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Bio::AnnotatableI.3pm

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