R/mergeTracks.R

In sojourner: Statistical analysis of single molecule trajectories

## mergeTracks-methods
##' @name mergeTracks
##' @aliases mergeTracks
##' @title mergeTracks
##' @rdname mergeTracks-methods
##' @docType methods

##' @description merge track lists in a list into one

##' @usage
##' mergeTracks(folder, trackll)

##' @param folder Full path to the output files.
##' @param trackll A list of track lists.
##' @return modified trackll
##' @examples
##' #Basic masking with folder path with image masks
##' folder = system.file('extdata', 'SWR1', package = 'sojourner')
##' trackll=createTrackll(folder=folder, input=3)
##' trackll.merged <- mergeTracks(folder = folder, trackll = trackll)


##' @details
##' IMPORTANT: Once a trackll has been merged, it cannot be masked using 
##' maskTracks().
##' 
##' Merging creates the following data structure: (1) first level is the 
##' folder name, (2) second level is a list of data.frames/tracks from all 
##' output files merged into one.
##' 
##' If not merged, track lists takes the name of individual files in the 
##' folder. If merged, the single merged track list takes the folder name.

##' @export mergeTracks

##-----------------------------------------------------------------------------
## 

mergeTracks = function(folder, trackll) {
    
    first.name = names(trackll)[[1]]
    pattern = substr(first.name, nchar(first.name) - 3, nchar(first.name))
    
    track.holder = c()
    
    # getting a file list of track files in a directory
    file.list = list.files(path = folder, pattern = pattern, full.names = TRUE)
    folder.name = basename(folder)
    
    # concatenate track list into one list of data.frames
    for (i in seq_along(file.list)) {
        track.holder = c(track.holder, trackll[[i]])
    }
    
    # rename indexPerTrackll of index extrac index
    Index = strsplit(names(track.holder), split = "[.]")  # split='\\.'
    
    # remove the last old indexPerTrackll
    Index = lapply(Index, function(x) {
        x = x[seq_len((length(x) - 1))]
        x = paste(x, collapse = ".")
    })
    
    # add indexPerTrackll to track name
    indexPerTrackll = seq_along(track.holder)
    names(track.holder) = mapply(paste, Index, indexPerTrackll, sep = ".")
    
    # make the result a list of list with length 1
    trackll = list()
    trackll[[1]] = track.holder
    names(trackll)[[1]] = folder.name
    
    cat(paste("\nMerging of folder", folder.name, "complete.\n", sep = " "))
    
    return(trackll)
}