Provided by: libbio-perl-perl_1.7.2-3_all
Bio::Search::Tiling::MapTileUtils - utilities for manipulating closed intervals for an HSP tiling algorithm
Not used directly.
Not used directly.
An "interval" in this module is defined as an arrayref "[$a0, $a1]", where "$a0, $a1" are scalar numbers satisfying "$a0 <= $a1".
Mark A. Jensen - maj -at- fortinbras -dot- us
interval_tiling Title : interval_tiling() Usage : @tiling = interval_tiling( \@array_of_intervals ) Function: Find minimal set of intervals covering the input set Returns : array of arrayrefs of the form ( [$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