Bio::Annotation Relation
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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
Bio::AnnotationI Bio::Root::Root
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
newDescriptionCode
as_textDescriptionCode
display_textDescriptionCode
hash_treeDescriptionCode
tagnameDescriptionCode
typeDescriptionCode
toDescriptionCode
confidenceDescriptionCode
confidence_typeDescriptionCode
tag_termDescriptionCode
Methods description
newcode    nextTop
 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]
as_textcodeprevnextTop
 Title   : as_text
Usage : my $text = $obj->as_text
Function: return the string "Value: $v" where $v is the value
Returns : string
Args : none
display_textcodeprevnextTop
 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
hash_treecodeprevnextTop
 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
tagnamecodeprevnextTop
 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)
type codeprevnextTop
 Title   : type 
Usage : $obj->type($newval)
Function: Get/Set the type
Returns : type of relation
Args : newtype (optional)
tocodeprevnextTop
 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)
confidencecodeprevnextTop
 Title   : confidence
Usage : $self->confidence($newval)
Function: Gives the confidence value.
Example :
Returns : value of confidence
Args : newvalue (optional)
confidence_typecodeprevnextTop
 Title   : confidence_type
Usage : $self->confidence_type($newtype)
Function: Gives the confidence type.
Example :
Returns : type of confidence
Args : newtype (optional)
tag_termcodeprevnextTop
 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
newdescriptionprevnextTop
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);

   # set the term first
defined $term && $self->tag_term($term); defined $type && $self->type($type); defined $to && $self->to($to); defined $tag && $self->tagname($tag); return $self;
}
as_textdescriptionprevnextTop
sub as_text {
   my ($self) = @_;

   return $self->type." to  ".$self->to->id;
}
display_textdescriptionprevnextTop
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);
  }
}
hash_treedescriptionprevnextTop
sub hash_tree {
    my $self = shift;

    my $h = {};
    $h->{'type'} = $self->type;
    $h->{'to'} = $self->to;
    return $h;
}
tagnamedescriptionprevnextTop
sub tagname {
    my $self = shift;

    # check for presence of an ontology term
if($self->{'_tag_term'}) { # keep a copy in case the term is removed later
$self->{'tagname'} = $_[0] if @_; # delegate to the ontology term object
return $self->tag_term->name(@_); } return $self->{'tagname'} = shift if @_; return $self->{'tagname'};
}
typedescriptionprevnextTop
sub type {
   my ($self,$type) = @_;

   if( defined $type) {
      $self->{'type'} = $type;
    }
    return $self->{'type'};
}
todescriptionprevnextTop
sub to {
   my ($self,$to) = @_;

   if( defined $to) {
      $self->{'to'} = $to;
    }
    return $self->{'to'};
}
confidencedescriptionprevnextTop
sub confidence {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'confidence'} = $value;
    }
    return $self->{'confidence'};
}
confidence_typedescriptionprevnextTop
sub confidence_type {
   my ($self,$type) = @_;
   if( defined $type) {
      $self->{'confidence_type'} = $type;
    }
    return $self->{'confidence_type'};
}
tag_termdescriptionprevnextTop
sub tag_term {
    my $self = shift;

    return $self->{'_tag_term'} = shift if @_;
    return $self->{'_tag_term'};
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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/
AUTHOR - Mira HanTop
Email mirhan@indiana.edu
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
AnnotationI implementing functionsTop
Specific accessors for RelationTop