TFBS
SiteSet
Summary
TFBS::SiteSet - a set of TFBS::Site objects
Package variables
No package variables defined.
Included modules
Inherit
Bio::Root::Root
Synopsis
my $site_set = TFBS::SiteSet->new(@list_of_site_objects);
# add a TFBS::Site object to set:
$site_set->add_site($site_obj);
# append another TFBS::SiteSet contents:
$site_pair_set->add_site_set($site_obj);
# create an iterator:
my $it = $site_set->Iterator(-sort_by => 'start');
Description
TFBS::SiteSet is an aggregate class that contains a collection
of TFBS::Site objects. It can be created anew and filled with
TFBS::Site object. It is also returned by search_seq() method call
of some TFBS::PatternI subclasses (e.g. TFBS::Matrix::PWM).
Methods
Methods description
Title : GFF
Usage : print $siteset->GFF();
: print $siteset->GFF($gff_formatter)
Function: returns a "standard" multiline GFF string
Returns : a string (multiline, newline terminated)
Args : a $gff_formatter function reference (optional) |
Title : Iterator
Usage : my $siteset_iterator =
$siteset->Iterator(-sort_by =>'start');
while (my $site = $siteset_iterator->next) {
# do whatever you want with individual matrix objects
}
Function: Returns an iterator object that can be used to go through
all members of the set (TFBS::Site objects)
Returns : an iterator object (currently undocumentened in TFBS -
but understands the 'next' method)
Args : -sort_by # optional - currently it accepts
# (default sort order in parenthetse)
# 'name' (pattern name, alphabetically)
# 'ID' (pattern/matrix ID, alphabetically)
# 'start' (site start in sequence,
# numerically,increasing order)
# 'end' (site end in sequence,
# numerically, increasing order)
# 'score' (numerically, decreasing order)
-reverse # optional - reverses the default sorting order if true |
Title : add_site
Usage : $siteset->add_site($site_object)
$siteset->add_site(@list_of_site_objects)
Function: adds TFBS::Site objects to an existing TFBS::SiteSet object
Returns : $sitepair object (usually ignored)
Args : A list of TFBS::Site objects to add |
Title : size
Usage : my $size = $siteset->size()
Function: returns a number of TFBS::Site objects contained in the set
Returns : a scalar (integer)
Args : none |
Methods code
sub AUTOLOAD
{ my ($self) = @_;
my %discontinued = (sort => 1,
sort_by_name => 1,
sort_reversed => 1,
reverse => 1,
next_site => 1,
reset => 1
);
$AUTOLOAD =~ /.+::(\w+)/;
if ($discontinued{$1}) {
$self->_no_more($1);
}
else {
$self->throw("$1: no such method");
}} | sub GFF
{ my ($self, %args) = @_;
my $site_iterator = $self->Iterator(-sort_by=>'start');
my $gff_string = "";
while (my $site = $site_iterator->next()) {
$gff_string .= $site->GFF(%args)."\n";
}
return $gff_string;
}
} | sub _no_more
{ $_[0]->throw("Method '$_[1]' is no longer available in ".
ref($_[0]).". Use the 'Iterator' method instead.");
}
1;} | sub add_site
{ my ($self, @site_list) = @_;
foreach my $site (@site_list) {
ref($site) =~ /TFBS::Site*/
or $self->throw("Attempted to add an element ".
"of a wrong type.");
push @{$self->{_site_array_ref}}, $site;
}
return 1;} | sub add_siteset
{ my ($self, @sitesets) = @_;
foreach my $siteset (@sitesets) {
ref($siteset) =~ /TFBS::Site.*Set/
or $self->throw("Attempted to add an element ".
"that is not a TFBS::SiteSet object.");
push @{$self->{_site_array_ref}},
@{ $siteset->{_site_array_ref} };
}
return $self;} | sub all_sites
{ my ($self,%args) = @_;
return @{$self->{_site_array_ref}} if @{$self->{_site_array_ref}};} | sub new
{ my ($class, @data) = @_;
my $self = bless {}, ref($class) || $class;
$self->{_site_array_ref} = [];
@data = @{$class->{site_list}} if !@data && ref($class);
$self->add_site(@data);
return $self;} | sub old_GFF
{ eval "require GFF::GeneFeatureSet;";
if ($@) { print STDERR "Failed to load GFF modules, stopped"; return; }
my ($self) = @_;
my $site_iterator = $self->Iterator(-sort_by=>'start');
my $GFFset = GFF::GeneFeatureSet->new(2);
while (my $site = $site_iterator->next()) {
$GFFset->addGeneFeature($site->GFF());
}
return $GFFset;
}
} | sub size
{ scalar @{ $_[0]->{_site_array_ref} };} | 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.
Title : add_site_set
Usage : $siteset->add_site_set($site_set_object)
$siteset->add_site(@list_of_site_set_objects)
Function: adds the contents of other TFBS::SiteSet objects
to an existing TFBS::SiteSet object
Returns : $siteset object (usually ignored)
Args : A list of TFBS::SiteSet objects whose contents should be
added to $siteset