[Bioperl-l] PrimarySeq POD changes

Sendu Bala bix at sendu.me.uk
Wed Sep 27 21:12:01 UTC 2006

Jason Stajich wrote:
> http://lists.open-bio.org/pipermail/bioperl-guts-l/2006-September/023408.html 
> This is wrong. Bio::PrimarySeq does take named  arguments - look at the 
> actual method code.

I did look at the method code:

sub seq {
    my ($obj, at args) = @_;

    if( scalar(@args) == 0 ) {
        return $obj->{'seq'};

    my ($value,$alphabet) = @args;

    if(@args) {
        if(defined($value) && (! $obj->validate_seq($value))) {
	   $obj->throw(" [...]

Unless I'm being blind, if the first argument supplied to the method 
isn't something that validates as a sequence, it throws. How can it 
accept named args? Or, where is the code that works out what named args 
have been supplied?

The new() method accepts named args if that's what you meant, but I 
didn't change the docs for new().

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