Bio::Search::Tiling::MapTileUtils(3pm)			User Contributed Perl Documentation		    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

   containing_hsps()
	Title	: containing_hsps
	Usage	: @hsps = containing_hsps($interval, @hsps_to_search)
	Function: Return a list of hsps whose coordinates completely contain the
		  given $interval
	Returns : Array of HSP objects
	Args	: $interval : [$int1, $int2],
		  array of HSP objects

   covering_groups()
	Title	: covering_groups
	Usage	:
	Function: divide a list of **ordered,disjoint** intervals (as from a
		  coverage map) into a set of disjoint covering groups
	Returns : array of arrayrefs, each arrayref a covering set of
		  intervals
	Args	: array of intervals

   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

   get_SeqFeatures
	Title	: get_SeqFeatures
	Usage	:
	Function: Get the feature objects held by this feature holder.

		  Features which are not top-level are subfeatures of one or
		  more of the returned feature objects, which means that you
		  must traverse the subfeature arrays of each top-level
		  feature object in order to traverse all features associated
		  with this sequence.

		  Top-level features can be obtained by tag, specified in
		  the argument.

		  Use get_all_SeqFeatures() if you want the feature tree
		  flattened into one single array.

	Example :
	Returns : an array of Bio::SeqFeatureI implementing objects
	Args	: [optional] scalar string (feature tag)

   feature_count
	Title	: feature_count
	Usage	: $seq->feature_count()
	Function: Return the number of SeqFeatures attached to a sequence
	Returns : integer representing the number of SeqFeatures
	Args	: None

   add_SeqFeature
	Title	: add_SeqFeature
	Usage	: $seq->add_SeqFeature($feat);
		  $seq->add_SeqFeature(@feat);
	Function: Adds the given feature object (or each of an array of feature
		  objects to the feature array of this
		  sequence. The object passed is required to implement the
		  Bio::SeqFeatureI interface.
	Returns : 1 on success
	Args	: A Bio::SeqFeatureI implementing object, or an array of such objects.

   remove_SeqFeatures
	Title	: remove_SeqFeatures
	Usage	: $seq->remove_SeqFeatures();
	Function: Flushes all attached SeqFeatureI objects.

		  To remove individual feature objects, delete those from the returned
		  array and re-add the rest.
	Example :
	Returns : The array of Bio::SeqFeatureI objects removed from this seq.
	Args	: None

perl v5.14.2							    2012-03-02				    Bio::Search::Tiling::MapTileUtils(3pm)