Mercurial > repos > matteoc > agame_custom_tools
view pfamScan/Bio/Pfam/HMM/HMMUnit.pm @ 0:68a3648c7d91 draft default tip
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author | matteoc |
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date | Thu, 22 Dec 2016 04:45:31 -0500 |
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package Bio::Pfam::HMM::HMMUnit; use strict; use warnings; use Moose; use Moose::Util::TypeConstraints; extends 'Bio::Pfam::HMM::HMMMatch'; subtype 'Domain' => as 'Int' => where { $_ > 0 }; #coerce 'Domain' # => from 'Str' # => via { # my $d; # if(/(\d+)\/\d+/){ # $d = $1; # } # return $d; # }; # #subtype 'proteinCoos' # => as 'Int' # => where { $_ > 0 && $_ < 100000 } # => message { 'Protein coordinates are expected to be positive and less the 100,000'}; has 'seqEvalue' => ( isa => 'Num', is => 'rw', ); has 'domain' => ( isa => 'Domain', is => 'rw' ); has 'seqFrom' => ( isa => 'Int', is => 'rw', required => 1 ); has 'seqTo' => ( isa => 'Int', is => 'rw', required => 1 ); #has 'indEvalue' => ( # isa => 'evalue', # is => 'rw', # required => 1, #); has 'domEvalue' => ( isa => 'evalue', is => 'rw', ); has 'hmmalign' => ( isa => 'HashRef', is => 'rw', default => sub { {} }, ); has 'hmmFrom' => ( isa => 'Int', is => 'rw', required => 1 ); has 'hmmTo' => ( isa => 'Int', is => 'rw', required => 1 ); has 'envFrom' => ( isa => 'Int', is => 'rw' ); has 'envTo' => ( isa => 'Int', is => 'rw' ); has 'coreFrom' => ( isa => 'Str', is => 'rw' ); has 'coreTo' => ( isa => 'Str', is => 'rw' ); has 'aliAcc' => ( isa => 'Num', is => 'rw' ); has 'sig' => ( isa => 'Int', is => 'rw' ); __PACKAGE__->meta->make_immutable; =head1 COPYRIGHT Copyright (c) 2007: Genome Research Ltd. Authors: Rob Finn (rdf@sanger.ac.uk), John Tate (jt6@sanger.ac.uk) This is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. =cut 1;