R/compareFolder.R

In snjy9182/smt-beta: Statistical analysis of single molecule trajectories

## compareFolder-methods
##' @name compareFolder
##' @aliases compareFolder
##' @title compareFolder
##' @rdname compareFolder-methods
##' @docType methods
##' 
##' @description compare folders with Diatrack output files. merge track files
##' in each folder into one item of a track list. This list can then be fed
##' into other functions for comparison. It keeps folder information as names
##' of the resulting list.

##' @usage compareFolder(folders,input=1,ab.track=FALSE,cores=1)
##' @param folders a vector storing paths to the folders location.'...'
##'   indicates multiple (unlimited) folders can be added into the function.
##' @param input Input file type (Diatrack .txt file = 1; Diatrack .mat session
##'   file = 2; ImageJ .csv file = 3; SlimFast .txt file = 4).
##' @param ab.track a Logical indicating if absolute coordinates should be 
##' used.
##' @param cores Number of cores used for parallel computation. This can be the
##'   cores on a workstation, or on a cluster.

##' @return
##' \itemize{
##' \item{trackll} A list of tracks, each item of a track list correspond to a
##' folder. This list can then be fed into other functions for comparison. }

##' @examples
##' folder1=system.file('extdata','SWR1',package='sojourner')
##' folder2=system.file('extdata','HTZ1',package='sojourner')
##' trackll=compareFolder(folders=c(folder1,folder2), input=3)
##' str(trackll,max.level=1)

##' @import reshape2
##' @export compareFolder
##'
## FUTURE: maybe plot on dt


compareFolder = function(folders, input = 1, ab.track = FALSE, cores = 1) {
    
    # the number of folder to compare can be extended using ...  statement
    # folder.list=list(folder1,folder2,folder3,folder4,folder5) remove null
    # folders by subsetting un-null folders
    # null.folder=sapply(folder.list,is.null)
    # folder.list=folder.list[!null.folder]
    
    folder.list = vapply(folders, list, FUN.VALUE=list(1))
    
    names(folder.list) = vapply(folder.list, basename, FUN.VALUE=character(1))
    
    sample.list = list()
    
    
    if (ab.track == TRUE) {
        
        for (i in seq_along(folder.list)) {
            sample.list[i] = mergeTracks(folder = folder.list[[i]], 
                createTrackll(folder = folder.list[[i]], 
                input = input, ab.track = TRUE, cores = cores))
            cat("\n...\n")  # seperator makes ouput clearer
            names(sample.list)[i] = names(folder.list)[i]
        }
        
    } else {
        
        for (i in seq_along(folder.list)) {
            # i=1
            sample.list[i] = mergeTracks(folder = folder.list[[i]],
                createTrackll(folder = folder.list[[i]], 
                input = input, ab.track = FALSE, cores = cores))
            cat("\n...\n")  # seperator makes ouput clearer
            names(sample.list)[i] = names(folder.list)[i]
        }
    }
    
    # names(sample.list)=names(folder.list)
    return(sample.list)
    
}