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Bio::Search::Tiling::MUserlContributed PerBio::Search::Tiling::MapTileUtils(3)

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 v5.32.1			  2019-12-Bio::Search::Tiling::MapTileUtils(3)

NAME | SYNOPSIS | DESCRIPTION | NOTE | AUTHOR | APPENDIX

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