diff variant_effect_predictor/Bio/EnsEMBL/MiscSet.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/MiscSet.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,187 @@
+=head1 LICENSE
+
+  Copyright (c) 1999-2012 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]>.
+
+=cut
+
+=head1 NAME
+
+Bio::EnsEMBL::MiscSet - This is a set representing a classification of
+a group of miscellaneuos features.
+
+=head1 SYNOPSIS
+
+  use Bio::EnsEMBL::MiscSet;
+
+  my $misc_set = Bio::EnsEMBL::MiscSet->new(
+    1234, $adaptor, 'tilepath',
+    'Assembly Tiling Path',
+    'The tiling path of clones', 1e6
+  );
+
+  my $misc_feature->add_set($misc_set);
+
+=head1 DESCRIPTION
+
+MiscSets represent classsifications or groupings of MiscFeatures.
+Features are classified into sets essentially to define what they are
+and how they may be used.  Generally MiscFeatures are retrieved on
+the basis of their associated sets. See Bio::EnsEMBL::MiscFeature,
+Bio::EnsEMBL::DBSQL::MiscFeatureAdaptor.
+
+Note that MiscSets and MiscFeatures were formerly known as MapSets and
+MapFrags
+
+=head1 METHODS
+
+=cut
+
+package Bio::EnsEMBL::MiscSet;
+
+use strict;
+
+use Bio::EnsEMBL::Storable;
+use Bio::EnsEMBL::Utils::Argument qw(rearrange);
+
+use vars qw(@ISA);
+
+@ISA = qw(Bio::EnsEMBL::Storable);
+
+
+=head2 new
+
+  Arg [1]    : int $misc_set_id
+               The internal identifier for this misc set
+  Arg [2]    : string $code
+               The unique code which identifies this set type
+  Arg [3]    : string $name
+               The human readable name of this set
+  Arg [4]    : string $desc
+               The description of this set
+  Arg [5]    : int $max_len
+               The maximum length of features of this mapset
+  Example    : $set = new Bio::EnsEMBL::MiscSet(1234, 'tilepath',
+                                                'Assembly Tiling Path',
+                                                'The tiling path of clones',
+                                                1e6);
+  Description: Instantiates a Bio::EnsEMBL::MiscSet
+  Returntype : Bio::EnsEMBL::MiscSet
+  Exceptions : none
+  Caller     : MiscFeatureAdaptor
+  Status     : Stable
+
+=cut
+
+sub new {
+  my $caller = shift;
+
+  my $class = ref($caller) || $caller;
+
+  my $self = $class->SUPER::new(@_);
+
+  my($code, $name, $desc, $max_len) =
+    rearrange([qw(CODE NAME DESCRIPTION LONGEST_FEATURE)], @_);
+
+  $self->{'code'} = $code;
+  $self->{'name'} = $name;
+  $self->{'description'} = $desc;
+  $self->{'longest_feature'} = $max_len;
+
+  return $self;
+}
+
+=head2 code
+
+  Arg [1]    : string $newval (optional) 
+               The new value to set the code attribute to
+  Example    : $code = $obj->code()
+  Description: Getter/Setter for the code attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub code{
+  my $self = shift;
+  $self->{'code'} = shift if(@_);
+  return $self->{'code'};
+}
+
+
+=head2 name
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the code attribute to
+  Example    : $name = $obj->name()
+  Description: Getter/Setter for the name attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub name {
+  my $self = shift;
+  $self->{'name'} = shift if(@_);
+  return $self->{'name'};
+}
+
+
+=head2 description
+
+  Arg [1]    : string $newval (optional)
+               The new value to set the description attribute to
+  Example    : $description = $obj->description()
+  Description: Getter/Setter for the description attribute
+  Returntype : string
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub description{
+  my $self = shift;
+  $self->{'description'} = shift if(@_);
+  return $self->{'description'};
+}
+
+
+=head2 longest_feature
+
+  Arg [1]    : int $newval (optional) 
+               The new value to set the longest_feature attribute to
+  Example    : $longest_feature = $obj->longest_feature()
+  Description: Getter/Setter for the longest_feature attribute
+  Returntype : int
+  Exceptions : none
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub longest_feature{
+  my $self = shift;
+  $self->{'longest_feature'} = shift if(@_);
+  return $self->{'longest_feature'};
+}
+
+
+1;