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merge_predict_res.py

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    reactId_ExchClass.R 7.27 KiB
    #  reactId_ExchClass.R
    #  FBA and friends with R.
    #
    #  Copyright (C) 2010-2014 Gabriel Gelius-Dietrich, Dpt. for Bioinformatics,
    #  Institute for Informatics, Heinrich-Heine-University, Duesseldorf, Germany.
    #  All right reserved.
    #  Email: geliudie@uni-duesseldorf.de
    #  
    #  This file is part of sybil.
    #
    #  Sybil is free software: you can redistribute it and/or modify
    #  it under the terms of the GNU General Public License as published by
    #  the Free Software Foundation, either version 3 of the License, or
    #  (at your option) any later version.
    #
    #  Sybil is distributed in the hope that it will be useful,
    #  but WITHOUT ANY WARRANTY; without even the implied warranty of
    #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    #  GNU General Public License for more details.
    #
    #  You should have received a copy of the GNU General Public License
    #  along with sybil.  If not, see <http://www.gnu.org/licenses/>.
    
    
    # reactId_ExchClass
    
    
    #------------------------------------------------------------------------------#
    #                   definition of the class reactId_Exch                       #
    #------------------------------------------------------------------------------#
    
    setClass("reactId_Exch",
             representation(
                  uptake  = "logical",
                  met_pos = "integer",
                  met_id  = "character",
                  lowbnd  = "numeric",
                  uppbnd  = "numeric"
             ),
             contains = "reactId",
             validity = .validreactId_Exch
    )
    
    
    #------------------------------------------------------------------------------#
    #                            default constructor                               #
    #------------------------------------------------------------------------------#
    
    setMethod(f = "initialize",
              signature = "reactId_Exch",
              definition = function(.Object, mod_id, mod_key = "",
                                    rpnt, rid, upt, mpnt, mid, lb, ub) {
    
                  if ( (!missing(mod_id))  ||
                       (!missing(mod_key)) ||
                       (!missing(rpnt))    ||
                       (!missing(rid))     ||
                       (!missing(upt))     ||
                       (!missing(mpnt))    ||
                       (!missing(mid))     ||
                       (!missing(lb))      ||
                       (!missing(ub)) ) {
                  
                      tmp <- new("reactId",
                                 mod_id  = mod_id,
                                 mod_key = mod_key,
                                 pnt     = rpnt,
                                 id      = rid)
                      as(.Object, "reactId_Exch") <- tmp
                  
                      .Object@uptake  <- as.logical(upt)
                      .Object@met_pos <- as.integer(mpnt)
                      .Object@met_id  <- as.character(mid)
                      .Object@lowbnd  <- as.numeric(lb)
                      .Object@uppbnd  <- as.numeric(ub)
                      validObject(.Object)
                  }
    
                  return(.Object)
              }
    )
    
    
    #------------------------------------------------------------------------------#
    #                            setters and getters                               #
    #------------------------------------------------------------------------------#
    
    # position
    setMethod("met_pos", signature(object = "reactId_Exch"),
              function(object) {
                  return(object@met_pos)
              }
    )
    
    setReplaceMethod("met_pos", signature = (object = "reactId_Exch"),
                     function(object, value) {
                         object@met_pos <- value
                         return(object)
                     }
    )
    
    
    # met_id
    setMethod("met_id", signature(object = "reactId_Exch"),
              function(object) {
                  return(object@met_id)
              }
    )
    
    setReplaceMethod("met_id", signature = (object = "reactId_Exch"),
                     function(object, value) {
                         object@met_id <- value
                         return(object)
                     }
    )
    
    
    # lowbnd
    setMethod("lowbnd", signature(object = "reactId_Exch"),
              function(object) {
                  return(object@lowbnd)
              }
    )
    
    setReplaceMethod("lowbnd", signature = (object = "reactId_Exch"),
                     function(object, value) {
                         object@lowbnd <- value
                         return(object)
                     }
    )
    
    
    # uppbnd
    setMethod("uppbnd", signature(object = "reactId_Exch"),
              function(object) {
                  return(object@uppbnd)
              }
    )
    
    setReplaceMethod("uppbnd", signature = (object = "reactId_Exch"),
                     function(object, value) {
                         object@uppbnd <- value
                         return(object)
                     }
    )
    
    
    # uptake
    setMethod("uptake", signature(object = "reactId_Exch"),
              function(object) {
                  return(object@uptake)
              }
    )
    
    setReplaceMethod("uptake", signature = (object = "reactId_Exch"),
                     function(object, value) {
                         object@uptake <- value
                         return(object)
                     }
    )
    
    
    #------------------------------------------------------------------------------#
    #                               other methods                                  #
    #------------------------------------------------------------------------------#
    
    setMethod("show", signature(object = "reactId_Exch"),
        function(object) {
            wcn <- trunc(log10(length(object))) + 3
            cn  <- paste("[", 1:length(object), "]", sep = "")
            lb <- ifelse(lowbnd(object) <= SYBIL_SETTINGS("MAXIMUM")*-1, -Inf, lowbnd(object))
            ub <- ifelse(uppbnd(object) >= SYBIL_SETTINGS("MAXIMUM"), Inf, uppbnd(object))
            cat(sprintf(paste("%", wcn, "s  ", "%-6s%-22s%-23s%-7s%6s %6s\n", sep = ""),
                "# ", "pos.", "reaction id", "metabolite id", "uptake", "lb", "ub"))
            cat(sprintf(paste("%", wcn, "s  ", "%-6s%-22s%-23s%-7s%6s %6s", sep = ""),
                        cn, react_pos(object), react_id(object),
                        met_id(object), uptake(object), lb, ub), sep = "\n")
            cat("\nnumber of exchange reactions: ", length(object), "\n", sep = "")
        }
    )
    
    
    # uptReact
    setMethod("uptReact", signature(object = "reactId_Exch"),
              function(object) {
                  return(object@react_id[object@uptake])
              }
    )
    
    
    # uptMet
    setMethod("uptMet", signature(object = "reactId_Exch"),
              function(object) {
                  return(object@met_id[object@uptake])
              }
    )
    
    
    # [
    setMethod("[", signature(x = "reactId_Exch"),
        function(x, i, j, ..., drop = FALSE) {
    
            if ( (missing(i)) || (length(i) == 0) ) {
                return(x)
            }
    
            if (is(i, "character")) {
                ind <- match(i, react_id(x))
            }
    #        else if (is(i, "reactId")) {
    #            ind <- which(react_pos(x) %in% react_pos(i))
    #        }
            else {
                ind <- i
            }
    
            if (max(ind, na.rm = TRUE) > length(x)) {
                stop("subscript out of bounds")
            }
    
            newRI <- new("reactId_Exch",
                         mod_id  = x@mod_id,
                         mod_key = x@mod_key,
                         rpnt    = x@react_pos[ind],
                         rid     = x@react_id[ind],
                         upt     = x@uptake[ind],
                         mpnt    = x@met_pos[ind],
                         mid     = x@met_id[ind],
                         lb      = x@lowbnd[ind],
                         ub      = x@uppbnd[ind])
    
            return(newRI)
    
        }
    )