Provided by: libtfbs-perl_0.7.1-2_amd64
TFBS::PatternI - interface definition for all pattern objects (currently includes matrices and word (consensus and regular expressions )
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.
Please send bug reports and other comments to the author.
AUTHOR - Boris Lenhard
Boris Lenhard <Boris.Lenhard@cgb.ki.se>
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)