tfbs::sitepair(3pm) [debian man page]

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

   pattern
	Title	: pattern
	Usage	: my $pattern = $sitepair->pattern();  # gets the pattern
						       # sets the pattern to $pwm
	Function: gets the pattern object associated with the site pair
	Returns : pattern object, here TFBS::Matrix::PWM object
	Args	: none (get-only method)

   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)

   site1 =head2 site2
	Title	: site1
		  site2
	Usage	: my $site1 = $sitepair->site1();

	Function:  Returns individual TFBS::Site objects, from the site pair
	Returns : a TFBS::Site
	Args	: none

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

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

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