Bio::AnnotatableI(3)

NAME
Bio::AnnotatableI - the base interface an annotatable object must implement

SYNOPSIS
    use Bio::SeqIO;
    # get an annotatable object somehow: for example, Bio::SeqI objects
    # are annotatable
    my $seqio = Bio::SeqIO->new(-fh => \*STDIN, -format => 'genbank');
    while (my $seq = $seqio->next_seq()) {
        # $seq is-a Bio::AnnotatableI, hence:
        my $ann_coll = $seq->annotation();
        # $ann_coll is-a Bio::AnnotationCollectionI, hence:
        my @all_anns = $ann_coll->get_Annotations();
        # do something with the annotation objects
    }

DESCRIPTION
This is the base interface that all annotatable objects must implement. A good example is Bio::Seq which is an AnnotableI 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 the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

  Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  http://bugzilla.open-bio.org/

AUTHOR
 Hilmar Lapp E<lt>hlapp@gmx.netE<gt>
 Allen Day E<lt>allenday@ucla.eduE<gt>

APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

  annotation
 Title   : annotation
 Usage   : $obj->annotation($newval)
 Function: Get the annotation collection for this annotatable object.
 Example :
 Returns : a Bio::AnnotationCollectionI implementing object, or undef
 Args    : on set, new value (a Bio::AnnotationCollectionI
           implementing object, optional) (an implementation may not
           support changing the annotation collection)

See Bio::AnnotationCollectionI

"*_tag_*" METHODS
The methods below allow mapping of the old "get_tag_values()"-style annotation access to Bio::AnnotationCollectionI. These need not be implemented in a Bio::AnnotationCollectionI compliant class, as they are built on top of the methods.

DEPRECATED: DO NOT USE THESE FOR FUTURE DEVELOPMENT.

  has_tag
 Usage   : $count = $obj->has_tag($tag)
 Function: returns the number of annotations corresponding to $tag
 Returns : an integer
 Args    : tag name
 Note    : DEPRECATED

Use "get_Annotations" instead.

  add_tag_value
 Usage   : See add_Annotation
 Function:
 Returns :
 Args    : DEPRECATED

See Bio::AnnotationCollectionI::add_Annotation

  get_Annotations
 Usage   : my $parent   = $obj->get_Annotations('Parent');
           my @parents = $obj->get_Annotations('Parent');
 Function: a wrapper around Bio::Annotation::Collection::get_Annotations().
 Returns : returns annotations as
           Bio::Annotation::Collection::get_Annotations() does, but
           additionally returns a single scalar in scalar context
           instead of list context so that if an annotation tag
           contains only a single value, you can do:

           $parent = $feature->get_Annotations('Parent');

           instead of:

           ($parent) = ($feature->get_Annotations('Parent'))[0];

           if the 'Parent' tag has multiple values and is called in a
           scalar context, the number of annotations is returned.

 Args    : an annotation tag name.

  get_tag_values
 Usage   : @annotations = $obj->get_tag_values($tag)
 Function: returns annotations corresponding to $tag
 Returns : a list of scalars
 Args    : tag name
 Note    : DEPRECATED

This method is essentially "get_Annotations", use it instead.

  get_tagset_values
 Usage   : @annotations = $obj->get_tagset_values($tag1,$tag2)
 Function: returns annotations corresponding to a list of tags.
           this is a convenience method equivalent to multiple calls
           to get_tag_values with each tag in the list.
 Returns : a list of Bio::AnnotationI objects.
 Args    : a list of tag names
 Note    : DEPRECATED

See Bio::AnnotationCollectionI::get_Annotations

  get_all_tags
 Usage   : @tags = $obj->get_all_tags()
 Function: returns a list of annotation tag names.
 Returns : a list of tag names
 Args    : none
 Note    : DEPRECATED

See Bio::AnnotationCollectionI::get_all_annotation_keys

  remove_tag
 Usage   : See remove_Annotations().
 Function:
 Returns :
 Args    : DEPRECATED
 Note    : Contrary to what the name suggests, this method removes
           all annotations corresponding to $tag, not just a
           single anntoation.

See Bio::AnnotationCollectionI::remove_Annotations