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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)