=head1 NAME

probability module - part of the Wise2 package

=head1 SYNOPSIS

This module contains helper functions for the Wise2 package

=head1 DESCRIPTION

=over

=item Probability_from_average_state_occupancy

&Wise2::Probability_from_average_state_occupancy(length)

  for single state (exponetial decays) takes an average length
  and converts that to a probability that will produce that
  length (on average) for the state. NB... this *assumes* that
  you want a single state exp decay.



  Argument length       [UNKN ] average length of state [double]
  Return [UNKN ] Undocumented return value [Probability]


=item state_occupancy_from_Probability

&Wise2::state_occupancy_from_Probability(p)

  If you have a single state then this will tak
  the probability for the state->state transition and
  give you back the average length in the state



  Argument p            [UNKN ] probability of staying in the state [double]
  Return [UNKN ] Undocumented return value [double]


=item Probability2Score

&Wise2::Probability2Score(p)

  maps probabilities to scores. Deals
  sensibly with 0's.



  Argument p            [UNKN ] Undocumented argument [Probability]
  Return [UNKN ] Undocumented return value [Score]


=item Score2Probability

&Wise2::Score2Probability(s)

  maps scores to probabilities



  Argument s            [UNKN ] Undocumented argument [Score]
  Return [UNKN ] Undocumented return value [Probability]


=item Score2Bits

&Wise2::Score2Bits(s)

  maps scores to bits



  Argument s            [UNKN ] Undocumented argument [Score]
  Return [UNKN ] Undocumented return value [Bits]


=item halfbit2Probability

&Wise2::halfbit2Probability(half_bit)

  maps halfbits (log2(prob*2) to
  probabilities



  Argument half_bit     [UNKN ] Undocumented argument [double]
  Return [UNKN ] Undocumented return value [Probability]


=back