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Bio::EnsEMBL::Map::Ditag Class Reference
Inheritance diagram for Bio::EnsEMBL::Map::Ditag:

List of all members.


Class Summary

Synopsis

  my $feature = Bio::EnsEMBL::Map::Ditag-\>new(
    -dbID      =\> $tag_id,
    -name      =\> $name,
    -type      =\> $type,
    -tag_count =\> $tag_count,
    -sequence  =\> $sequence,
    -adaptor   =\> $dbAdaptor
  );

Description

Represents an unmapped ditag object in the EnsEMBL database.
Corresponds to original tag containing the full sequence. This can be
a single piece of sequence like CAGE tags or a ditag with concatenated
sequence from 5' and 3' end like GIS or GSC tags.
 

Definition at line 28 of file Ditag.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Int dbID ()
public get_all_DAS_Features ()
public Listref get_ditagFeatures ()
public Boolean is_stored ()
public Text name ()
public Bio::EnsEMBL::Map::Ditag new ()
public Text sequence ()
public Int tag_count ()
public Text type ()

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:
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public Int Bio::EnsEMBL::Map::Ditag::dbID ( )
  Arg [1]    : (optional) int id
  Example    : $ditag_id = $ditag->dbID;
  Description: Getter/Setter for the dbID of a ditag
  Returntype : int
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::Storable::get_all_DAS_Features ( ) [inherited]

Undocumented method

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

public Listref Bio::EnsEMBL::Map::Ditag::get_ditagFeatures ( )
  Arg        : none
  Example    : @features = @{$ditag->get_ditagFeatures};
  Description: Fetch ditag_features created from this ditag
  Returntype : listref of Bio::EnsEMBL::Map::DitagFeature
  Caller     : general
 
Code:
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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:
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public Text Bio::EnsEMBL::Map::Ditag::name ( )
  Arg [1]    : (optional) string $type
  Example    : $type = $ditag->name;
  Description: Getter/Setter for the name of a ditag
  Returntype : text
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Map::Ditag Bio::EnsEMBL::Map::Ditag::new ( )
  Arg [1]    : (optional) int $dbID
  Arg [2]    : (optional) string name
  Arg [3]    : (optional) string type
  Arg [4]    : (optional) int tag_count
  Arg [5]    : (optional) string sequence
  Arg [6]    : (optional) Bio::EnsEMBL::Map::DBSQL::DitagAdaptor $adaptor
  Description: Creates a new ditag
  Returntype : Bio::EnsEMBL::Map::Ditag
  Exceptions : none
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::Storable.

public Text Bio::EnsEMBL::Map::Ditag::sequence ( )
  Arg [1]    : (optional) string $sequence
  Example    : $sequence = $ditag->sequence;
  Description: Getter/Setter for the sequence of a ditag
  Returntype : text
  Caller     : general
 
Code:
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public Int Bio::EnsEMBL::Map::Ditag::tag_count ( )
  Arg [1]    : (optional) string $tag_count
  Example    : $type = $ditag->tag_count;
  Description: Getter/Setter for the tag_count of a ditag
  Returntype : int
  Caller     : general
 
Code:
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public Text Bio::EnsEMBL::Map::Ditag::type ( )
  Arg [1]    : (optional) string $type
  Example    : $type = $ditag->type;
  Description: Getter/Setter for the type of a ditag
  Returntype : text
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: