway"}
 \description{ A class to represent KEGG pathway}
 \section{Objects from the Class}{
 Objects can be created by calls of the form \code{new("KEGGPathway",
   ...)} . Normally they are created by \code{\link{parseKGML}}.
 }
 \section{Slots}{
 	 \describe{
     \item{\code{pathwayInfo}:}{ An object of \code{\link{KEGGPathwayInfo-class}}}
     \item{\code{nodes}:}{ List of objects of \code{\link{KEGGNode-class}}}
     \item{\code{edges}:}{  List of objects of
       \code{\link{KEGGEdge-class}} }
     \item{\code{reactions}:}{ List of objects of
       \code{\link{KEGGReaction-class}} }
   }
 }
 \section{Methods}{
   \describe{
     \item{edges}{\code{signature(object = "KEGGPathway", which =
 	"ANY")}: KEGGEdges of the pathway}
     \item{edges<-}{\code{signature(object = "KEGGPathway")}: setting edges}
     \item{getName}{\code{signature(object = "KEGGPathway")}: getting
       pathway name }
     \item{getTitle}{\code{signature(object = "KEGGPathway")}: getting
       pathway title }
     \item{nodes<-}{\code{signature(object = "KEGGPathway", value =
 	"ANY")}: setting nodes}
     \item{nodes}{\code{signature(object = "KEGGPathway")}: KEGGNodes of
       the pathway }
     \item{getPathwayInfo}{\code{signature(object = "KEGGPathway")}: getting
     KEGGPathwayInfo}
     \item{getTitle}{\code{signature(object = "KEGGPathway")}: getting
       title of the pathway }
     \item{show}{\code{signature(object = "KEGGPathway")}: display method }
 	 }
 }

 \references{ KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/} }

 \author{ Jitao David Zhang \url{mailto:[email protected]} }

 
 \seealso{\code{\link{parseKGML}},
   \code{\link{KEGGEdge-class}}, \code{\link{KEGGNode-class}},
   \code{\link{KEGGReaction-class}}
 }
 
 \examples{
 ## We show how to extract information from KEGGPathway objects
 ## Parse KGML file into a 'KEGGPathway' object
 mapfile <- system.file("extdata/map00260.xml", package="KEGGgraph")
 maptest <- parseKGML(mapfile)
 
 ## short summary of the pathway
 maptest
 
 ## get information of the pathway
 getPathwayInfo(maptest)
 
 ## nodes of the pathway
 nodes <- nodes(maptest)
 node <- nodes[[3]]
 getName(node)
 getType(node)
 getDisplayName(node)
 
 ## edges of the pathway
 edges <- edges(maptest)
 edge <- edges[[3]]
 getEntryID(edge)
 getSubtype(edge)
 }
 \keyword{classes}