TFBS
PatternI
Summary
TFBS::PatternI - interface definition for all pattern objects (currently
includes matrices and word (consensus and regular expressions )
Package variables
No package variables defined.
Included modules
Inherit
Bio::Root::Root
Synopsis
No synopsis!
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.
Methods
Methods description
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 : 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 : 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 : delete_tag
Usage : $pfm->delete_tag('score');
Function: get a hash of all tags for a matrix
Returns : nothing
Args : a string (tag 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 |
Title : tag
Usage : my $acc = $pwm->tag('acc')
$pfm->tag(source => "Gibbs");
Function: Get/set on the structural class of the pattern
Returns : tag value (a scalar/reference)
Args : tag name (string) for get,
tag name (string) and value (any scalar/reference) for set |
Methods code
sub ID
{ my ($self, $ID) = @_;
$self->{'ID'} = $ID if $ID;
return $self->{'ID'};} | sub all_tags
{ return %{$_[0]->{'tags'}};} | sub class
{ my ($self, $class) = @_;
$self->{'class'} = $class if $class;
return $self->{'class'};} | sub delete_tag
{ my ($self, $tag) = @_;
delete $self->{'tags'}->{$tag};
}
1;} | sub name
{ my ($self, $name) = @_;
$self->{'name'} = $name if $name;
return $self->{'name'};} | sub tag
{ my $self = shift;
my $tag = shift || return;
if (scalar @_) {
$self->{'tags'}->{$tag} =shift;
}
return $self->{'tags'}->{$tag};} | General documentation
Please send bug reports and other comments to the author.
| AUTHOR - Boris Lenhard | Top |
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.