Linux Certif

Toute la documentation sur la certification Linux LPI

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)