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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pfamScan/Bio/Pfam/HMM/HMMSequence.pm	Thu Dec 22 04:45:31 2016 -0500
@@ -0,0 +1,102 @@
+
+package Bio::Pfam::HMM::HMMSequence;
+
+use strict;
+use warnings;
+
+use Moose;
+use Moose::Util::TypeConstraints;
+
+extends 'Bio::Pfam::HMM::HMMMatch';
+
+
+has sumEvalue => (
+  isa      => 'evalue',
+  is       => 'rw',
+);
+
+
+has H2mode => (
+  isa => 'Str',
+  is  => 'rw'
+);
+
+has sumScore => (
+  isa      => 'Num',
+  is       => 'rw',
+);
+
+has desc => (
+  isa      => 'Str',
+  is       => 'rw',
+  required => 1
+);
+
+has numberHits => (
+  isa      => 'Int',
+  is       => 'rw',
+  required => 1
+);
+
+
+
+has 'exp' => (
+  isa => 'Num',
+  is  => 'rw'
+);
+
+
+has hmmUnits => (
+  isa => "ArrayRef[ Bio::Pfam::HMM::HMMUnit ]",
+  is  => 'rw',
+  default => sub { [] }
+);
+
+
+#-------------------------------------------------------------------------------
+=head1 Subroutines
+
+=head2 addHMMUnit 
+
+  Title    : addHMMUnit
+  Usage    : $hmmseq->addHMMUnit($hmmUnit) 
+  Function : Adds a hmmUnit to a sequence. It checks that the variable passed in is a Bio::Pfam::HMM::HMMUnit oject
+  Args     : A Bio::Pfam::HMM::HMMUnit oject
+  Returns  : Nothing
+  
+=cut
+
+sub addHMMUnit {
+  my ( $self, $hmmUnit ) = @_;
+  if($hmmUnit->isa("Bio::Pfam::HMM::HMMUnit")){
+    push(@{$self->hmmUnits}, $hmmUnit);
+  }else{
+    warn "$hmmUnit is not a Bio::Pfam::HMM::HMMUnit, not added\n"; 
+  }
+}
+
+
+  __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;