Fixed MSA output; Added randomOrder and thresholdType

MSA output:
  Added function (parse_alignments) for reading MSA output
  Now including preconsensus in MSA output
  Fixed both sequence names and which alignment string in each output line

thresholdType:
  ArgumentValidator - added test_threshold_type()
  CommandLineParser - added parameter
  ConsensusFilterFactory - init param and logic to set count threshold

randomOrder:
  CommandLineParser - added parameter
  MultipleSequenceDriver - added param to init, in build_preconsensus used to check whether to "shuffle" (made copy of self.queries and used the copy)