NAME

Bio::Annotation::Relation - Relationship (pairwise) with other objects SeqI and NodeI;

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

FEEDBACK

Mailing Lists

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

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 Bugs

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://github.com/bioperl/bioperl-live/issues

AUTHOR - Mira Han

Email mirhan@indiana.edu

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

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]

AnnotationI implementing functions

as_text

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_text

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_tree

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

tagname

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)

Specific accessors for Relation

type

Title   : type 
Usage   : $obj->type($newval)
Function: Get/Set the type
Returns : type of relation
Args    : newtype (optional)

to

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)

confidence

Title   : confidence
Usage   : $self->confidence($newval)
Function: Gives the confidence value.
Example :
Returns : value of confidence
Args    : newvalue (optional)

confidence_type

Title   : confidence_type
Usage   : $self->confidence_type($newtype)
Function: Gives the confidence type.
Example :
Returns : type of confidence
Args    : newtype (optional)

tag_term

Title   : tag_term
Usage   : $obj->tag_term($newval)
Function: Get/set the L<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 L<Bio::Ontology::TermI> compliant object, or undef
Args    : on set, new value (a L<Bio::Ontology::TermI> compliant
          object or undef, optional)

cpanm Bio::Seq

perl -MCPAN -e shell
install Bio::Seq