Bio::EnsEMBL
MiscSet
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Summary
Bio::EnsEMBL::MiscSet - This is a set representing a classification of
a group of miscellaneuos features.
Package variables
No package variables defined.
Included modules
Inherit
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);
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
Methods
Methods description
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 |
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 |
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 |
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 |
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 |
Methods code
sub code
{ my $self = shift;
$self->{'code'} = shift if(@_);
return $self->{'code'};} | sub description
{ my $self = shift;
$self->{'description'} = shift if(@_);
return $self->{'description'};} | sub longest_feature
{ my $self = shift;
$self->{'longest_feature'} = shift if(@_);
return $self->{'longest_feature'};
}
1;} | sub name
{ my $self = shift;
$self->{'name'} = shift if(@_);
return $self->{'name'};} | 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;} | General documentation
Copyright (c) 1999-2009 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
/info/about/code_licence.html