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