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

NAME

       TFBS::PatternI - interface definition for all pattern objects (currently includes matrices and word (consensus and regular expressions )

DESCRIPTION

       TFBS::PatternI is a draft class that should contain general interface for matrix and other (future) pattern objects. It is not defined and
       not used yet, as I need to ponder over certain unresolved issues in general pattern definition. User feedback is more than welcome.

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.

   ID
	Title	: ID
	Usage	: my $ID = $icm->ID()
		  $pfm->ID('M00119');
	Function: Get/set on the ID of the pattern (unique in a DB or a set)
	Returns : pattern ID (a string)
	Args	: none for get, string for set

   name
	Title	: name
	Usage	: my $name = $pwm->name()
		  $pfm->name('PPARgamma');
	Function: Get/set on the name of the pattern
	Returns : pattern name (a string)
	Args	: none for get, string for set

   class
	Title	: class
	Usage	: my $class = $pwm->class()
		  $pfm->class('forkhead');
	Function: Get/set on the structural class of the pattern
	Returns : class name (a string)
	Args	: none for get, string for set

   tag
	Title	: tag
	Usage	: my $acc = $pwm->tag('acc')
		  $pfm->tag(source => "Gibbs");
	Function: Get/set on the structural class of the pattern
	Returns : tag value (a scalar/reference)
	Args	: tag name (string) for get,
		  tag name (string) and value (any scalar/reference) for set

   all_tags
	Title	: all_tags
	Usage	: my %tag = $pfm->all_tags();
	Function: get a hash of all tags for a matrix
	Returns : a hash of all tag values keyed by tag name
	Args	: none

   delete_tag
	Title	: delete_tag
	Usage	: $pfm->delete_tag('score');
	Function: get a hash of all tags for a matrix
	Returns : nothing
	Args	: a string (tag name)

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