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Bio::EnsEMBL::RepeatConsensus Class Reference
Inheritance diagram for Bio::EnsEMBL::RepeatConsensus:

List of all members.


Class Summary

Definition at line 6 of file RepeatConsensus.pm.

Available Methods

public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
adaptor ()
public Int dbID ()
public String desc ()
public get_all_DAS_Features ()
public Boolean is_stored ()
public Int length ()
public String name ()
public
Bio::EnsEMBL::RepeatConsensus 
new ()
public
Bio::EnsEMBL::RepeatConsensus 
new_fast ()
public String repeat_class ()
public String repeat_consensus ()
public String repeat_type ()
public String seq ()

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

public String Bio::EnsEMBL::RepeatConsensus::desc ( )
  Arg [1]    : none
  Example    : $desc = $repeat_consensus->desc()
  Description: Getter for the description of this repeat consensus as extracted
               from the repeat_class.  This method is probably useless.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Medium risk
 
Code:
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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 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 Int Bio::EnsEMBL::RepeatConsensus::length ( )
  Arg [1]    : int $length (optional)
  Example    : $length = $repeat_consensus->length()
  Description: Getter/Setter for the length of this repeat_consensus
  Returntype : int
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::RepeatConsensus::name ( )
  Arg [1]    : string $name (optional)
  Example    : $name = $repeat_consensus->name()
  Description: Getter/Setter for the name of this repeat_consensus
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::RepeatConsensus::new ( )
  Arg [NAME] : string (optional)
               The name of this repeat consensus
  Arg [LENGTH]: int (optional)
               The length of the repeat consensus sequence
  Arg [REPEAT_CLASS]: string (optional)
               The type of repeat consensus
  Arg [REPEAT_CONSENSUS]: string (optional)
               The sequence of this repeat consensus
  Arg [REPEAT_TYPE]: string 
               Its like class only more general
  Arg [...]: Named arguments to superclass constructor
             (see Bio::EnsEMBL::Storable)
  Example    : $rc = Bio::EnsEMBL::RepeatConsensus->new
                       (-REPEAT_CONSENSUS => 'AATG'
                        -NAME => '(AATG)n',
                        -REPEAT_CLASS => 'Simple_repeat',
                        -LENGTH => '4',
                        -DBID => 1023,
                        -ADAPTOR => $rc_adaptor);
  Description: Creates a new Bio::EnsEMBL::RepeatConsensus object
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : RepeatFeatureAdaptors
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::Storable.

public Bio::EnsEMBL::RepeatConsensus Bio::EnsEMBL::RepeatConsensus::new_fast ( )
  Arg [1] : hashref to bless as a new RepeatConsensus
  Description: Creates a new Bio::EnsEMBL::RepeatConsensus object
  Returntype : Bio::EnsEMBL::RepeatConsensus
  Exceptions : none
  Caller     : internal
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::RepeatConsensus::repeat_class ( )
  Arg [1]    : string $class (optional)
               The class of 
  Example    : $class = $repeat_consensus->repeat_class()
  Description: Getter/Setter for the class of this repeat_consensus
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public String Bio::EnsEMBL::RepeatConsensus::repeat_consensus ( )
  Arg [1]    : string $consensus_seq (optional)
               The sequence of this repeat consensus
  Example    : $consensus = $repeat_consensus->repeat_consensus();
  Description: Getter/Setter for the sequence of this repeat_consensus.
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::RepeatConsensus::repeat_type ( )
  Arg [1]    : string $type (optional)
               The type of the consensus 
  Example    : $type = $repeat_consensus->repeat_type()
  Description: Getter/Setter for the type of this repeat_consensus
  Returntype : string
  Exceptions : none
  Caller     : general
 
Code:
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public String Bio::EnsEMBL::RepeatConsensus::seq ( )
  Arg [1]    : none
  Example    : none
  Description: Returns the repeat consensus.  This method is useless - Use
               repeat_consensus() instead.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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The documentation for this class was generated from the following file: