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

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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