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)