LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

CONTACT

Please email comments or questions to the public Ensembl
developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.

Questions may also be sent to the Ensembl help desk at
<http://www.ensembl.org/Help/Contact>.

NAME

Bio::EnsEMBL::MiscSet - This is a set representing a classification of a group of miscellaneuos features.

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

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

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

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

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

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