Bio::Annotation::Comment(3pm) User Contributed Perl Documentation Bio::Annotation::Comment(3pm)NAME
Bio::Annotation::Comment - A comment object, holding text
SYNOPSIS
$comment = Bio::Annotation::Comment->new();
$comment->text("This is the text of this comment");
$annotation->add_Annotation('comment', $comment);
DESCRIPTION
A holder for comments in annotations, just plain text. This is a very simple object, and justifiably so.
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 : $comment = Bio::Annotation::Comment->new( '-text' => 'some text for this comment');
Function: This returns a new comment object, optionally with
text filed
Example :
Returns : a Bio::Annotation::Comment object
Args : a hash with -text optionally set
AnnotationI implementing functions
as_text
Title : as_text
Usage :
Function:
Example :
Returns :
Args :
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 :
Function:
Example :
Returns :
Args :
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 Bio::AnnotationCollectionI when adding
this object. When obtaining an AnnotationI object from the
collection, the collection will set the value to the tag
under which it was stored unless the object has a tag
stored already.
Example :
Returns : value of tagname (a scalar)
Args : new value (a scalar, optional)
Specific accessors for Comments
text
Title : text
Usage : $value = $self->text($newval)
Function: get/set for the text field. A comment object
just holds a single string which is accessible through
this method
Example :
Returns : value of text
Args : newvalue (optional)
value
Title : value
Usage : $value = $self->value($newval)
Function: Alias of the 'text' method
Example :
Returns : value of text
Args : newvalue (optional)
type
Title : type
Usage : $value = $self->type($newval)
Function: get/set for the comment type field. The comment type
is normally found as a subfield within comment sections
in some files, such as SwissProt
Example :
Returns : value of text
Args : newvalue (optional)
perl v5.14.2 2012-03-02 Bio::Annotation::Comment(3pm)
Check Out this Related Man Page
Bio::Annotation::Reference(3pm) User Contributed Perl Documentation Bio::Annotation::Reference(3pm)NAME
Bio::Annotation::Reference - Specialised DBLink object for Literature References
SYNOPSIS
$reg = Bio::Annotation::Reference->new( -title => 'title line',
-location => 'location line',
-authors => 'author line',
-medline => 998122 );
DESCRIPTION
Object which presents a literature reference. This is considered to be a specialised form of database link. The additional methods provided
are all set/get methods to store strings commonly associated with references, in particular title, location (ie, journal page) and authors
line.
There is no attempt to do anything more than store these things as strings for processing elsewhere. This is mainly because parsing these
things suck and generally are specific to the specific format one is using. To provide an easy route to go format --> object --> format
without losing data, we keep them as strings. Feel free to post the list for a better solution, but in general this gets very messy very
fast...
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 : $ref = Bio::Annotation::Reference->new( -title => 'title line',
-authors => 'author line',
-location => 'location line',
-medline => 9988812);
Function:
Example :
Returns : a new Bio::Annotation::Reference object
Args : a hash with optional title, authors, location, medline, pubmed,
start, end, consortium, rp and rg attributes
AnnotationI implementing functions
as_text
Title : as_text
Usage :
Function:
Example :
Returns :
Args :
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 :
Function:
Example :
Returns :
Args :
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 Bio::AnnotationCollectionI when adding this object. When
obtaining an AnnotationI object from the collection, the collection
will set the value to the tag under which it was stored unless the
object has a tag stored already.
Example :
Returns : value of tagname (a scalar)
Args : new value (a scalar, optional)
Specific accessors for References
start
Title : start
Usage : $self->start($newval)
Function: Gives the reference start base
Example :
Returns : value of start
Args : newvalue (optional)
end
Title : end
Usage : $self->end($newval)
Function: Gives the reference end base
Example :
Returns : value of end
Args : newvalue (optional)
rp
Title : rp
Usage : $self->rp($newval)
Function: Gives the RP line. No attempt is made to parse this line.
Example :
Returns : value of rp
Args : newvalue (optional)
rg
Title : rg
Usage : $obj->rg($newval)
Function: Gives the RG line. This is Swissprot/Uniprot specific, and
if set will usually be identical to the authors attribute,
but the swissprot manual does allow both RG and RA (author)
to be present for the same reference.
Example :
Returns : value of rg (a scalar)
Args : on set, new value (a scalar or undef, optional)
authors
Title : authors
Usage : $self->authors($newval)
Function: Gives the author line. No attempt is made to parse the author line
Example :
Returns : value of authors
Args : newvalue (optional)
location
Title : location
Usage : $self->location($newval)
Function: Gives the location line. No attempt is made to parse the location line
Example :
Returns : value of location
Args : newvalue (optional)
title
Title : title
Usage : $self->title($newval)
Function: Gives the title line (if exists)
Example :
Returns : value of title
Args : newvalue (optional)
medline
Title : medline
Usage : $self->medline($newval)
Function: Gives the medline number
Example :
Returns : value of medline
Args : newvalue (optional)
pubmed
Title : pubmed
Usage : $refobj->pubmed($newval)
Function: Get/Set the PubMed number, if it is different from the MedLine
number.
Example :
Returns : value of medline
Args : newvalue (optional)
database
Title : database
Usage :
Function: Overrides DBLink database to be hard coded to 'MEDLINE' (or 'PUBMED'
if only pubmed id has been supplied), unless the database has been
set explicitly before.
Example :
Returns :
Args :
primary_id
Title : primary_id
Usage :
Function: Overrides DBLink primary_id to provide medline number, or pubmed
number if only that has been defined
Example :
Returns :
Args :
optional_id
Title : optional_id
Usage :
Function: Overrides DBLink optional_id to provide the PubMed number.
Example :
Returns :
Args :
publisher
Title : publisher
Usage : $self->publisher($newval)
Function: Gives the publisher line. No attempt is made to parse the publisher line
Example :
Returns : value of publisher
Args : newvalue (optional)
editors
Title : editors
Usage : $self->editors($newval)
Function: Gives the editors line. No attempt is made to parse the editors line
Example :
Returns : value of editors
Args : newvalue (optional)
encoded_ref
Title : encoded_ref
Usage : $self->encoded_ref($newval)
Function: Gives the encoded_ref line. No attempt is made to parse the encoded_ref line
(this is added for reading PDB records (REFN record), where this contains
ISBN/ISSN/ASTM code)
Example :
Returns : value of encoded_ref
Args : newvalue (optional)
doi
Title : doi
Usage : $self->doi($newval)
Function: Gives the DOI (Digital Object Identifier) from the International
DOI Foundation (http://www.doi.org/), which can be used to resolve
URL links for the full-text documents using:
http://dx.doi.org/<doi>
Example :
Returns : value of doi
Args : newvalue (optional)
consortium
Title : consortium
Usage : $self->consortium($newval)
Function: Gives the consortium line. No attempt is made to parse the consortium line
Example :
Returns : value of consortium
Args : newvalue (optional)
gb_reference
Title : gb_reference
Usage : $obj->gb_reference($newval)
Function: Gives the generic GenBank REFERENCE line. This is GenBank-specific.
If set, this includes everything on the reference line except
the REFERENCE tag and the reference count. This is mainly a
fallback for the few instances when REFERENCE lines have unusual
additional information such as split sequence locations, feature
references, etc. See Bug 2020 in Bugzilla for more information.
Example :
Returns : value of gb_reference (a scalar)
Args : on set, new value (a scalar or undef, optional)
perl v5.14.2 2012-03-02 Bio::Annotation::Reference(3pm)