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 listsSupport
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/issuesAUTHOR - 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 : noneBio::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 : noneget_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 : noneImplementation 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 toremove_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 givenBio::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 : nonedisplay_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] callbackhash_tree
Title : hash_tree
Usage :
Function: See L<Bio::AnnotationI>
Example :
Returns : a hash reference
Args : nonetagname
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)