| TFBS::PatternI(3pm) | User Contributed Perl Documentation | TFBS::PatternI(3pm) |
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.
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.
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
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
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
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
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
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)
| 2018-11-02 | perl v5.28.0 |