R/getReaction.R

In TPEA: A Novel Topology-Based Pathway Enrichment Analysis Approach

getReaction <-
function(reaction){
     reactionlist<-list()
     substrate<-list()
     product<-list()
     childrenlength<-0
     sk<-0
     pk<-0
	 xml_children<-xmlChildren(reaction)
     childrenlength<-length(xml_children)
     if(childrenlength>=1){
         for(i in 1:childrenlength){
		      xml_children_i<-xml_children[[i]]
		      xml_name<-xmlName(xml_children_i)
              if(xml_name=="substrate"){
                  sk<-sk+1
				  substrate[[sk]]<-getSubstrate(xml_children_i)
              }
              if(xml_name=="product"){
                  pk<-pk+1
				  product[[pk]]<-getProduct(xml_children_i)
              }
          }
		  if(sk<1){substrate[[1]]<-getUnknowSubstrate()}
		  if(pk<1){product[[1]]<-getUnknowProduct()}
      }
	 else{
	     substrate[[1]]<-getUnknowSubstrate()
		 product[[1]]<-getUnknowProduct()
	 }
	 reactionlist[[1]]<-xmlGetAttr(reaction,"id","unknow")
     reactionlist[[2]]<-xmlGetAttr(reaction,"name","unknow")
     reactionlist[[3]]<-xmlGetAttr(reaction,"type","unknow")
     reactionlist[[4]]<-substrate
     reactionlist[[5]]<-product
     names(reactionlist)<-c("id","name","type","substrate","product")
     return(reactionlist)
}