From 38adee4621c4adbccfefc652163ac0ce3820a9ca Mon Sep 17 00:00:00 2001 From: Brian Osborne Date: Sat, 27 Sep 2014 22:49:24 -0400 Subject: [PATCH] Reformat, correct docs, for legibility --- Bio/OntologyIO/obo.pm | 73 +++++++++++++++++++------------------------ 1 file changed, 32 insertions(+), 41 deletions(-) diff --git a/Bio/OntologyIO/obo.pm b/Bio/OntologyIO/obo.pm index 85d69c596c..92bf0db5e1 100644 --- a/Bio/OntologyIO/obo.pm +++ b/Bio/OntologyIO/obo.pm @@ -199,25 +199,24 @@ sub ontology_name { sub parse { my $self = shift; - # setup the default term factory if not done by anyone yet - $self->term_factory( - Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::OBOterm" ) ) + # Setup the default term factory if not done by anyone yet + $self->term_factory(Bio::Ontology::TermFactory->new( -type => "Bio::Ontology::OBOterm" ) ) unless $self->term_factory(); - ## Parse the file header + # Parse the file header my $annotations_collection = $self->_header(); - # create the default ontology object itself + # Create the default ontology object itself my $ont = Bio::Ontology::Ontology->new( -name => $self->ontology_name(), -engine => $self->_ont_engine() ); - ## Assign the file headers + # Assign the file headers $ont->annotation($annotations_collection); - # set up the ontology of the relationship types - foreach ( + # Set up the ontology of the relationship types + for ( $self->_part_of_relationship(), $self->_is_a_relationship(), $self->_related_to_relationship(), @@ -229,14 +228,12 @@ sub parse { $_->ontology($ont); } -################################## $self->_add_ontology($ont); -################################## - ### Adding new terms + # Adding new terms while ( my $term = $self->_next_term() ) { - ### CHeck if the terms has a valid ID and NAME otherwise ignore the term + # Check if the terms has a valid ID and NAME otherwise ignore the term if ( !$term->identifier() || !$term->name() ) { $self->throw( "OBO File Format Error on line " . $self->{'_current_line_no'} @@ -245,24 +242,23 @@ sub parse { next; } - #print $term->identifier(),"\t",$term->name(),"\n"; - - my $new_ontology_flag = 1; + my $new_ontology_flag = 1; my $ontologies_array_ref = $self->{'_ontologies'}; - foreach my $ontology (@$ontologies_array_ref) { - my ($oname, $t_ns) = ($ontology->name(), $term->namespace() ); - next unless (defined($oname) && defined($t_ns)); + + for my $ontology ( @$ontologies_array_ref ) { + my ($oname, $t_ns) = ( $ontology->name, $term->namespace ); + next unless ( defined($oname) && defined($t_ns) ); if ( $oname eq $t_ns ) { - ### No need to create new ontology + # No need to create new ontology $new_ontology_flag = 0; - $ont = $ontology; + $ont = $ontology; } } - if ( $new_ontology_flag && $term->namespace() ) { + if ( $new_ontology_flag && $term->namespace ) { my $new_ont = Bio::Ontology::Ontology->new( - -name => $term->namespace(), - -engine => $self->_ont_engine() + -name => $term->namespace, + -engine => $self->_ont_engine ); $new_ont->annotation($annotations_collection); $self->_add_ontology($new_ont); @@ -272,10 +268,10 @@ sub parse { $self->_add_term( $term, $ont ); - #### Addding the IS_A relationship + # Adding the IS_A relationship my $isa_parents_array_ref = $self->{'_isa_parents'}; foreach my $parent_term (@$isa_parents_array_ref) { - ### Check if parent exist, if not then add the term to the graph. + # Check if parent exists, if not then add the term to the graph. if ( !( $self->_has_term($parent_term) ) ) { $self->_add_term( $parent_term, $ont ); } @@ -284,41 +280,37 @@ sub parse { $self->_is_a_relationship(), $ont ); } - #### Addding the other relationships like part_of, realted_to, develpos_from + # Adding the other relationships like part_of, related_to, develops_from my $relationship_hash_ref = $self->{'_relationships'}; - foreach my $relationship ( keys %$relationship_hash_ref ) { + for my $relationship ( keys %$relationship_hash_ref ) { my $reltype; - #### Check if relationship exist, if not add it. + # Check if relationship exists, if not add it if ( $self->_ont_engine->get_relationship_type($relationship) ) { - $reltype = - $self->_ont_engine->get_relationship_type($relationship); + $reltype = $self->_ont_engine->get_relationship_type($relationship); } else { - $self->_ont_engine->add_relationship_type( $relationship, - $ont ); - $reltype = - $self->_ont_engine->get_relationship_type($relationship); + $self->_ont_engine->add_relationship_type( $relationship, $ont ); + $reltype = $self->_ont_engine->get_relationship_type($relationship); } - #### Check if the id already exist in the graph + # Check if the id already exists in the graph my $id_array_ref = $$relationship_hash_ref{$relationship}; - foreach my $id (@$id_array_ref) { + for my $id (@$id_array_ref) { my $parent_term = $self->_create_term_object(); $parent_term->identifier($id); $parent_term->ontology($ont); - if ( !( $self->_has_term($parent_term) ) ) { + if ( ! $self->_has_term($parent_term) ) { $self->_add_term( $parent_term, $ont ); } $self->_add_relationship( $parent_term, $term, $reltype, $ont ); } - } - } + return $self->_ont_engine(); -} # parse +} =head2 next_ontology @@ -573,7 +565,6 @@ sub _next_term { my $line_counter = $self->{'_current_line_no'}; while ( my $line = $self->_readline() ) { - #print $line."\n"; ++$line_counter; my $line = $self->_filter_line($line); if ( !$line && $term ) {