diff pfamScan/Bio/Pfam/HMM/HMMUnit.pm @ 0:68a3648c7d91 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pfamScan/Bio/Pfam/HMM/HMMUnit.pm	Thu Dec 22 04:45:31 2016 -0500
@@ -0,0 +1,138 @@
+
+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 ([e-mail]), John Tate ([e-mail])
+
+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;