Christopher Fields > BioPerl-1.6.923 > Bio::Search::Tiling::MapTileUtils

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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
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