| Bio::Annotation::Collection(3pm) | User Contributed Perl Documentation | Bio::Annotation::Collection(3pm) |
Bio::Annotation::Collection - Default Perl implementation of AnnotationCollectionI
# 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();
}
}
Bioperl implementation for Bio::AnnotationCollectionI
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The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
Title : new Usage : $coll = Bio::Annotation::Collection->new() Function: Makes a new Annotation::Collection object. Returns : Bio::Annotation::Collection Args : none
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
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)
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.
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)
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
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
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)
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
This is to allow nested annotation: you can use a collection as an annotation object for an annotation collection.
Title : as_text Usage : Function: See L<Bio::AnnotationI> Example : Returns : a string Args : none
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
Title : hash_tree Usage : Function: See L<Bio::AnnotationI> Example : Returns : a hash reference Args : none
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)
Functions put in for backward compatibility with old Bio::Annotation.pm stuff
Title : description Usage : Function: Example : Returns : Args :
Title : add_gene_name Usage : Function: Example : Returns : Args :
Title : each_gene_name Usage : Function: Example : Returns : Args :
Title : add_Reference Usage : Function: Example : Returns : Args :
Title : each_Reference Usage : Function: Example : Returns : Args :
Title : add_Comment Usage : Function: Example : Returns : Args :
Title : each_Comment Usage : Function: Example : Returns : Args :
Title : add_DBLink Usage : Function: Example : Returns : Args :
Title : each_DBLink Usage : Function: Example : Returns : Args :
Title : _typemap Usage : $obj->_typemap($newval) Function: Example : Returns : value of _typemap Args : newvalue (optional)
| 2021-08-15 | perl v5.32.1 |