--- a/charts.r	Fri May 09 00:58:44 2014 -0400
+++ b/charts.r	Fri May 09 00:58:55 2014 -0400
@@ -1,358 +1,7 @@
 #!/usr/bin/Rscript
 
-#' Returns file name of calling Rscript
-#'
-#' \code{get_Rscript_filename} returns the file name of calling Rscript 
-#' @return A string with the filename of the calling script.
-#'      If not found (i.e. you are in a interactive session) returns NA.
-#'
-#' @export
-get_Rscript_filename <- function() {
-    prog <- sub("--file=", "", grep("--file=", commandArgs(), value=TRUE)[1])
-    if( .Platform$OS.type == "windows") { 
-        prog <- gsub("\\\\", "\\\\\\\\", prog)
-    }
-    prog
-}
-
-#' Recursively sorts a list
-#'
-#' \code{sort_list} returns a sorted list
-#' @param unsorted_list A list.
-#' @return A sorted list.
-#' @export
-sort_list <- function(unsorted_list) {
-    for(ii in seq(along=unsorted_list)) {
-        if(is.list(unsorted_list[[ii]])) {
-            unsorted_list[[ii]] <- sort_list(unsorted_list[[ii]])
-        }
-    }
-    unsorted_list[sort(names(unsorted_list))] 
-}
-
-#' #!/path/to/Rscript
-#' library('getopt');
-#' #get options, using the spec as defined by the enclosed list.
-#' #we read the options from the default: commandArgs(TRUE).
-#' spec = matrix(c(
-#'   'verbose', 'v', 2, "integer",
-#'   'help'   , 'h', 0, "logical",
-#'   'count'  , 'c', 1, "integer",
-#'   'mean'   , 'm', 1, "double",
-#'   'sd'     , 's', 1, "double"
-#' ), byrow=TRUE, ncol=4);
-#' opt = getopt(spec);
-#' 
-#' # if help was asked for print a friendly message 
-#' # and exit with a non-zero error code
-#' if ( !is.null(opt$help) ) {
-#'   cat(getopt(spec, usage=TRUE));
-#'   q(status=1);
-#' }
-#' 
-#' #set some reasonable defaults for the options that are needed,
-#' #but were not specified.
-#' if ( is.null(opt$mean    ) ) { opt$mean    = 0     }
-#' if ( is.null(opt$sd      ) ) { opt$sd      = 1     }
-#' if ( is.null(opt$count   ) ) { opt$count   = 10    }
-#' if ( is.null(opt$verbose ) ) { opt$verbose = FALSE }
-#' 
-#' #print some progress messages to stderr, if requested.
-#' if ( opt$verbose ) { write("writing...",stderr()); }
-#' 
-#' #do some operation based on user input.
-#' cat(paste(rnorm(opt$count,mean=opt$mean,sd=opt$sd),collapse="\n"));
-#' cat("\n");
-#' 
-#' #signal success and exit.
-#' #q(status=0);
-getopt = function (spec=NULL,opt=commandArgs(TRUE),command=get_Rscript_filename(),usage=FALSE,debug=FALSE) {
-
-  # littler compatibility - map argv vector to opt
-  if (exists("argv", where = .GlobalEnv, inherits = FALSE)) {
-    opt = get("argv", envir = .GlobalEnv);
-  }
-
-  ncol=4;
-  maxcol=6;
-  col.long.name    = 1;
-  col.short.name   = 2;
-  col.has.argument = 3;
-  col.mode         = 4;
-  col.description  = 5;
-
-  flag.no.argument = 0;
-  flag.required.argument = 1;
-  flag.optional.argument = 2;
-
-  result = list();
-  result$ARGS = vector(mode="character");
-
-  #no spec.  fail.
-  if ( is.null(spec) ) {
-    stop('argument "spec" must be non-null.');
-
-  #spec is not a matrix.  attempt to coerce, if possible.  issue a warning.
