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)