R/bp2.find.proteins.R

In microbiome/biopax2: BioPAX level 2 S4 object model

## Copyright (c) 2010 Ossi Koivistoinen

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bp2.find.proteins <- function(physical.entities)
  {
    uniprot.ids <- lapply(physical.entities, function(p)
                          {
                            if(length(p) > 0)
                              {
                                objs <- bp2.ids2objects(p)
                                prots <- objs[sapply(objs, function(x) {is(x, "bp2.protein")})]
                                if(length(prots) > 0)
                                  {
                                    return(levels(bp2.get.uniprot.ids(prots)[,2]))
                                  }
                              }
                            return(character())
                          })
    names(uniprot.ids) <- names(physical.entities)
    uniprot.ids
  }