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Bio::Search::Tiling::MapTileUtils.3pm

NAME

Bio::Search::Tiling::MapTileUtils - utilities for manipulating closed intervals for an HSP tiling algorithm

SYNOPSIS

Not used directly.

DESCRIPTION

Not used directly.

NOTE

An ``interval'' in this module is defined as an arrayref "[$a0, $a1]", where "$a0, $a1" are scalar numbers satisfying "$a0 <= $a1".

AUTHOR

Mark A. Jensen - maj -at- fortinbras -dot- us

APPENDIX

interval_tiling

  Title   : interval_tiling()
  Usage   : @tiling = interval_tiling( \@array_of_intervals )
  Function: Find minimal set of intervals covering the input set
  Returns : array of arrayrefs of the form
   ( [$interval => [ @indices_of_collapsed_input_intervals ]], ...)
  Args    : arrayref of intervals
 
 

decompose_interval

  Title   : decompose_interval
  Usage   : @decomposition = decompose_interval( \@overlappers )
  Function: Calculate the disjoint decomposition of a set of
            overlapping intervals, each annotated with a list of
            covering intervals
  Returns : array of arrayrefs of the form
            ( [[@interval] => [@indices_of_coverers]], ... )
  Args    : arrayref of intervals (arrayrefs like [$a0, $a1], with
  Note    : Each returned interval is associated with a list of indices of the
            original intervals that cover that decomposition component
            (scalar size of this list could be called the 'coverage coefficient')
  Note    : Coverage: each component of the decomp is completely contained
            in the input intervals that overlap it, by construction.
  Caveat  : This routine expects the members of @overlappers to overlap,
            but doesn't check this.
 
 

are_disjoint

  Title   : are_disjoint
  Usage   : are_disjoint( [$a0, $a1], [$b0, $b1] )
  Function: Determine if two intervals are disjoint
  Returns : True if the intervals are disjoint, false if they overlap
  Args    : array of two intervals
 
 

min_covering_interval

  Title   : min_covering_interval 
  Usage   : $interval = min_covering_interval( [$a0,$a1],[$b0,$b1] )
  Function: Determine the minimal covering interval for two intervals
  Returns : an interval
  Args    : two intervals
 
 

get_intervals_from_hsps

  Title   : get_intervals_from_hsps
  Usage   : @intervals = get_intervals_from_hsps($type, @hsp_objects)
  Function: Return array of intervals of the form [ $start, $end ],
            from an array of hsp objects
  Returns : an array of intervals
  Args    : scalar $type, array of HSPI objects; where $type is one of 'hit',
            'subject', 'query'
 
 

_allowable_filters

  Title   : _allowable_filters
  Usage   : _allowable_filters($Bio_Search_Hit_HitI, $type)
  Function: Return the HSP filters (strand, frame) allowed, 
            based on the reported algorithm
  Returns : String encoding allowable filters: 
            s = strand, f = frame
            Empty string if no filters allowed
            undef if algorithm unrecognized
  Args    : A Bio::Search::Hit::HitI object,
            scalar $type, one of 'hit', 'subject', 'query';
            default is 'query'
 
 

_set_attributes

  Title   : _set_attributes
  Usage   : $tiling->_set_attributes()
  Function: Sets attributes for invocant
            that depend on algorithm name
  Returns : True on success
  Args    : none
  Note    : setting based on the configuration table
            %alg_lookup
 
 

matches_MT

  Title   : matches_MT
  Usage   : $hsp->matches($type, $action, $start, $end)
  Purpose   : Get the total number of identical or conserved matches 
              in the query or sbjct sequence for the given HSP. Optionally can
              report data within a defined interval along the seq.
  Returns   : scalar int 
  Args      : 
  Comments  : Relies on seq_str('match') to get the string of alignment symbols
              between the query and sbjct lines which are used for determining
              the number of identical and conservative matches.
  Note      : Modeled on Bio::Search::HSP::HSPI::matches