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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pfamScan/Bio/Pfam/HMM/HMM.pm	Thu Dec 22 04:45:31 2016 -0500
@@ -0,0 +1,266 @@
+# HMM.pm
+#
+# Author:        finnr
+# Maintainer:    $Id: HMM.pm,v 1.1 2009-10-08 12:27:28 jt6 Exp $
+# Version:       $Revision: 1.1 $
+# Created:       Nov 24, 2008
+# Last Modified: $Date: 2009-10-08 12:27:28 $
+=head1 NAME
+
+Template - a short description of the class
+
+=cut
+
+package Bio::Pfam::HMM::HMM;
+
+=head1 DESCRIPTION
+
+A more detailed description of what this class does and how it does it.
+
+$Id: HMM.pm,v 1.1 2009-10-08 12:27:28 jt6 Exp $
+
+=head1 COPYRIGHT
+
+File: HMM.pm
+
+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, write to the Free Software
+ Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
+ or see the on-line version at http://www.gnu.org/copyleft/gpl.txt
+ 
+=cut
+
+use strict;
+use warnings;
+
+use Moose;
+use Moose::Util::TypeConstraints;
+use Carp;
+
+#-------------------------------------------------------------------------------
+
+=head1 METHODS
+
+=cut
+
+
+subtype 'hmmVersion'
+  => as Str
+  => where { $_ =~ m/^HMMER3\/f\s+\[3\.\d+[ab](\d+)?\s+|\s+\[.*\]/ }
+  => message { "|$_| does not look like as HMMER3 version" };
+
+subtype 'hmmName'
+  => as Str
+  => where { $_ =~ m/\S{1,15}/ }
+  => message { "|$_| does not look like Pfam name or SEED" };
+
+subtype 'hmmAcc'
+  => as Str
+  => where { $_ =~ m/PF\d{5}/ }
+  => message { "|$_| does not look like Pfam accession" };
+
+
+subtype 'hmmAlpha'
+  => as Str
+  => where { $_ eq 'amino' or $_ eq 'nucleic'  }
+  => message { "|$_| does not look like a HMMER3 alphabet" };
+
+
+subtype 'hmmMsvStats'
+  => as HashRef
+  => where { defined ($_->{mu}) and defined ($_->{lambda}) and ($_->{lambda} <= 0.8) and ($_->{lambda} >= 0.5) }
+  => message { "Mu |$_->{mu}| and lambda |$_->{lambda}| must be defined and lambda must be between 0.5 and 0.8" };
+
+  
+subtype 'hmmViterbiStats'
+  => as HashRef
+  => where { defined ($_->{mu}) and defined ($_->{lambda}) and ($_->{lambda} <= 0.8) and ($_->{lambda} >= 0.5) }
+  => message { "Mu |$_->{mu}| and lambda |$_->{lambda}| must be defined and lambda must be between 0.5 and 0.8" };
+
+subtype 'hmmForwardStats'
+  => as HashRef
+  => where { defined ($_->{tau}) and defined ($_->{lambda}) and ($_->{lambda} <= 0.8) and ($_->{lambda} >= 0.5) }
+  => message { "Tau |$_->{tau}| and lambda |$_->{lambda}| must be defined and lambda must be between 0.5 and 0.8" };
+  
+has 'version' => (
+  isa      => 'hmmVersion',
+  is       => 'rw',
+  required => 1
+);
+
+has 'name' => (
+  isa => 'hmmName',
+  is  => 'rw',
+  required => 1
+);
+
+has 'accession' => (
+  isa => 'hmmAcc',
+  is  => 'rw'
+);
+
+has 'description' => (
+  isa => 'Str',
+  is  => 'rw'
+);
+
+has 'length' => (
+  isa  => 'Int',
+  is   => 'rw',
+  required => 1
+);
+
+has 'alpha' => (
+  isa  => 'hmmAlpha',
+  is   => 'rw',
+  required => 1,
+);
+
+has 'rf' => (
+  isa  => 'Bool',
+  is   => 'rw',
+  required => 1
+);
+
+has 'mm' => (
+  isa  => 'Bool',
+  is   => 'rw',
+);
+
+has 'cons' => (
+  isa  => 'Bool',
+  is   => 'rw',
+);
+
+has 'cs' => (
+  isa  => 'Bool',
+  is   => 'rw',
+  required => 1
+);
+
+has 'map' => (
+  isa  => 'Bool',
+  is   => 'rw',
+  required => 1
+);
+
+has 'date' => (
+  isa  => 'Str',
+  is   => 'rw',
+  required => 1
+);
+
+has 'buildLine' => (
+  isa => 'HashRef[Str]',
+  is  => 'rw',
+  required => 1,
+  default => sub { {} },
+);
+
+has 'searchMethod' => (
+  isa => 'Str',
+  is  => 'rw',
+);
+
+has 'nSeq' => (
+  isa  => 'Int',
+  is   => 'rw',
+  required => 1
+);
+
+has 'msvStats' => (
+  isa => 'hmmMsvStats',
+  is => 'rw',
+  required => 1
+);
+
+has 'viterbiStats' => (
+  isa => 'hmmViterbiStats',
+  is => 'rw',
+  required => 1
+);
+
+has 'forwardStats' => (
+  isa => 'hmmForwardStats',
+  is => 'rw',
+  required => 1
+);
+
+
+has 'effn' => (
+  isa  => 'Num',
+  is   => 'rw',
+  required => 1
+);
+
+has 'cksum' => (
+  isa => 'Int',
+  is  => 'rw',
+  required => 1
+);
+
+has 'seqGA' => (
+  isa => 'Num',
+  is  => 'rw',
+);
+
+has 'domGA' => (
+  isa => 'Num',
+  is  => 'rw',
+);
+
+has 'seqTC' => (
+  isa => 'Num',
+  is  => 'rw',
+);
+
+has 'domTC' => (
+  isa => 'Num',
+  is  => 'rw',
+);
+
+has 'seqNC' => (
+  isa => 'Num',
+  is  => 'rw',
+);
+
+has 'domNC' => (
+  isa => 'Num',
+  is  => 'rw',
+);
+
+has 'emissionLines' => (
+  isa => 'ArrayRef[ArrayRef]',
+  is  => 'rw',
+  default => sub { [] },
+);
+
+has 'mapPos'=> (
+  isa => 'ArrayRef[Int]',
+  is  => 'rw',
+  default => sub{ [] }
+);
+
+has 'compLines' => (
+  isa => 'ArrayRef[Str]',
+  is  => 'rw',
+  default => sub { [] },
+);
+
+__PACKAGE__->meta->make_immutable;
+1;
+