From 76916bfac7886794380c51849b1bd87fef728bf0 Mon Sep 17 00:00:00 2001
From: Chris Fields <cjfields@bioperl.org>
Date: Wed, 6 Apr 2011 12:56:13 -0500
Subject: [PATCH] * 'use vars' -> our * run-time modification of @ISA is
 extremely evil and points to a problem that should be fixed in other ways. 
 Commenting this out still passes tests; I openly implore anyone who used such
 evilness to please find a better fix

---
 Bio/Seq/Meta/Array.pm | 29 ++++++++++++++---------------
 Bio/Seq/Quality.pm    | 13 +++----------
 2 files changed, 17 insertions(+), 25 deletions(-)

diff --git a/Bio/Seq/Meta/Array.pm b/Bio/Seq/Meta/Array.pm
index b4feff7f6..b5f94f2b0 100644
--- a/Bio/Seq/Meta/Array.pm
+++ b/Bio/Seq/Meta/Array.pm
@@ -134,19 +134,13 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Seq::Meta::Array;
-use vars qw(@ISA $DEFAULT_NAME $GAP $META_GAP);
 use strict;
 
-#use overload '""' => \&to_string;
-
 use base qw(Bio::LocatableSeq Bio::Seq Bio::Seq::MetaI);
 
-BEGIN {
-
-    $DEFAULT_NAME = 'DEFAULT';
-    $GAP = '-';
-    $META_GAP = 0;
-}
+our $DEFAULT_NAME = 'DEFAULT';
+our $GAP = '-';
+our $META_GAP = 0;
 
 =head2 new
 
@@ -165,14 +159,19 @@ BEGIN {
 
 sub new {
     my ($class, %args) = @_;
+    
+    # run-time modification of @ISA is extremely evil (you should't pick your
+    # interface on the fly); this has no obvious effect on any tests so
+    # commenting out - cjfields 2011-4-6
+    
 	#defined inheritance according to stated baseclass,
 	#if undefined then will be PrimarySeq
-	if (defined($args{'-baseclass'})) {
-		@ISA = ($args{'-baseclass'},"Bio::Seq::MetaI");
-		}
-	else {
-		@ISA = qw( Bio::LocatableSeq Bio::Seq Bio::Seq::MetaI );
-		}
+	#if (defined($args{'-baseclass'})) {
+	#	@ISA = ($args{'-baseclass'},"Bio::Seq::MetaI");
+	#	}
+	#else {
+	#	@ISA = qw( Bio::LocatableSeq Bio::Seq Bio::Seq::MetaI );
+	#	}
 
     my $self = $class->SUPER::new(%args);
 
diff --git a/Bio/Seq/Quality.pm b/Bio/Seq/Quality.pm
index ed2704f4f..99870e241 100644
--- a/Bio/Seq/Quality.pm
+++ b/Bio/Seq/Quality.pm
@@ -170,22 +170,15 @@ Internal methods are usually preceded with a _
 
 
 package Bio::Seq::Quality;
-use vars qw($DEFAULT_NAME $GAP $META_GAP);
 use strict;
 
-#use overload '""' => \&to_string;
-
 use base qw(Bio::Seq::Meta::Array);
 
 ## Is this the right place (and way) to define this?
 our $MASK_CHAR = 'X';
-
-BEGIN {
-
-    $DEFAULT_NAME = 'DEFAULT';
-    $GAP = '-';
-    $META_GAP = ' ';
-}
+our $DEFAULT_NAME = 'DEFAULT';
+our $GAP = '-';
+our $META_GAP = ' ';
 
 =head2 new
 
-- 
2.11.4.GIT