Bio::Search::Tiling::MapTileUtils man page on Fedora

Man page or keyword search:  
man Server   31170 pages
apropos Keyword Search (all sections)
Output format
Fedora logo
[printable version]

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

   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

perl v5.14.1			  2011-07-Bio::Search::Tiling::MapTileUtils(3)
[top]

List of man pages available for Fedora

Copyright (c) for man pages and the logo by the respective OS vendor.

For those who want to learn more, the polarhome community provides shell access and support.

[legal] [privacy] [GNU] [policy] [cookies] [netiquette] [sponsors] [FAQ]
Tweet
Polarhome, production since 1999.
Member of Polarhome portal.
Based on Fawad Halim's script.
....................................................................
Vote for polarhome
Free Shell Accounts :: the biggest list on the net