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)