NAME

Bio::Annotation::SimpleValue - A simple scalar

SYNOPSIS

use Bio::Annotation::SimpleValue;
use Bio::Annotation::Collection;

my $col = Bio::Annotation::Collection->new();
my $sv = Bio::Annotation::SimpleValue->new(-value => 'someval');
$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 - Ewan Birney

Email birney@ebi.ac.uk

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::SimpleValue->new();
Function: Instantiate a new SimpleValue object
Returns : Bio::Annotation::SimpleValue object
Args    : -value    => $value to initialize the object data field [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 SimpleValue

value

Title   : value
Usage   : $obj->value($newval)
Function: Get/Set the value for simplevalue
Returns : value of value
Args    : newvalue (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