From 68dcb70b77c5e9b67d611a64af3e418d567df2fc Mon Sep 17 00:00:00 2001
From: Brian Osborne <briano@bioteam.net>
Date: Sun, 28 Sep 2014 01:09:55 -0400
Subject: [PATCH] Minor edits

---
 Bio/Ontology/OBOEngine.pm | 14 ++++++--------
 Bio/OntologyIO/obo.pm     | 13 ++++++-------
 2 files changed, 12 insertions(+), 15 deletions(-)

diff --git a/Bio/Ontology/OBOEngine.pm b/Bio/Ontology/OBOEngine.pm
index 16460dac1..2997a6eae 100644
--- a/Bio/Ontology/OBOEngine.pm
+++ b/Bio/Ontology/OBOEngine.pm
@@ -296,7 +296,7 @@ sub negatively_regulates_relationship {
  Function: Adds a Bio::Ontology::TermI to this engine
  Returns : true if the term was added and false otherwise (e.g., if the
            term already existed in the ontology engine)
- Args    : Bio::Ontology::TermI
+ Args    : Bio::Ontology::TermI`
 
 =cut
 
@@ -972,8 +972,7 @@ sub _get_id {
     if ( ref($term) ) {
 
         # use TermI standard API
-        $self->throw(
-            "Object doesn't implement Bio::Ontology::TermI. " . "Bummer." )
+        $self->throw( "Object doesn't implement Bio::Ontology::TermI" )
           unless $term->isa("Bio::Ontology::TermI");
         $id = $term->identifier();
 
@@ -986,10 +985,8 @@ sub _get_id {
         }
     }
 
-    return $id
-
-#        if $term->isa("Bio::Ontology::GOterm")||($id =~ /^[A-Z_]{1,8}:\d{1,}$/);
-      if $term->isa("Bio::Ontology::OBOterm") || ( $id =~ /^\w+:\w+$/ );
+    # if $term->isa("Bio::Ontology::GOterm")||($id =~ /^[A-Z_]{1,8}:\d{1,}$/);
+    return $id if $term->isa("Bio::Ontology::OBOterm") || ( $id =~ /^\w+:\w+$/ );
 
     # prefix with something if only numbers
     #     if($id =~ /^\d+$/) {
@@ -1000,8 +997,9 @@ sub _get_id {
     # we shouldn't have gotten here if it's at least a remotely decent ID
     $self->throw( ref($self) . ": non-standard identifier '$id'\n" )
       unless $id =~ /\|/;
+
     return $id;
-}    # _get_id
+} 
 
 # Helper for getting children and parent terms
 sub _get_child_parent_terms_helper {
diff --git a/Bio/OntologyIO/obo.pm b/Bio/OntologyIO/obo.pm
index 92bf0db5e..843d6f7e8 100644
--- a/Bio/OntologyIO/obo.pm
+++ b/Bio/OntologyIO/obo.pm
@@ -265,15 +265,13 @@ sub parse {
             $ont = $new_ont;
         }
 
-
         $self->_add_term( $term, $ont );
 
         # Adding the IS_A relationship
-        my $isa_parents_array_ref = $self->{'_isa_parents'};
-        foreach my $parent_term (@$isa_parents_array_ref) {
+        for my $parent_term ( @{$self->{'_isa_parents'}} ) {
             # 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 );
+            if ( ! $self->_has_term($parent_term) ) {
+                $self->_add_term( $parent_term, $ont ); # !
             }
 
             $self->_add_relationship( $parent_term, $term,
@@ -282,7 +280,7 @@ sub parse {
 
         # Adding the other relationships like part_of, related_to, develops_from
         my $relationship_hash_ref = $self->{'_relationships'};
-        for my $relationship ( keys %$relationship_hash_ref ) {
+        for my $relationship ( keys %{$relationship_hash_ref} ) {
             my $reltype;
             # Check if relationship exists, if not add it
             if ( $self->_ont_engine->get_relationship_type($relationship) ) {
@@ -695,7 +693,8 @@ sub _next_term {
             }
         }
     }
-    return $term;
+
+    $term;
 }
 
 # Creates a Bio::Ontology::OBOterm object
-- 
2.11.4.GIT