Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::MiscSet Class Reference
Inheritance diagram for Bio::EnsEMBL::MiscSet:

List of all members.


Class Summary

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
 

Definition at line 31 of file MiscSet.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public String code ()
public Int dbID ()
public String description ()
public get_all_DAS_Features ()
public Boolean is_stored ()
public Int longest_feature ()
public String name ()
public Bio::EnsEMBL::MiscSet new ()

Method Documentation

public Bio::EnsEMBL::DBSQL::BaseAdaptor Bio::EnsEMBL::Storable::adaptor ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::BaseAdaptor $adaptor
  Example    : none
  Description: get/set for this objects Adaptor
  Returntype : Bio::EnsEMBL::DBSQL::BaseAdaptor
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
click to view
public String Bio::EnsEMBL::MiscSet::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
 
Code:
click to view
public Int Bio::EnsEMBL::Storable::dbID ( ) [inherited]
  Arg [1]    : int $dbID
  Example    : none
  Description: getter/setter for the database internal id
  Returntype : int
  Exceptions : none
  Caller     : general, set from adaptor on store
  Status     : Stable
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::Map::Ditag, and Bio::EnsEMBL::Map::DitagFeature.

public String Bio::EnsEMBL::MiscSet::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
 
Code:
click to view
public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

Code:
click to view

Reimplemented in Bio::EnsEMBL::Gene, Bio::EnsEMBL::Transcript, and Bio::EnsEMBL::Translation.

public Boolean Bio::EnsEMBL::Storable::is_stored ( ) [inherited]
  Arg [1]    : Bio::EnsEMBL::DBSQL::DBConnection 
             : or Bio::EnsEMBL::DBSQL::DBAdaptor
  Example    : do_something if($object->is_stored($db));
  Description: Returns true if this object is stored in the provided database.
               This works under the assumption that if the adaptor and dbID are
               set and the database of the adaptor shares the port, dbname and
               hostname with the provided database, this object is stored in
               that database.
  Returntype : 1 or 0
  Exceptions : throw if dbID is set but adaptor is not
               throw if adaptor is set but dbID is not
               throw if incorrect argument is passed
  Caller     : store methods
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::MiscSet::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
 
Code:
click to view
public String Bio::EnsEMBL::MiscSet::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
 
Code:
click to view
public Bio::EnsEMBL::MiscSet Bio::EnsEMBL::MiscSet::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:
click to view

Reimplemented from Bio::EnsEMBL::Storable.


The documentation for this class was generated from the following file: