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AMEN: v.1.1.2 released, four changes & three bugs fixed !
07-25-2008
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Bio::Annotation::SimpleValue(3pm) User Contributed Perl Documentation Bio::Annotation::SimpleValue(3pm) 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://redmine.open-bio.org/projects/bioperl/ 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) perl v5.14.2 2012-03-02 Bio::Annotation::SimpleValue(3pm)