-  } else if ( !is.matrix(spec) ) {
-    if ( length(spec)/4 == as.integer(length(spec)/4) ) {
-      warning('argument "spec" was coerced to a 4-column (row-major) matrix.  use a matrix to prevent the coercion');
-      spec = matrix( spec, ncol=ncol, byrow=TRUE );
-    } else {
-      stop('argument "spec" must be a matrix, or a character vector with length divisible by 4, rtfm.');
-    }
-
-  #spec is a matrix, but it has too few columns.
-  } else if ( dim(spec)[2] < ncol ) {
-    stop(paste('"spec" should have at least ",ncol," columns.',sep=''));
-
-  #spec is a matrix, but it has too many columns.
-  } else if ( dim(spec)[2] > maxcol ) {
-    stop(paste('"spec" should have no more than ",maxcol," columns.',sep=''));
-
-  #spec is a matrix, and it has some optional columns.
-  } else if ( dim(spec)[2] != ncol ) {
-    ncol = dim(spec)[2];
-  }
-
-  #sanity check.  make sure long names are unique, and short names are unique.
-  if ( length(unique(spec[,col.long.name])) != length(spec[,col.long.name]) ) {
-    stop(paste('redundant long names for flags (column ',col.long.name,').',sep=''));
-  }
-  if ( length(na.omit(unique(spec[,col.short.name]))) != length(na.omit(spec[,col.short.name])) ) {
-    stop(paste('redundant short names for flags (column ',col.short.name,').',sep=''));
-  }
-  # convert numeric type to double type
-  spec[,4] <- gsub("numeric", "double", spec[,4])
-
-  # if usage=TRUE, don't process opt, but generate a usage string from the data in spec
-  if ( usage ) {
-    ret = '';
-    ret = paste(ret,"Usage: ",command,sep='');
-    for ( j in 1:(dim(spec))[1] ) {
-      ret = paste(ret,' [-[-',spec[j,col.long.name],'|',spec[j,col.short.name],']',sep='');
-      if (spec[j,col.has.argument] == flag.no.argument) {
-        ret = paste(ret,']',sep='');
-      } else if (spec[j,col.has.argument] == flag.required.argument) {
-        ret = paste(ret,' <',spec[j,col.mode],'>]',sep='');
-      } else if (spec[j,col.has.argument] == flag.optional.argument) {
-        ret = paste(ret,' [<',spec[j,col.mode],'>]]',sep='');
-      }
-    }
-    # include usage strings
-    if ( ncol >= 5 ) {
-      max.long = max(apply(cbind(spec[,col.long.name]),1,function(x)length(strsplit(x,'')[[1]])));
-      ret = paste(ret,"\n",sep='');
-      for (j in 1:(dim(spec))[1] ) {
-        ret = paste(ret,sprintf(paste("    -%s|--%-",max.long,"s    %s\n",sep=''),
-          spec[j,col.short.name],spec[j,col.long.name],spec[j,col.description]
-        ),sep='');
-      }
-    }
-    else {
-      ret = paste(ret,"\n",sep='');
-    }
-    return(ret);
-  }
-
-  #XXX check spec validity here.  e.g. column three should be convertible to integer
-
-  i = 1;
-
-  while ( i <= length(opt) ) {
-    if ( debug ) print(paste("processing",opt[i]));
-
-    current.flag = 0; #XXX use NA
-    optstring = opt[i];
-
-
-    #long flag
-    if ( substr(optstring, 1, 2) == '--' ) {
-      if ( debug ) print(paste("  long option:",opt[i]));
-
-      optstring = substring(optstring,3);
-
-      this.flag = NA;
-      this.argument = NA;
-      kv = strsplit(optstring, '=')[[1]];
-      if ( !is.na(kv[2]) ) {
-        this.flag = kv[1];
-        this.argument = paste(kv[-1], collapse="=");
-      } else {
-        this.flag = optstring;
-      }
-
-      rowmatch = grep( this.flag, spec[,col.long.name],fixed=TRUE );
-
-      #long flag is invalid, matches no options
-      if ( length(rowmatch) == 0 ) {
-        stop(paste('long flag "', this.flag, '" is invalid', sep=''));
-
-      #long flag is ambiguous, matches too many options
-      } else if ( length(rowmatch) > 1 ) {
-        # check if there is an exact match and use that
-        rowmatch = which(this.flag == spec[,col.long.name])
