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Reformat, correct docs, for legibility
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@bosborne
bosborne committed Sep 28, 2014
1 parent a7f4b29 commit 38adee4
Showing 1 changed file with 32 additions and 41 deletions.
73 changes: 32 additions & 41 deletions Bio/OntologyIO/obo.pm
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Expand Up @@ -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(),
Expand All @@ -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'}
Expand All @@ -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);
Expand All @@ -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 );
}
Expand All @@ -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
Expand Down Expand Up @@ -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 ) {
Expand Down

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