Tuesday, July 6, 2010

Enable multiple/toggle selection feature in Bio::SimpleAlign

One major new feature in Bio::SimpleAlign is to enable multiple and toggle selection for methods selecting sequences or columns. The new ways of doing can be :

$newaln=$aln->select_Seqs([4..10,20..35,37]);
$newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37]);

Or you can toggle selection(reverse selection) using:
$newaln=$aln->select_Seqs([4..10,20..35,37],1);
$newaln=$aln->select_Seqs(-selection=>[4..10,20..35,37],-toggle=>1);

The coordinates of the sequences or columns are 1-based. This new feature will make the selection much easier for users.And, it will affect methods such as:

select_Seqs
remove_Seqs
select_columns
remove_columns
mask_columns

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