-        if(length(rowmatch) == 0) {
-          stop(paste('long flag "', this.flag, '" is ambiguous', sep=''));
-        }
-      }
-
-      #if we have an argument
-      if ( !is.na(this.argument) ) {
-        #if we can't accept the argument, bail out
-        if ( spec[rowmatch, col.has.argument] == flag.no.argument ) {
-          stop(paste('long flag "', this.flag, '" accepts no arguments', sep=''));
-
-        #otherwise assign the argument to the flag
-        } else {
-          storage.mode(this.argument) = spec[rowmatch, col.mode];
-          result[spec[rowmatch, col.long.name]] = this.argument;
-	  i = i + 1;
-	  next;
-        }
-
-      #otherwise, we don't have an argument
-      } else {
-        #if we require an argument, bail out
-        ###if ( spec[rowmatch, col.has.argument] == flag.required.argument ) {
-        ###  stop(paste('long flag "', this.flag, '" requires an argument', sep=''));
-
-        #long flag has no attached argument. set flag as present.  set current.flag so we can peek ahead later and consume the argument if it's there
-        ###} else {
-          result[spec[rowmatch, col.long.name]] = TRUE;
-          current.flag = rowmatch;
-        ###}
-      }
-
-    #short flag(s)
-    } else if ( substr(optstring, 1, 1) == '-' ) {
-      if ( debug ) print(paste("  short option:",opt[i]));
-
-      these.flags = strsplit(optstring,'')[[1]];
-
-      done = FALSE;
-      for ( j in 2:length(these.flags) ) {
-        this.flag = these.flags[j];
-        rowmatch = grep( this.flag, spec[,col.short.name],fixed=TRUE );
-
-        #short flag is invalid, matches no options
-        if ( length(rowmatch) == 0 ) {
-          stop(paste('short flag "', this.flag, '" is invalid', sep=''));
-
-        #short flag is ambiguous, matches too many options
-        } else if ( length(rowmatch) > 1 ) {
-          stop(paste('short flag "', this.flag, '" is ambiguous', sep=''));
-
-        #short flag has an argument, but is not the last in a compound flag string
-        } else if ( j < length(these.flags) & spec[rowmatch,col.has.argument] == flag.required.argument ) {
-          stop(paste('short flag "', this.flag, '" requires an argument, but has none', sep=''));
-
-        #short flag has no argument, flag it as present
-        } else if ( spec[rowmatch,col.has.argument] == flag.no.argument ) {
-          result[spec[rowmatch, col.long.name]] = TRUE;
-	  done = TRUE;
-
-        #can't definitively process this flag yet, need to see if next option is an argument or not
-        } else {
-          result[spec[rowmatch, col.long.name]] = TRUE;
-          current.flag = rowmatch;
-          done = FALSE;
-        }
-      }
-      if ( done ) {
-        i = i + 1;
-        next;
-      }
-    }
-
-    #invalid opt
-    if ( current.flag == 0 ) {
-      stop(paste('"', optstring, '" is not a valid option, or does not support an argument', sep=''));
-      #TBD support for positional args
-      #if ( debug ) print(paste('"', optstring, '" not a valid option.  It is appended to getopt(...)$ARGS', sep=''));
-      #result$ARGS = append(result$ARGS, optstring);
-
-    # some dangling flag, handle it
-    } else if ( current.flag > 0 ) {
-      if ( debug ) print('    dangling flag');
-      if ( length(opt) > i ) {
-        peek.optstring = opt[i + 1];
-        if ( debug ) print(paste('      peeking ahead at: "',peek.optstring,'"',sep=''));
-
-        #got an argument.  attach it, increment the index, and move on to the next option.  we don't allow arguments beginning with '-' UNLESS
-	#specfile indicates the value is an "integer" or "double", in which case we allow a leading dash (and verify trailing digits/decimals).
