--- name: "Bio::Annotation" section: "3pm" platform: "linux" package: "bioperl" version: "1.0-1" release: "Debian 3.0 (Woody)" platforms: ["linux"] url: "https://new.carta.tech/Bio::Annotation" --- # Bio::Annotation(3pm) Bio::Annotation - A generic object for annotations. ``` use Bio::Annotation; use Bio::Annotation::DBLink; use Bio::Annotation::Comment; ``` ``` my $link = new Bio::Annotation::DBLink(-database => 'TSC', -primary_id => 'TSC0000030' ); my $ann = Bio::Annotation->new('-description' => 'some description'); $ann->add_DBLink($link); ``` ``` my $comment = Bio::Annotation::Comment->new('-text' => 'Text of comment'); my $comment2 = Bio::Annotation::Comment->new('-text' => 'Second comment'); $ann->add_Comment($comment); $ann->add_Comment($comment2); ``` ``` my $ref = Bio::Annotation::Reference->new( '-authors' => 'author line', '-title' => 'title line', '-location'=> 'location line', '-start' => 12); $ann->add_Reference($ref); ``` ``` # description is a simple, one line description print "Description is ",$ann->description, "\n"; ``` ``` foreach $comment ( $ann->each_Comment ) { # $comment is a Bio::Annotation::Comment object print "Comment: ", $comment->text(), "\n"; } ``` ``` foreach $link ( $ann->each_DBLink ) { # link is a Bio::Annotation::DBLink object print "Link to ",$link->primary_id, " in database", $link->database,"\n"; } ``` ``` foreach $ref ( $ann->each_Reference ) { # link is a Bio::Annotation::Reference object print "Reference title ", $ref->title , "\n"; } ``` The object represents generic biological annotation of an object. It has the ability to provide ``` a brief, one line description free text comments links to other biological objects references to literature ``` It does not have the following abilities ``` The basis (experimental/non experimental/homology) of the annotation. This is considered to be part of the object which owns the annotation. This is because the type of relevant basis is usually dependent on the object ``` ``` The previous revisions of the object This should be a property of whatever database this object comes from ``` **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://bio.perl.org/MailList.html - About the mailing lists ``` **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 email or the web: ``` bioperl-bugs@bio.perl.org http://bio.perl.org/bioperl-bugs/ ``` Email birney@ebi.ac.uk The rest of the documentation details each of the object methods. Internal methods are usually preceded with a \_\ **new** ``` Title : new Usage : $annotation = Bio::Annotation->new( '-description' => 'a description line'); Function: Makes a new Annotation object. The main thing you will want to do with this is add comment objects and dblink objects, with calls like ``` ``` $annotation->add_Comment($comment); $annotation->add_DBLink($dblink); ``` ``` Example : Returns : a new Bio::Annotation Object Args : hash, potentially with one field, -description ``` **description** ``` Title : description Usage : $obj->description($newval) Function: Example : Returns : value of description Args : newvalue (optional) ``` **add\_gene\_name** ``` Title : add_gene_name Usage : $self->add_gene_name($name1[,$name2,...]) Function: adds a reference object Example : Returns : Args : a string, or a list of strings ``` **remove\_gene\_name** ``` Title : remove_gene_name Usage : $self->remove_gene_name($index) Function: removes a particular gene name Example : Returns : Args : index of the name to remove ``` **each\_gene\_name** ``` Title : each_gene_name Usage : foreach $genename ( $self->each_gene_name() ) { print "seq has gene name $genename\n"; } Function: gets the array of gene names Example : Returns : an array of strings Args : ``` **add\_Reference** ``` Title : add_Reference Usage : $self->add_Reference($ref1[,$ref2,...]) Function: adds a reference object Example : Returns : Args : a Bio::Annotation::Reference or derived object ``` **remove\_Reference** ``` Title : remove_Reference Usage : $self->remove_Reference($index) Function: removes a reference object Example : Returns : Args : index number from references array ``` **each\_Reference** ``` Title : each_Reference Usage : foreach $ref ( $self->each_Reference() ) Function: gets an array of reference Example : Returns : an array of Bio::Annotation::Reference or derived objects Args : ``` **add\_Comment** ``` Title : add_Comment Usage : $self->add_Comment($ref) Function: adds a Comment object Example : Returns : Args : a Bio::Annotation::Comment or derived object ``` **remove\_Comment** ``` Title : remove_Comment Usage : $self->remove_Comment($index) Function: removes a comment object Example : Returns : Args : index number from comments array ``` **each\_Comment** ``` Title : each_Comment Usage : foreach $ref ( $self->each_Comment() ) Function: gets an array of Comment of objects Example : Returns : an array of Bio::Annotation::Comment or derived objects Args : none ``` **add\_DBLink** ``` Title : add_DBLink Usage : $self->add_DBLink($ref) Function: adds a link object Example : Returns : Args : a Bio::Annotation::DBLink or derived object ``` **remove\_DBLink** ``` Title : remove_DBLink Usage : $self->remove_DBLink($index) Function: removes a DBLink object Example : Returns : Args : index number from links array ``` **each\_DBLink** ``` Title : each_DBLink Usage : foreach $ref ( $self->each_DBlink() ) Function: gets an array of DBlink of objects Example : Returns : an array of Bio::Annotation::DBlink or derived objects Args : ```