hacmp

TFBS::SiteSet(3pm)					User Contributed Perl Documentation					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)

perl v5.14.2							    2008-01-24							TFBS::SiteSet(3pm)