### This function can be used to merge in a single folders, files that are
### placed in multiple subfolders.

### from: folder which contains a bunch of sub-folders
### to: folder where all the files are going to be merged
### patternFromDir: pattern to select only a subset of all the sub-folders
### patternFiles: operate the merging only on a particular set of files
### quiet: if FALSE ask for confirmation before merging files in destination folder


### Example:
### mergeFilesInFolder(getwd(), "../mergedPhotos", patternFromDir="[0-9]", patternFiles="JPG|NEF", quiet=T)


mergeFilesInFolder <- function(from, to, patternFromDir="[0-9]",
                               patternFiles="JPG|NEF", quiet=F) {

    listDirFrom <- list.files(from, patternFromDir)
    listDirFrom <- listDirFrom[file.info(listDirFrom)$isdir]

    if(substr(from, nchar(from), nchar(from)) == "/")
        substr(from, nchar(from), nchar(from)) <- ""
    if(substr(to, nchar(to), nchar(to)) == "/")
        substr(to, nchar(to), nchar(to)) <- ""

    for(eachDir in listDirFrom) {
        fromDir <- paste(from, eachDir, sep="/")
        listFiles <- list.files(fromDir, patternFiles)
        listFilesFrom <- paste(fromDir, listFiles, sep="/")
        destFiles <- paste(to, listFiles, sep="/")
        filesToMove <- cbind(listFilesFrom, destFiles)

        if(!quiet) {
            print(filesToMove)
            prt <- readline("Proceed? (yes/no) \n")
            if(! identical(prt, "yes") )
                stop("Stopped by user.")
        }

        if(any(file.exists(destFiles)))
            stop("destination file already exist")

        #browser()
        rslt <- apply(filesToMove, 1, function(x)
                      file.copy(x[1], x[2]))

        if(!all(rslt)) warning("Something went wrong in folder ", eachDir)
    }

    invisible()
}