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)