diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/Channel.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Channel.pm	Fri Aug 03 10:04:48 2012 -0400
@@ -0,0 +1,207 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::Channel
+#
+# You may distribute this module under the same terms as Perl itself
+
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2011 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <[e-mail]>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <[e-mail]>.
+
+
+=head1 NAME
+
+Bio::EnsEMBL::Funcgen::Channel - A module to represent a single channel of an ExperimentalChip
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::Channel;
+
+my $array = Bio::EnsEMBL::Funcgen::Channel->new(
+                   			        -EXPERIMENTAL_CHIP_ID => $ec_id,
+			        	        -SAMPLE_ID            => $sample_id,
+					        -TYPE                 => $type,
+						-DYE                  => $dye,
+					       );
+
+#-replace TYPE with DENOMINATOR?
+
+my $db_adaptor = Bio::EnsEMBL::Funcgen::DBSQL::DBAdaptor->new(...);
+my $chan_a = $db_adaptor->get_ChannelAdaptor();
+my $chan = $chan_a->fetch_by_type_ExperimentalChip($type, $ExpChip);
+
+=head1 DESCRIPTION
+
+A Channel object represents a single channel on an ExperimentalChip. The data
+are stored in the channel table, and associated expermental variables are
+stored in the experimental_variable table.
+
+=cut
+
+use strict;
+use warnings;
+
+
+package Bio::EnsEMBL::Funcgen::Channel;
+
+
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw warning );
+use Bio::EnsEMBL::Funcgen::Storable;
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
+
+
+=head2 new
+
+  Arg [-EXPERIMENTAL_CHIP_ID]:  int - the experimental chip dbID
+
+
+
+  Example    : my $array = Bio::EnsEMBL::Funcgen::Channel->new(
+	                   			       -EXPERIMENTAL_CHIP_ID => $ec_id,
+                                   	               -SAMPLE_ID            => $sample_id,
+					               -TYPE                 => $type,
+					               -DYE                  => $dye,
+					                     );
+  Description: Creates a new Bio::EnsEMBL::Funcgen::Channel object.
+  Returntype : Bio::EnsEMBL::Funcgen::Channel
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub new {
+	my $caller = shift;
+
+	my $class = ref($caller) || $caller;
+
+	my $self = $class->SUPER::new(@_);
+
+	#can we lc these?
+	my ($ec_id, $sample_id, $type, $dye)
+		= rearrange( ['EXPERIMENTAL_CHIP_ID', 'SAMPLE_ID', 'TYPE', 'DYE'], @_ );
+	
+	$self->sample_id($sample_id)          if defined $sample_id;
+	$self->experimental_chip_id($ec_id)          if defined $ec_id;
+	$self->type($type)    if defined $type;
+	$self->dye($dye)    if defined $dye;
+
+
+	return $self;
+}
+
+=head2 sample_id
+
+  Arg [1]    : (optional) string - the sample id for this Channel
+  Example    : my $sample_id = $chan->sample_id();
+  Description: Getter, setter and lazy loader of sample_id attribute.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub sample_id {
+	my $self = shift;
+	$self->{'sample_id'} = shift if @_;
+
+	if ( ! exists $self->{'sample_id'} && $self->dbID() && $self->adaptor() ) {
+		$self->adaptor->fetch_attributes($self);
+	}
+
+	return $self->{'sample_id'};
+}
+
+
+
+=head2 experimental_chip_id
+
+  Arg [1]    : (optional) int - the experimenta chip dbID
+  Example    : my $ec_id = $chan->experimental_chip_id();
+  Description: Getter, setter and lazy loader of experimental_chip_id attribute
+  Returntype : int
+  Exceptions : None
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub experimental_chip_id {
+	my $self = shift;
+
+	$self->{'experimental_chip_id'} = shift if @_;
+	if ( !exists $self->{'experimental_chip_id'} && $self->dbID() && $self->adaptor() ) {
+		$self->adaptor->fetch_attributes($self);
+	}
+	return $self->{'experimental_chip_id'};
+}
+
+=head2 type
+
+  Arg [1]    : (optional) string - the channel type e.g. EXPERIMENTAL or CONTROL
+  Example    : my $type = $chan->type();
+  Description: Getter, setter and lazy loader of type attribute
+  Returntype : string
+  Exceptions : 
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub type {
+  my $self = shift;
+
+  $self->{'type'} = shift if @_;
+
+  #warn "we need to control EXPERIMENTAL OR CONTROL here or enum on DB";
+  
+  if ( !exists $self->{'type'} && $self->dbID() && $self->adaptor() ) {
+    $self->adaptor->fetch_attributes($self);
+  }
+  return $self->{'type'};
+}
+
+=head2 dye
+
+  Arg [1]    : (optional) string - the channel type e.g. EXPERIMENTAL or CONTROL
+  Example    : my $dye = $chan->dye();
+  Description: Getter, setter and lazy loader of dye attribute
+  Returntype : string
+  Exceptions : 
+  Caller     : General
+  Status     : Medium Risk
+
+=cut
+
+sub dye {
+  my $self = shift;
+
+  $self->{'dye'} = shift if @_;
+  
+  #if ( !exists $self->{'dye'} && $self->dbID() && $self->adaptor() ) {
+  #  $self->adaptor->fetch_attributes($self);
+  #}
+  return $self->{'dye'};
+}
+
+
+1;
+