Bio::Annotation
Relation
Toolbar
Summary
Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI;
Package variables
Privates (from "my" definitions)
$DEFAULT_CB = sub { return $_[0]->type." to ".$_[0]->to->id }
Inherit
Synopsis
use Bio::Annotation::Relation;
use Bio::Annotation::Collection;
my $col = Bio::Annotation::Collection->new();
my $sv = Bio::Annotation::Relation->new(-type => "paralogy" -to => "someSeqI");
$col->add_Annotation('tagname', $sv);
Description
Scalar value annotation object
Methods
Methods description
Title : new
Usage : my $sv = Bio::Annotation::Relation->new();
Function: Instantiate a new Relation object
Returns : Bio::Annotation::Relation object
Args : -type => $type of relation [optional]
-to => $obj which $self is in relation to [optional]
-tagname => $tag to initialize the tagname [optional]
-tag_term => ontology term representation of the tag [optional] |
Title : as_text
Usage : my $text = $obj->as_text
Function: return the string "Value: $v" where $v is the value
Returns : string
Args : none |
Title : display_text
Usage : my $str = $ann->display_text();
Function: returns a string. Unlike as_text(), this method returns a string
formatted as would be expected for te specific implementation.
One can pass a callback as an argument which allows custom text
generation; the callback is passed the current instance and any text
returned
Example :
Returns : a string
Args : [optional] callback |
Title : hash_tree
Usage : my $hashtree = $value->hash_tree
Function: For supporting the AnnotationI interface just returns the value
as a hashref with the key 'value' pointing to the value
Returns : hashrf
Args : none |
Title : tagname
Usage : $obj->tagname($newval)
Function: Get/set the tagname for this annotation value.
Setting this is optional. If set, it obviates the need to
provide a tag to AnnotationCollection when adding this
object.
Example :
Returns : value of tagname (a scalar)
Args : new value (a scalar, optional) |
Title : type
Usage : $obj->type($newval)
Function: Get/Set the type
Returns : type of relation
Args : newtype (optional) |
Title : to
Usage : $obj->to($newval)
Function: Get/Set the object which $self is in relation to
Returns : the object which the relation applies to
Args : new target object (optional) |
Title : confidence
Usage : $self->confidence($newval)
Function: Gives the confidence value.
Example :
Returns : value of confidence
Args : newvalue (optional) |
Title : confidence_type
Usage : $self->confidence_type($newtype)
Function: Gives the confidence type.
Example :
Returns : type of confidence
Args : newtype (optional) |
Title : tag_term
Usage : $obj->tag_term($newval)
Function: Get/set the Bio::Ontology::TermI object representing
the tag name.
This is so you can specifically relate the tag of this
annotation to an entry in an ontology. You may want to do
this to associate an identifier with the tag, or a
particular category, such that you can better match the tag
against a controlled vocabulary.
This accessor will return undef if it has never been set
before in order to allow this annotation to stay
light-weight if an ontology term representation of the tag
is not needed. Once it is set to a valid value, tagname()
will actually delegate to the name() of this term.
Example :
Returns : a Bio::Ontology::TermI compliant object, or undef
Args : on set, new value (a Bio::Ontology::TermI compliant
object or undef, optional) |
Methods code
sub new
{ my ($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($type, $to, $tag, $term) =
$self->_rearrange([qw(TYPE TO TAGNAME TAG_TERM)], @args);
defined $term && $self->tag_term($term);
defined $type && $self->type($type);
defined $to && $self->to($to);
defined $tag && $self->tagname($tag);
return $self;} | sub as_text
{ my ($self) = @_;
return $self->type." to ".$self->to->id; } | sub display_text
{ my ($self, $cb) = @_;
$cb ||= $DEFAULT_CB;
$self->throw("Callback must be a code reference") if ref $cb ne 'CODE';
return $cb->($self);
}} | sub hash_tree
{ my $self = shift;
my $h = {};
$h->{'type'} = $self->type;
$h->{'to'} = $self->to;
return $h;} | sub tagname
{ my $self = shift;
if($self->{'_tag_term'}) {
$self->{'tagname'} = $_[0] if @_;
return $self->tag_term->name(@_);
}
return $self->{'tagname'} = shift if @_;
return $self->{'tagname'};} | sub type
{ my ($self,$type) = @_;
if( defined $type) {
$self->{'type'} = $type;
}
return $self->{'type'};} | sub to
{ my ($self,$to) = @_;
if( defined $to) {
$self->{'to'} = $to;
}
return $self->{'to'};} | sub confidence
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'confidence'} = $value;
}
return $self->{'confidence'};} | sub confidence_type
{ my ($self,$type) = @_;
if( defined $type) {
$self->{'confidence_type'} = $type;
}
return $self->{'confidence_type'};} | sub tag_term
{ my $self = shift;
return $self->{'_tag_term'} = shift if @_;
return $self->{'_tag_term'};
}
1;} | General documentation
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to one
of the Bioperl mailing lists. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
| AnnotationI implementing functions | Top |
| Specific accessors for Relation | Top |