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merge Brian Osborne commits from HEAD to 1.5.1 branch
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svn path=/bioperl-live/branches/bioperl-branch-1-5-1/; revision=9357
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@hyphaltip
hyphaltip committed Oct 13, 2005
1 parent 3fb811a commit b9bdd26
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Showing 17 changed files with 293 additions and 362 deletions.
16 changes: 9 additions & 7 deletions Bio/Ontology/DocumentRegistry.pm
View file
Expand Up @@ -28,7 +28,7 @@ Allows lookups by name.
=head1 DESCRIPTION
Don't use this directly, use Bio::Ontology::OntologyStore instead.
Do not use this directly, use Bio::Ontology::OntologyStore instead.
Bio::Ontology::OntologyStore uses Bio::Ontology::DocumentRegistry to
load and cache ontologies as object graphs, you can just ask it for
what you want by name. See L<Bio::Ontology::OntologyStore> for
Expand Down Expand Up @@ -120,15 +120,15 @@ sub new {
=item Usage
my $singleton = Bio::Ontology::DocumentRegistry->get_instance();
my $singleton = Bio::Ontology::DocumentRegistry->get_instance();
=item Function
constructor
=item Returns
the Bio::Ontology::DocumentRegistry singleton.
The Bio::Ontology::DocumentRegistry singleton.
=item Arguments
Expand All @@ -148,23 +148,25 @@ sub get_instance {
=item Usage
my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology');
my($ontology_url, $definitions_url, $format) = $obj->documents('Sequence Ontology');
=item Function
maps an ontology name to a list of (local or) remote URIs where the files can be located.
Maps an ontology name to a list of (local or) remote URIs where the files
can be located.
=item Returns
a 3-item list:
A 3-item list:
(1) URI for the ontology file
(2) URI for the ontology definitions file
(3) format of the files (dagedit, obo, etc)
=item Arguments
name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component (Gene Ontology)'
Name of an ontology, e.g. 'Sequence Ontology', or 'Cellular Component
(Gene Ontology)'
=back
Expand Down
15 changes: 6 additions & 9 deletions Bio/Ontology/GOterm.pm
View file
Expand Up @@ -108,11 +108,12 @@ use constant FALSE => 0;
=head2 new
Title : new
Usage : $term = Bio::Ontology::GOterm->new( -go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Usage : $term = Bio::Ontology::GOterm->new(
-go_id => "GO:0016847",
-name => "1-aminocyclopropane-1-carboxylate synthase",
-definition => "Catalysis of ...",
-is_obsolete => 0,
-comment => "" );
Function: Creates a new Bio::Ontology::GOterm.
Returns : A new Bio::Ontology::GOterm object.
Args : -go_id => the goid of this GO term [GO:nnnnnnn]
Expand Down Expand Up @@ -168,8 +169,6 @@ sub init {
} # init




=head2 GO_id
Title : GO_id
Expand Down Expand Up @@ -262,8 +261,6 @@ sub remove_secondary_GO_ids {
} # remove_secondary_GO_ids




=head2 to_string
Title : to_string()
Expand Down
29 changes: 12 additions & 17 deletions Bio/Ontology/Ontology.pm
View file
Expand Up @@ -294,10 +294,11 @@ sub close{
Function: Get/set the ontology engine to which all the query methods
delegate.
Example :
Returns : an object implementing L<Bio::Ontology::OntologyEngineI>
Returns : an object implementing Bio::Ontology::OntologyEngineI
Args : on set, new value (an object implementing
L<Bio::Ontology::OntologyEngineI>, or undef)
Bio::Ontology::OntologyEngineI, or undef)
See L<Bio::Ontology::OntologyEngineI>.
=cut