-        if ( substr(peek.optstring, 1, 1) != '-' |
-	  #match negative double
-	  ( substr(peek.optstring, 1, 1) == '-'
-	  & regexpr('^-[0123456789]*\\.?[0123456789]+$',peek.optstring) > 0
-	  & spec[current.flag, col.mode]== 'double'
-	  ) |
-	  #match negative integer
-	  ( substr(peek.optstring, 1, 1) == '-'
-	  & regexpr('^-[0123456789]+$',peek.optstring) > 0
-	  & spec[current.flag, col.mode]== 'integer'
-	  )
-	) {
-          if ( debug ) print(paste('        consuming argument *',peek.optstring,'*',sep=''));
-
-          storage.mode(peek.optstring) = spec[current.flag, col.mode];
-          result[spec[current.flag, col.long.name]] = peek.optstring;
-          i = i + 1;
-
-	#a lone dash
-	} else if ( substr(peek.optstring, 1, 1) == '-' & length(strsplit(peek.optstring,'')[[1]]) == 1 ) {
-          if ( debug ) print('        consuming "lone dash" argument');
-          storage.mode(peek.optstring) = spec[current.flag, col.mode];
-          result[spec[current.flag, col.long.name]] = peek.optstring;
-          i = i + 1;
-
-        #no argument
-        } else {
-          if ( debug ) print('        no argument!');
-
-          #if we require an argument, bail out
-          if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
-            stop(paste('flag "', this.flag, '" requires an argument', sep=''));
-
-          #otherwise set flag as present.
-          } else if (
-	    spec[current.flag, col.has.argument] == flag.optional.argument |
-	    spec[current.flag, col.has.argument] == flag.no.argument 
-	  ) {
-  	    x = TRUE;
-  	    storage.mode(x) = spec[current.flag, col.mode];
-            result[spec[current.flag, col.long.name]] = x;
-          } else {
-            stop(paste("This should never happen.",
-              "Is your spec argument correct?  Maybe you forgot to set",
-              "ncol=4, byrow=TRUE in your matrix call?"));
-	  }
-        }
-      #trailing flag without required argument
-      } else if ( spec[current.flag, col.has.argument] == flag.required.argument ) {
-        stop(paste('flag "', this.flag, '" requires an argument', sep=''));
-
-      #trailing flag without optional argument
-      } else if ( spec[current.flag, col.has.argument] == flag.optional.argument ) {
-        x = TRUE;
-        storage.mode(x) = spec[current.flag, col.mode];
-        result[spec[current.flag, col.long.name]] = x;
-
-      #trailing flag without argument
-      } else if ( spec[current.flag, col.has.argument] == flag.no.argument ) {
-        x = TRUE;
-        storage.mode(x) = spec[current.flag, col.mode];
-        result[spec[current.flag, col.long.name]] = x;
-      } else {
-        stop("this should never happen (2).  please inform the author.");
-      }
-    #no dangling flag, nothing to do.
-    } else {
-    }
-
-    i = i+1;
-  }
-  return(result);
-}
+# load getopt library
+library('getopt');
 
 # convert multi parameter string (i.e. key1: value, key2: value, ...) to object
 split <- function(argument){
@@ -421,7 +70,7 @@
 header_settings <- paste('# settings -', opt$settings, sep=' ')
 header_columns <- paste('# columns -', opt$columns, sep=' ')
 
-# fill gaps
+# check result
 if (length(l) > 0) {
     # print details
     if (!is.null(opt$verbose)) {
@@ -451,6 +100,7 @@
     # close file
     close(output)
 } else {
+    # print details
     print ('Columns:')
     print (columns)
     print ('Settings:')