don't use Bioinform::Parameters, use accessors instead;
use CollectionParser to load data from stdin (due to changes in a shortcoming release of bioinform lib;
new lines in the end of files
remove parameters from Collection, make a subclass Macroape::ThresholdingParametersCollection from Bioinform::Collection
make use of Parameter-less motif model, subclass Motif
don't use PM bang-methods
comply to move of .choose moved to Parser
move PWMCounting to a separate class; make use of novel data models, backgrounds  and conversion algorithms
comply with augment-->augmented method renaming
use expect instead of should in specs
move inverf from bioinform (it's removed from there); replace collect_hash with common ruby idiom
refactor naming models
remove test about loading from motifs for scannong from a collection of pm-s without thresholds (because it isn't an option any more)
fix pwms to be obtained from pcm using exact count of column, not a common one (discrepancies in 10th digit or so)
Fix yaml-s to comply with new formats and model types
make use of Motif and Collection classes created from scratch, not derived from bioinform's classes
don't use choose_parser_for_collection because it's always the same
rename converters to their actual names
finally remove Bioinform::PM - old models
remove parsing motifs from stdin as unusable and misleading feature
Parser#parse now returns a Hash instead of OpenStruct so fix it
partial_sums was removed from bioinform
explicitly split motifs