TFBS
SitePair
No package variables defined. |
Bio::SeqFeature::FeaturePair |
strict |
Bio::SeqFeature::FeaturePair |
Methods description
Title : GFF
Usage : print $site->GFF();
: print $site->GFF($gff_formatter)
Function: returns a "standard" multiline GFF string
Returns : a string (multiline, newline terminated)
Args : a $gff_formatter function reference (optional)
Title : pattern
Usage : my $pattern = $sitepair->pattern(); # gets the pattern
# sets the pattern to $pwm
Function: gets the pattern object associated with the site pair
Returns : pattern object, here TFBS::Matrix::PWM object
Args : none (get-only method)
Title : site1
site2
Usage : my $site1 = $sitepair->site1();
Function: Returns individual TFBS::Site objects, from the site pair
Returns : a TFBS::Site
Args : none
Methods code
sub GFF
{ return join "\n", $_[0]->site1->GFF, $_[0]->site2->GFF;
}
sub new
{ my ($caller, $site1, $site2) = @_;
if ($Bio::Root::Root::VERSION < 1.4) {
return $caller->SUPER::new($site1, $site2);
}
else {
return $caller->SUPER::new(-feature1 => $site1,
-feature2 => $site2);
}
}
sub pattern
{ $_[0]->feature1();
}
sub site1
{ $_[0]->feature1();
}
sub site2
{ $_[0]->feature2();
}
General documentation
No general documentation available.