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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)