[Bioperl-l] Interface of the method

[Dave Messina]

Hi Jun,

Great! Glad to hear you're taking on this project.


> This may cause some confusion.So I propose that we should use a more
> consistent way for similar functions.
> 
> For example, the methods of
> 
> select_Seq
> 
> select_columns
> 
> remove_Seq
> 
> remove_columns
> 
> mask_columns
> 
> .
> 
> should have the same interface.

Agreed, absolutely. Consistency is important. I would further propose that select_Seq be select_seqs, if indeed multiple seqs are to be selected with this method. Also, capital letters are typically not used in BioPerl method names. For example, eachSeq was deprecated in favor of each_seq.



> So I suggest, we can do 
> 
> $new_aln=$aln->select_Seq([1,3,5..10,15],"toggle")
> 
> Or
> 
> $new_aln=$aln->select_columns([2.25,34,52..60])


BioPerl tends to use named parameters passed as a hash, e.g.:

	my $in = Bio::SeqIO->new('-format' => 'fasta', '-file' => 'my.fasta');


So something more like:

	$new_aln = $aln->select_seqs('-seqs' => (1, 3, 5..10,15), -toggle => 'yes);
	$new_aln = $aln->select_columns('-columns' => (2, 25, 45, 52..60);


Admittedly, it's redundant to say -seqs when the method is named select_seqs, and maybe less redundant labels can be chosen.

Also, and this is perhaps a minor point, using () instead of [] here for the set of seqs or columns is better, since [] implies indexing into an array, which isn't what's being done.


Dave