#' wrapper around cat
 #' @keywords
 #'
 #' @description cleans up message printing
 #' @param allParams all cogaps parameters
 #' @param ... arguments forwarded to cat
 #' @return displays text
 gapsCat <- function(allParams, ...)
 {
     if (allParams$messages)
         cat(...)
 }
 
 #' checks if file is supported
 #' @keywords internal
 #'
 #' @param file path to file
 #' @return TRUE if file is supported, FALSE if not
 #' @importFrom tools file_ext
 supported <- function(file)
 {
     if (!is(file, "character"))
         return(FALSE)

     return(tools::file_ext(file) %in% c("tsv", "csv", "mtx", "gct"))

 }
 
 #' get number of rows from supported file name or matrix
 #' @keywords internal
 #'
 #' @param data either a file name or a matrix
 #' @return number of rows
 #' @importFrom data.table fread
 #' @importFrom tools file_ext
 nrowHelper <- function(data)
 {
     if (is(data, "character"))
     {
         return(switch(tools::file_ext(data),
             "csv" = nrow(data.table::fread(data, select=1)),
             "tsv" = nrow(data.table::fread(data, select=1)),

             "mtx" = as.numeric(data.table::fread(data, nrows=1, fill=TRUE)[1,1]),
             "gct" = as.numeric(strsplit(as.matrix(data.table::fread(data, nrows=1, sep='\t')), "\\s+")[[1]][1])

         ))
     }
     return(nrow(data))
 }
 
 #' get number of columns from supported file name or matrix
 #' @keywords internal
 #'
 #' @param data either a file name or a matrix
 #' @return number of columns
 #' @importFrom data.table fread
 #' @importFrom tools file_ext
 ncolHelper <- function(data)
 {
     if (is(data, "character"))
     {
         return(switch(tools::file_ext(data),
             "csv" = ncol(data.table::fread(data, nrows=1)) - 1,
             "tsv" = ncol(data.table::fread(data, nrows=1)) - 1,

             "mtx" = as.numeric(data.table::fread(data, nrows=1, fill=TRUE)[1,2]),
             "gct" = as.numeric(strsplit(as.matrix(data.table::fread(data, nrows=1, sep='\t')), "\\s+")[[1]][2])

         ))
     }
     return(ncol(data))
 }
 
 #' extract gene names from data
 #' @keywords internal
 getGeneNames <- function(data, transpose)
 {
     nGenes <- ifelse(transpose, ncolHelper(data), nrowHelper(data))
     return(paste("Gene", 1:nGenes, sep="_"))
 }
 
 #' extract sample names from data
 #' @keywords internal
 getSampleNames <- function(data, transpose)
 {
     nSamples <- ifelse(transpose, nrowHelper(data), ncolHelper(data))
     return(paste("Sample", 1:nSamples, sep="_"))
 }
 
 #' write start up message
 #' @keywords internal
 #'
 #' @param data data set
 #' @param allParams list of all parameters
 #' @return message displayed to screen
 #' @importFrom methods show
 startupMessage <- function(data, allParams)
 {
     nGenes <- ifelse(allParams$transposeData, ncolHelper(data), nrowHelper(data))
     nSamples <- ifelse(allParams$transposeData, nrowHelper(data), ncolHelper(data))
 
     dist_message <- "Standard"
     if (!is.null(allParams$gaps@distributed))
         dist_message <- allParams$gaps@distributed
 
     cat("Running", dist_message, "CoGAPS on", nGenes, "genes and",
         nSamples, "samples")
 
     if (allParams$messages)
     {
         cat(" with parameters:\n\n")
         methods::show(allParams$gaps)
     }
     cat("\n")
 }
 
 #' parse parameters passed through the ... variable
 #' @keywords internal
 #'
 #' @param allParams list of all parameters
 #' @param extraParams list of parameters in ...
 #' @return allParams with any valid parameters in extraParams added
 #' @note will halt with an error if any parameters in extraParams are invalid
 #' @importFrom methods slotNames
 parseExtraParams <- function(allParams, extraParams)
 {
     # parse direct params
     for (s in slotNames(allParams$gaps))
     {
         if (!is.null(extraParams[[s]]))
         {
             allParams$gaps <- setParam(allParams$gaps, s, extraParams[[s]])
             extraParams[[s]] <- NULL
         }
     }
 
     # check for unrecognized options
     if (length(extraParams) > 0)
         stop(paste("unrecognized argument:", names(extraParams)[1]))
 
     return(allParams)
 }
 
 #' check that provided data is valid
 #' @keywords internal
 #'
 #' @param data data matrix
 #' @param uncertainty uncertainty matrix, can be null
 #' @param params CogapsParams object
 #' @return throws an error if data has problems
 checkDataMatrix <- function(data, uncertainty, params)
 {
     if (sum(data < 0) > 0 | sum(uncertainty < 0) > 0)
         stop("negative values in data and/or uncertainty matrix")
     if (nrow(data) <= params@nPatterns | ncol(data) <= params@nPatterns)
         stop("nPatterns must be less than dimensions of data")
     if (sum(uncertainty < 1e-5) > 0)
         warning("small values in uncertainty matrix detected")
 }