[Bioperl-l] some not-so-good perl practice in bioperl

[Juguang Xiao]

Hi all,

I was Java programmer learning Perl from Bioperl code. I did learn a 
lot for you ushers. Recently, I decide to read Programming Perl, the 
Perl Bible, and found some common-sense code in bioperl is not the 
best. Here are my findings.

1) getset

Months ago, Hilmar gave us a tip for the getter/setter to accept undef. 
The code is like

sub name {
	my $self=shift;
	return $self->{_name} = shift if @_;
	return $self->{_name};
}

It is no fault about it until this super or sub module have a method 
with different name but use the same hash key.  So choosing the hash 
key is not on your own ease. Here is the code in Section 12.7

sub name {
     my $self = shift;
     my $field = __PACKAGE__ . "::name";
     if (@_) { $self->{$field} = shift }
     return $self->{$field};
}

Your getset generator may need to be updated. ;-)
##############################################
2) use vars (@ISA);

This is copied from Chapter 31.

31.21. use vars

use vars qw($frobbed @munge %seen);


This pragma, once used to declare a global variable, is now somewhat 
deprecated in favor of the our modifier.  The previous declaration  is 
better accomplished using:

our($frobbed, @munge, %seen);

   or even:
our $frobbed = "F";
our @munge = "A" .. $frobbed;
our %seen = ();

#########################################
3) auto getset, again

I really cannot stand individual getset any more, after I read Section 
12.7. Do yourself a favor, read it, please. One year ago, I suggest to 
use AUTOLOAD replace all getset methods. The idea was mercilessly 
extinguish. Now I have big boss's support in his book. Anyone wants to 
say anything? ;-) ( I do not mean to use AUTOLOAD again, but the rest 
ways in that section should be discussed) Just do not stay your Perl 
wisdom and braveness at high school, though your bioinformatics 
achievement reach above the Ph. D height.

I prefer the idea on Section 12.7.4. Generating Accessors with 
Closures. It is listsub'able.


my $0.02

Juguang