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)