require(rhdf5)

setClass ( 
  Class = "GROUP_INFO" , 
  representation =representation (
    fid="H5IdComponent" ,gid="H5IdComponent" , gname="character"
  ),
  prototype = prototype (
    fid = NULL, gid = NULL, gname = ""),
    
  validity = function ( object ){
    cat ( "------- GROUP_INFO : method inspector --------  \n " )
    if(is( object@gid, "H5IdComponent") == FALSE ){
      stop ( " [ GROUP_INFO : inspector ] Error in the group name")
      }else{}
    return(TRUE)
}
)

group_info <- function(fid, gname){
  cat("------- GROUP_INFO : method constructor --------\n")
  if (missing(fid))
    stop("Missing the H5 file identifier")
  if (missing(gname))
    stop("Missing group name")
  new(Class="GROUP_INFO", fileid = fid, groupname = gname)
  }

setMethod(
  f = "initialize",
  signature = "GROUP_INFO",
  definition = function(.Object, fileid, groupname){
    cat("------- GROUP_INFO : initializator --------\n")
    .Object@gname <- groupname
    .Object@fid <- fileid
    tmp <- H5Gopen(fileid, groupname)
    .Object@gid <- tmp  
    validObject (.Object)
    return(.Object)
  }
) 


setGeneric(
  # Get the number of group attributes
  name = "getNGroupAttr",
  def = function(object){
    standardGeneric("getNGroupAttr")}
)
setMethod(f = "getNGroupAttr", 
	  signature = "GROUP_INFO",
          definition = function (object) {
	    cat ( "------- GROUP_INFO : method  getNGroupAttr --------\n " )
	    return(H5Oget_num_attrs(object@gid))    
	    cat ( "------- End method getNGroupAttr --------\n " )
          }
) 


setGeneric(
  # Get a group attribute
  name = "getGroupAttr",
  def = function(object, attr){
    standardGeneric("getGroupAttr")}
)
setMethod(f = "getGroupAttr", 
	  signature = "GROUP_INFO",
          definition = function (object, attr) {
	    cat ( "------- GROUP_INFO : method  getGroupAttr --------\n " )
	    id <- H5Aopen( object@gid, attr)
	    value = H5Aread(id)
	    return(value)
	    H5Aclose(id) 
	    cat ( "------- End method getGroupAttr --------\n " )
          }
)


setGeneric(
  # Get a dataset attribute
  name = "getSdsAttr",
  def = function(object, sdsName, attr){
    standardGeneric("getSdsAttr")}
)
setMethod(f = "getSdsAttr", 
	  signature = "GROUP_INFO",
          definition = function (object, sdsName, attr) {
	    cat ( "------- GROUP_INFO : method  getSdsAttr --------\n " )
	    sid <- H5Dopen(object@gid, sdsName)
	    id <- H5Aopen( sid, attr)
	    value = H5Aread(id)
	    return(value)
	    H5Aclose(id) 
	    cat ( "------- End method getSdsAttr --------\n " )
          }
)


setGeneric(
  # Display sub groups names
  name = "listSubGroups",
  def = function(object){
    standardGeneric("listSubGroups")}
)
 setMethod(f = "listSubGroups", 
	   signature = "GROUP_INFO",
	   definition = function (object) {
	    cat ( "------- GROUP_INFO : method  listSubGroups * * * \n " )
	    L = list()
	    br = h5ls(object@gid)
	    for (i in 1:dim(br)[1]){	
	      if ((br$otype[i] == "H5I_GROUP") & (br$group[i] != "/")) {
		  L[length(L) + 1] <- paste0(br$group[i],"/", br$name[i])
	      }
	    }
	    return(L)
	    cat ( "------- End method lisSubtGroups * * * \n " )
          }
) 


setGeneric(
  # Get a datasets names list of a group
  name = "listSds",
  def = function(object){
    standardGeneric("listSds")}
)
setMethod(f = "listSds", 
	  signature = "GROUP_INFO",
          definition = function (object) {
	    cat ( "------- GROUP_INFO : method  listSds * * * \n " )
	    L = list()
	    br = h5ls(object@gid)
	    for (i in 1:dim(br)[1]){	
	      if (br$otype[i] == "H5I_DATASET") {
		if (br$group[i] != "/")
		  L[length(L) + 1] <- paste0(br$group[i],"/", br$name[i])
		else 
		  L[length(L) + 1] <- br$name[i]	
	      }
	  }
	  return(L)
	  cat ( "------- End method lisSdss * * * \n " )
          }
) 


setGeneric(
  # Read sds binary data
  name = "readBinaryData",
  def = function(object, sdsName, ... ){
    standardGeneric("readBinaryData")}
)
setMethod(f = "readBinaryData", 
	  signature = "GROUP_INFO",
          definition = function (object, sdsName, ...) {
	    cat ( "------- GROUP_INFO : method  readBinaryData --------\n " )
	    loc = paste0(object@gname, "/",sdsName)
	    data <- h5read(object@fid, loc,...)
	    return(t(data))
	    cat ( "------- End method readBinaryData --------\n " )
          }
)


setGeneric(
  # Read sds scaled data
  name = "readScaledData",
  def = function(object, sdsName, ... ){
    standardGeneric("readScaledData")}
)
setMethod(f = "readScaledData", 
	  signature = "GROUP_INFO",
          definition = function (object, sdsName, ...) {
	    cat ( "------- GROUP_INFO : method  readScaledData --------\n " )	
	    if((H5Aexists(object@fid, "/sds/_FillValue") == TRUE ) && (H5Aexists(object@fid, "/sds/scale_factor") == TRUE ) && (H5Aexists(object@fid, "/sds/add_offset") == TRUE )){
	      fill = getSdsAttr(object, sdsName, "_FillValue")
	      scale_factor =  getSdsAttr(object, sdsName, "scale_factor")
	      offset = getSdsAttr(object, sdsName, "add_offset")
	    } else{ 
	      cat ("------- Calling metohd ReadBinaryData --------\n ")
	      newData = readBinaryData(object, sdsName, ...)
	      return(newData)
	      stop("------- End method readScaledData --------\n ")
	    }
	    loc = paste0(object@gname, "/",sdsName)
	    data <- h5read(object@fid, loc,...)
	    newData = as.numeric(scale_factor) * (data - as.numeric(offset))
	    return(t(newData))
	    cat ( "------- End method readScaledData --------\n " )
          }
)