readLines<-function (con = stdin(), n = -1L, ok = TRUE, warn = FALSE, encoding = "unknown") 
{
    # Small change in realLines defaults  
    if (is.character(con)) {
        con <- file(con, "r")
        on.exit(close(con))
    }
    .Internal(readLines(con, n, ok, warn, encoding))
}

read.table.nowarn<-function(...){
  tryCatch.W.E <- function(expr)
  {
    W <- NULL
    w.handler <- function(w){ # warning handler
      if(!grepl('incomplete final line',w))W<<-w
      invokeRestart("muffleWarning")
    }
    list(value = withCallingHandlers(tryCatch(expr, error = function(e) e),warning = w.handler),warning = W)
  }
  lis<-tryCatch.W.E(read.table(...))
  if(!is.null(lis$warning))warning(lis$warning)
  lis$value
}

is.whole.positive.number <- function(x, tol = .Machine$double.eps^0.5){
  (abs(x - round(x)) < tol)&(x>=0)
}

read.ices<-function(filen, testonly=FALSE){
  # Function to read ices data files and validate if input makes sense 
  # 
  # First two lines are ignored and can be used for comments. 
  # Can read formats 1 full, 2 row, 3 scalar, and 5 column
  #
  # Tests: 
  # Formatcode is valid, years and ages are pos. integers 
  # minimum <= maximum for years and ages
  # number of rows and coulmns match year and age ranges
  # data contains only numbers.  
  # 
  # Returns: A validated data matrix.
  
  if(!file.exists(filen)){
    stop(paste("File",filen, "does not exsist"))
  }
  
  head<-scan(filen, skip=2, n=5, quiet=TRUE)
  minY<-head[1]
  maxY<-head[2]
  minA<-head[3]
  maxA<-head[4]
  datatype<-head[5]

  if(!is.whole.positive.number(minY)){
    stop(paste("In file",filen, ": Minimum year is expected to be a positive integer number"))
  }
  if(!is.whole.positive.number(maxY)){
    stop(paste("In file",filen, ": Maximum year is expected to be a positive integer number"))
  }
  if(!is.whole.positive.number(minA)){
    stop(paste("In file",filen, ": Minimum age is expected to be a positive integer number"))
  }
  if(!is.whole.positive.number(maxA)){
    stop(paste("In file",filen, ": Maximum age is expected to be a positive integer number"))
  }

  if(!(datatype%in%c(1,2,3,5))){
    stop(paste("In file",filen, ": Datatype code is expected to be one of the numbers 1, 2, 3, or 5"))
  }

  if(minY>maxY){
    stop(paste("In file",filen, ": Minimum year is expected to be less than maximum year"))
  }
  if(minA>maxA){
    stop(paste("In file",filen, ": Minimum age is expected to be less than maximum age"))
  }

  C<-as.matrix(read.table.nowarn(filen, skip=5, header=FALSE))

  if(datatype==1){
    if((maxY-minY+1)!=nrow(C)){
      stop(paste("In file",filen, ": Number of rows does not match the year range given"))
    }
    if((maxA-minA+1)>ncol(C)){
      stop(paste("In file",filen, ": Fewer columns than the age range given"))
    }
  }

  if(datatype==2){
    C<-as.matrix(read.table.nowarn(filen, skip=5, header=FALSE))
    if(1!=nrow(C)){
      stop(paste("In file",filen, ": For datatype 2 only one row of data is expected"))
    }
    if((maxA-minA+1)>ncol(C)){
      stop(paste("In file",filen, ": Fewer columns than the age range given"))
    }
    C<-C[rep(1,maxY-minY+1),]
  }

  if(datatype==3){
    C<-as.matrix(read.table.nowarn(filen, skip=5, header=FALSE))
    if(1!=nrow(C)){
      stop(paste("In file",filen, ": For datatype 3 only one row of data is expected"))
    }
    if(1!=ncol(C)){
      stop(paste("In file",filen, ": For datatype 3 only one column of data is expected"))
    }
    C<-C[rep(1,maxY-minY+1),rep(1,maxA-minA+1)]
  }

  if(datatype==5){
    C<-as.matrix(read.table.nowarn(filen, skip=5, header=FALSE))
    if((maxY-minY+1)!=nrow(C)){
      stop(paste("In file",filen, ": Number of rows does not match the year range given"))
    }
    if(1!=ncol(C)){
      stop(paste("In file",filen, ": For datatype 5 only one column of data is expected"))
    }
    C<-C[,rep(1,maxA-minA+1)]
  }
  rownames(C)<-minY:maxY
  C<-C[,1:length(minA:maxA)]
  colnames(C)<-minA:maxA

  if(!is.numeric(C)){
      stop(paste("In file",filen, ": Non numeric data values detected (could for instance be comma used as decimal operator)"))
  }

  return(C)
}