Skip site navigation (1)Skip section navigation (2)

FreeBSD Manual Pages

  
 
  

home | help
Bio::Annotation::ColleUsernContributed Perl DocuBio::Annotation::Collection(3)

NAME
       Bio::Annotation::Collection - Default Perl implementation of
       AnnotationCollectionI

SYNOPSIS
	  # get	an AnnotationCollectionI somehow, eg

	  $ac =	$seq->annotation();

	  foreach $key ( $ac->get_all_annotation_keys()	) {
	      @values =	$ac->get_Annotations($key);
	      foreach $value ( @values ) {
		 # value is an Bio::AnnotationI, and defines a "as_text" method
		 print "Annotation ",$key," stringified	value ",$value->as_text,"\n";

		 # also	defined	hash_tree method, which	allows data orientated
		 # access into this object
		 $hash = $value->hash_tree();
	      }
	  }

DESCRIPTION
       Bioperl implementation for Bio::AnnotationCollectionI

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 one
       of the Bioperl mailing lists. Your participation	is much	appreciated.

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

   Support
       Please direct usage questions or	support	issues to the mailing list:

       bioperl-l@bioperl.org

       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.

   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:

	 https://github.com/bioperl/bioperl-live/issues

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	: $coll	= Bio::Annotation::Collection->new()
	Function: Makes	a new Annotation::Collection object.
	Returns	: Bio::Annotation::Collection
	Args	: none

Bio::AnnotationCollectionI implementing	methods
   get_all_annotation_keys
	Title	: get_all_annotation_keys
	Usage	: $ac->get_all_annotation_keys()
	Function: gives	back a list of annotation keys,	which are simple text strings
	Returns	: list of strings
	Args	: none

   get_Annotations
	Title	: get_Annotations
	Usage	: my @annotations = $collection->get_Annotations('key')
	Function: Retrieves all	the Bio::AnnotationI objects for one or	more
		  specific key(s).

		  If no	key is given, returns all annotation objects.

		  The returned objects will have their tagname() attribute set to
		  the key under	which they were	attached, unless the tagname was
		  already set.

	Returns	: list of Bio::AnnotationI - empty if no objects stored	for a key
	Args	: keys (list of	strings) for annotations (optional)

   get_nested_Annotations
	Title	: get_nested_Annotations
	Usage	: my @annotations = $collection->get_nested_Annotations(
				       '-key' => \@keys,
				       '-recursive => 1);
	Function: Retrieves all	the Bio::AnnotationI objects for one or	more
		  specific key(s). If -recursive is set	to true, traverses the nested
		  annotation collections recursively and returns all annotations
		  matching the key(s).

		  If no	key is given, returns all annotation objects.

		  The returned objects will have their tagname() attribute set to
		  the key under	which they were	attached, unless the tagname was
		  already set.

	Returns	: list of Bio::AnnotationI - empty if no objects stored	for a key
	Args	: -keys	     =>	arrayref of keys to search for (optional)
		  -recursive =>	boolean, whether or not	to recursively traverse	the
		   nested annotations and return annotations with matching keys.

   get_all_Annotations
	Title	: get_all_Annotations
	Usage	:
	Function: Similar to get_Annotations, but traverses and	flattens nested
		  annotation collections. This means that collections in the
		  tree will be replaced	by their components.

		  Keys will not	be passed on to	nested collections. I.e., if the
		  tag name of a	nested collection matches the key, it will be
		  flattened in its entirety.

		  Hence, for un-nested annotation collections this will	be identical
		  to get_Annotations.
	Example	:
	Returns	: an array of L<Bio::AnnotationI> compliant objects
	Args	: keys (list of	strings) for annotations (optional)

   get_num_of_annotations
	Title	: get_num_of_annotations
	Usage	: my $count = $collection->get_num_of_annotations()
	Function: Returns the count of all annotations stored in this collection
	Returns	: integer
	Args	: none

Implementation specific	functions - mainly for adding
   add_Annotation
	Title	: add_Annotation
	Usage	: $self->add_Annotation('reference',$object);
		  $self->add_Annotation($object,'Bio::MyInterface::DiseaseI');
		  $self->add_Annotation($object);
		  $self->add_Annotation('disease',$object,'Bio::MyInterface::DiseaseI');
	Function: Adds an annotation for a specific key.

		  If the key is	omitted, the object to be added	must provide a value
		  via its tagname().

		  If the archetype is provided,	this and future	objects	added under
		  that tag have	to comply with the archetype and will be rejected
		  otherwise.

	Returns	: none
	Args	: annotation key ('disease', 'dblink', ...)
		  object to store (must	be Bio::AnnotationI compliant)
		  [optional] object archetype to map future storage of object
			     of	these types to

   remove_Annotations
	Title	: remove_Annotations
	Usage	:
	Function: Remove the annotations for the specified key from this collection.
	Example	:
	Returns	: an array Bio::AnnotationI compliant objects which were stored
		  under	the given key(s)
	Args	: the key(s) (tag name(s), one or more strings)	for which to
		  remove annotations (optional;	if none	given, flushes all
		  annotations)

   flatten_Annotations
	Title	: flatten_Annotations
	Usage	:
	Function: Flattens part	or all of the annotations in this collection.

		  This is a convenience	method for getting the flattened
		  annotation for the given keys, removing the annotation for
		  those	keys, and adding back the flattened array.

		  This should not change anything for un-nested	collections.
	Example	:
	Returns	: an array Bio::AnnotationI compliant objects which were stored
		  under	the given key(s)
	Args	: list of keys (strings) the annotation	for which to flatten,
		  defaults to all keys if not given

Bio::AnnotationI methods implementations
	  This is to allow nested annotation: you can use a collection as an
	  annotation object for	an annotation collection.

   as_text
	Title	: as_text
	Usage	:
	Function: See L<Bio::AnnotationI>
	Example	:
	Returns	: a string
	Args	: none

   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: See L<Bio::AnnotationI>
	Example	:
	Returns	: a hash reference
	Args	: none

   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)

Backward compatible functions
       Functions put in	for backward compatibility with	old Bio::Annotation.pm
       stuff

   description
	Title	: description
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   add_gene_name
	Title	: add_gene_name
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   each_gene_name
	Title	: each_gene_name
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   add_Reference
	Title	: add_Reference
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   each_Reference
	Title	: each_Reference
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   add_Comment
	Title	: add_Comment
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   each_Comment
	Title	: each_Comment
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   add_DBLink
	Title	: add_DBLink
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

   each_DBLink
	Title	: each_DBLink
	Usage	:
	Function:
	Example	:
	Returns	:
	Args	:

Implementation management functions
   _typemap
	Title	: _typemap
	Usage	: $obj->_typemap($newval)
	Function:
	Example	:
	Returns	: value	of _typemap
	Args	: newvalue (optional)

perl v5.32.0			  2019-12-07	Bio::Annotation::Collection(3)

NAME | SYNOPSIS | DESCRIPTION | FEEDBACK | AUTHOR - Ewan Birney | APPENDIX | Bio::AnnotationCollectionI implementing methods | Implementation specific functions - mainly for adding | Bio::AnnotationI methods implementations | Backward compatible functions | Implementation management functions

Want to link to this manual page? Use this URL:
<https://www.freebsd.org/cgi/man.cgi?query=Bio::Annotation::Collection&sektion=3&manpath=FreeBSD+12.2-RELEASE+and+Ports>

home | help