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tfbs::siteset(3pm) [debian man page]

TFBS::SiteSet(3pm)					User Contributed Perl Documentation					TFBS::SiteSet(3pm)

NAME
TFBS::SiteSet - a set of TFBS::Site objects SYNOPSIS
my $site_set = TFBS::SiteSet->new(@list_of_site_objects); # add a TFBS::Site object to set: $site_set->add_site($site_obj); # append another TFBS::SiteSet contents: $site_pair_set->add_site_set($site_obj); # create an iterator: my $it = $site_set->Iterator(-sort_by => 'start'); DESCRIPTION
TFBS::SiteSet is an aggregate class that contains a collection of TFBS::Site objects. It can be created anew and filled with TFBS::Site object. It is also returned by search_seq() method call of some TFBS::PatternI subclasses (e.g. TFBS::Matrix::PWM). FEEDBACK
Please send bug reports and other comments to the author. AUTHOR - Boris Lenhard Boris Lenhard <Boris.Lenhard@cgb.ki.se> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore. add_site Title : add_site Usage : $siteset->add_site($site_object) $siteset->add_site(@list_of_site_objects) Function: adds TFBS::Site objects to an existing TFBS::SiteSet object Returns : $sitepair object (usually ignored) Args : A list of TFBS::Site objects to add add_site_set Title : add_site_set Usage : $siteset->add_site_set($site_set_object) $siteset->add_site(@list_of_site_set_objects) Function: adds the contents of other TFBS::SiteSet objects to an existing TFBS::SiteSet object Returns : $siteset object (usually ignored) Args : A list of TFBS::SiteSet objects whose contents should be added to $siteset size Title : size Usage : my $size = $siteset->size() Function: returns a number of TFBS::Site objects contained in the set Returns : a scalar (integer) Args : none Iterator Title : Iterator Usage : my $siteset_iterator = $siteset->Iterator(-sort_by =>'start'); while (my $site = $siteset_iterator->next) { # do whatever you want with individual matrix objects } Function: Returns an iterator object that can be used to go through all members of the set (TFBS::Site objects) Returns : an iterator object (currently undocumentened in TFBS - but understands the 'next' method) Args : -sort_by # optional - currently it accepts # (default sort order in parenthetse) # 'name' (pattern name, alphabetically) # 'ID' (pattern/matrix ID, alphabetically) # 'start' (site start in sequence, # numerically,increasing order) # 'end' (site end in sequence, # numerically, increasing order) # 'score' (numerically, decreasing order) -reverse # optional - reverses the default sorting order if true GFF Title : GFF Usage : print $siteset->GFF(); : print $siteset->GFF($gff_formatter) Function: returns a "standard" multiline GFF string Returns : a string (multiline, newline terminated) Args : a $gff_formatter function reference (optional) perl v5.14.2 2008-01-24 TFBS::SiteSet(3pm)

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TFBS::SitePairSet(3pm)					User Contributed Perl Documentation				    TFBS::SitePairSet(3pm)

NAME
TFBS::SitePairSet - a set of TFBS::SitePair objects SYNOPSIS
my $site_pair_set = TFBS::SitePairSet->new(@list_of_site_pair_objects); # add a TFBS::SitePair object to set: $site_pair_set->add_site_pair($site_pair_obj); # append another TFBS::SitePairSet contents: $site_pair_set->add_site_pair_set($site_pair_obj); # create an iterator: my $it = $site_pair_set->Iterator(-sort_by => 'start'); DESCRIPTION
TFBS::SitePairSet is an aggregate class that contains a collection of TFBS::SitePair objects. It can be created anew and filled with TFBS::Site::Pair object. It is also returned by search_aln() method call of TFBS::PatternI subclasses (e.g. TFBS::Matrix::PWM). FEEDBACK
Please send bug reports and other comments to the author. AUTHOR - Boris Lenhard Boris Lenhard <Boris.Lenhard@cgb.ki.se> APPENDIX
The rest of the documentation details each of the object methods. Internal methods are preceded with an underscore. size Title : size Usage : my $size = $sitepairset->size() Function: returns a number of TFBS::SitePair objects contained in the set Returns : a scalar (integer) Args : none add_site_pair Title : add_site_pair Usage : $sitepairset->add_site_pair($site_pair_object) $sitepairset->add_site_pair(@list_of_site_pair_objects) Function: adds TFBS::SitePair objects to an existing TFBS::SitePairSet object Returns : $sitepairset object (usually ignored) Args : A list of TFBS::SitePair objects to add add_site_pair_set Title : add_site_pair_set Usage : $sitepairset->add_site_pair_set($site_pair_set_object) $sitepairset->add_site_pair(@list_of_site_pair_set_objects) Function: adds the contents of other TFBS::SitePairSet objects to an existing TFBS::SitePairSet object Returns : $sitepairset object (usually ignored) Args : A list of TFBS::SitePairSet objects whose contents should be added to $sitepairset Iterator Title : Iterator Usage : my $it = $sitepairset->Iterator(-sort_by=>'start'); while (my $site_pair = $it->next()) { #... Function: Returns an iterator object, used to iterate thorugh elements (TFBS::SitePair objects) Returns : a TFBS::_Iterator object Args : -sort_by # optional - currently it accepts # (default sort order in parenthetse) # 'name' (pattern name, alphabetically) # 'ID' (pattern/matrix ID, alphabetically) # 'start' (site start in sequence, # numerically,increasing order) # 'end' (site end in sequence, # numerically, increasing order) # 'score' (1st site in pair, # numerically, decreasing order) -reverse # optional - reverses the default sorting order if true set1 set2 Title : set1 set2 Usage : my $siteset1 = $sitepairset->set1(); : my $siteset2 = $sitepairset->set2() Function: Returns individual TFBS::SiteSet objects, from the site set pair Returns : A TFBS::SiteSet object Args : none GFF Title : GFF Usage : print $site->GFF(); : print $site->GFF($gff_formatter) Function: returns a "standard" multiline GFF string Returns : a string (multiline, newline terminated) Args : a $gff_formatter function reference (optional) perl v5.14.2 2008-01-24 TFBS::SitePairSet(3pm)

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