Expand Down Expand Up @@ -364,7 +365,7 @@ sub add_term{
Title : add_relationship
Usage : add_relationship(RelationshipI relationship): RelationshipI
add_relatioship(TermI subject, TermI predicate, TermI object)
add_relatioship(TermI subject, TermI predicate, TermI object)
Function: Adds a relationship object to the ontology engine.
Example :
Returns : Its argument.
Expand Down Expand Up @@ -425,7 +426,7 @@ sub get_relationships {
=head2 get_predicate_terms
Title : get_predicate_terms
Usage : get_predicate_terms(): TermI[]
Usage : get_predicate_terms(): TermI
Function: Retrieves all relationship types.
Example :
Returns : Array of TermI objects
Expand All @@ -444,7 +445,7 @@ sub get_predicate_terms{
=head2 get_child_terms
Title : get_child_terms
Usage : get_child_terms(TermI term, TermI[] predicate_terms): TermI[]
Usage : get_child_terms(TermI term, TermI predicate_terms): TermI
Function: Retrieves all child terms of a given term, that satisfy a
relationship among those that are specified in the second
argument or undef otherwise. get_child_terms is a special
Expand Down Expand Up @@ -472,7 +473,7 @@ sub get_child_terms{
=head2 get_descendant_terms
Title : get_descendant_terms
Usage : get_descendant_terms(TermI term, TermI[] rel_types): TermI[]
Usage : get_descendant_terms(TermI term, TermI rel_types): TermI
Function: Retrieves all descendant terms of a given term, that
satisfy a relationship among those that are specified in
the second argument or undef otherwise.
Expand All @@ -498,7 +499,7 @@ sub get_descendant_terms{
=head2 get_parent_terms
Title : get_parent_terms
Usage : get_parent_terms(TermI term, TermI[] predicate_terms): TermI[]
Usage : get_parent_terms(TermI term, TermI predicate_terms): TermI
Function: Retrieves all parent terms of a given term, that satisfy a
relationship among those that are specified in the second
argument or undef otherwise. get_parent_terms is a special
Expand Down Expand Up @@ -526,7 +527,7 @@ sub get_parent_terms{
=head2 get_ancestor_terms
Title : get_ancestor_terms
Usage : get_ancestor_terms(TermI term, TermI[] predicate_terms): TermI[]
Usage : get_ancestor_terms(TermI term, TermI predicate_terms): TermI
Function: Retrieves all ancestor terms of a given term, that satisfy
a relationship among those that are specified in the second
argument or undef otherwise.
Expand All @@ -552,15 +553,14 @@ sub get_ancestor_terms{
=head2 get_leaf_terms
Title : get_leaf_terms
Usage : get_leaf_terms(): TermI[]
Usage : get_leaf_terms(): TermI
Function: Retrieves all leaf terms from the ontology. Leaf term is a
term w/o descendants.
Example : @leaf_terms = $obj->get_leaf_terms()
Returns : Array of TermI objects.
Args :
=cut

sub get_leaf_terms{
Expand All @@ -577,15 +577,14 @@ sub get_leaf_terms{
=head2 get_root_terms()
Title : get_root_terms
Usage : get_root_terms(): TermI[]
Usage : get_root_terms(): TermI
Function: Retrieves all root terms from the ontology. Root term is a
term w/o descendants.
Example : @root_terms = $obj->get_root_terms()
Returns : Array of TermI objects.
Args :
=cut

sub get_root_terms{
Expand All @@ -602,7 +601,7 @@ sub get_root_terms{
=head2 get_all_terms
Title : get_all_terms
Usage : get_all_terms: TermI[]
Usage : get_all_terms: TermI
Function: Retrieves all terms from the ontology.
We do not mandate an order here in which the terms are
Expand All @@ -613,7 +612,6 @@ sub get_root_terms{
Returns : Array of TermI objects.
Args :
=cut

sub get_all_terms{
Expand Down Expand Up @@ -646,7 +644,6 @@ sub get_all_terms{
-identifier query by the given identifier
-name query by the given name
=cut

sub find_terms{
Expand All @@ -672,7 +669,6 @@ sub find_terms{
compliant object)
Args :
=cut

sub relationship_factory{
Expand All @@ -692,7 +688,6 @@ sub relationship_factory{
compliant object)
Args :
=cut

sub term_factory{
Expand Down

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