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 v5.10.1 2008-01-24 TFBS::SiteSet(3pm)