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.\" ========================================================================
.\"
.IX Title "Bio::Annotation::SimpleValue 3pm"
.TH Bio::Annotation::SimpleValue 3pm "2021-08-15" "perl v5.32.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Annotation::SimpleValue \- A simple scalar
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\&   use Bio::Annotation::SimpleValue;
\&   use Bio::Annotation::Collection;
\&
\&   my $col = Bio::Annotation::Collection\->new();
\&   my $sv = Bio::Annotation::SimpleValue\->new(\-value => \*(Aqsomeval\*(Aq);
\&   $col\->add_Annotation(\*(Aqtagname\*(Aq, $sv);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Scalar value annotation object
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR  \- Ewan Birney"
.IX Header "AUTHOR - Ewan Birney"
Email birney@ebi.ac.uk
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 7
\& 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]
.Ve
.SH "AnnotationI implementing functions"
.IX Header "AnnotationI implementing functions"
.SS "as_text"
.IX Subsection "as_text"
.Vb 5
\& Title   : as_text
\& Usage   : my $text = $obj\->as_text
\& Function: return the string "Value: $v" where $v is the value
\& Returns : string
\& Args    : none
.Ve
.SS "display_text"
.IX Subsection "display_text"
.Vb 4
\& 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
.Ve
.SS "hash_tree"
.IX Subsection "hash_tree"
.Vb 6
\& 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 \*(Aqvalue\*(Aq pointing to the value
\& Returns : hashrf
\& Args    : none
.Ve
.SS "tagname"
.IX Subsection "tagname"
.Vb 3
\& 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)
.Ve
.SH "Specific accessors for SimpleValue"
.IX Header "Specific accessors for SimpleValue"
.SS "value"
.IX Subsection "value"
.Vb 5
\& Title   : value
\& Usage   : $obj\->value($newval)
\& Function: Get/Set the value for simplevalue
\& Returns : value of value
\& Args    : newvalue (optional)
.Ve
.SS "tag_term"
.IX Subsection "tag_term"
.Vb 4
\& 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)
.Ve