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Bio::EnsEMBL::Compara::DnaFrag Class Reference

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::DnaFrag; 
  my $dnafrag = new Bio::EnsEMBL::Compara::DnaFrag(
          -dbID =\> 1,
          -adaptor =\> $dnafrag_adaptor,
          -length =\> 256,
          -name =\> "19",
          -genome_db =\> $genome_db,
          -coord_system_name =\> "chromosome"
        );


SET VALUES
  $dnafrag-\>dbID(1);
  $dnafrag-\>adaptor($dnafrag_adaptor);
  $dnafrag-\>length(256);
  $dnafrag-\>genome_db($genome_db);
  $dnafrag-\>genome_db_id(123);
  $dnafrag-\>coord_system_name("chromosome");
  $dnafrag-\>name("19");

GET VALUES
  $dbID = $dnafrag-\>dbID;
  $dnafrag_adaptor = $dnafrag-\>adaptor;
  $length = $dnafrag-\>length;
  $genome_db = $dnafrag-\>genome_db;
  $genome_db_id = $dnafrag-\>genome_db_id;
  $coord_system_name = $dnafrag-\>coord_system_name;
  $name = $dnafrag-\>name;

Description

The DnaFrag object stores information on the toplevel sequences such as the name, coordinate system, length and species.
 

Definition at line 43 of file DnaFrag.pm.

Available Methods

public
Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor 
adaptor ()
public String coord_system_name ()
public Int dbID ()
public String display_id ()
public Int end ()
public
Bio::EnsEMBL::Compara::GenomeDB 
genome_db ()
public Int genome_db_id ()
public Bool is_reference ()
public Int length ()
public String name ()
public
Bio::EnsEMBL::Compara::DnaFrag 
new ()
public new_fast ()
public Bio::EnsEMBL::Slice slice ()
public Int start ()

Method Documentation

public Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor Bio::EnsEMBL::Compara::DnaFrag::adaptor ( )
 Arg [1]   : Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor $dnafrag_adaptor
 Example   : $dnafrag_adaptor = $dnafrag->adaptor()
 Example   : $dnafrag->adaptor($dnafrag_adaptor)
 Function  : get/set adaptor attribute.
 Returns   : Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor object
 Exeption  : thrown if argument is not a Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor
             object
 Caller    : $object->adaptor
 Status    : Stable
 
Code:
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public String Bio::EnsEMBL::Compara::DnaFrag::coord_system_name ( )
 Arg [1]   : string $coord_system_name
 Example   : $coord_system_name = $dnafrag->coord_system_name()
 Example   : $dnafrag->coord_system_name("chromosome")
 Function  : get/set coord_system_name attribute. Use "" or 0 as argument to
             clear this attribute.
 Returns   : string
 Exeption  : none
 Caller    : $object->coord_system_name
 Status    : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFrag::dbID ( )
 Arg [1]   : int $dbID
 Example   : $dbID = $dnafrag->dbID()
 Example   : $dnafrag->dbID(1)
 Function  : get/set dbID attribute.
 Returns   : integer
 Exeption  : none
 Caller    : $object->dbID
 Status    : Stable
 
Code:
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public String Bio::EnsEMBL::Compara::DnaFrag::display_id ( )
  Args       : none
  Example    : my $id = $dnafrag->display_id;
  Description: returns string describing this chunk which can be used
               as display_id of a Bio::Seq object or in a fasta file.
               Uses dnafrag information in addition to start and end.
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFrag::end ( )
 
Deprecated:
! Use Bio::EnsEMBL::Compara::DnaFrag->length() method instead
  Arg [1]    : int $end
  Example    : $dnafrag->end(42);
  Description: Getter/Setter for the start attribute
  Returntype : int
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::GenomeDB Bio::EnsEMBL::Compara::DnaFrag::genome_db ( )
 Arg [1]   : Bio::EnsEMBL::Compara::GenomeDB $genome_db
 Example   : $genome_db = $dnafrag->genome_db()
 Example   : $dnafrag->genome_db($genome_db)
 Function  : get/set genome_db attribute. If no argument is given and the genome_db
             is not defined, it tries to get the data from other sources like the
             database using the genome_db_id.
 Returns   : Bio::EnsEMBL::Compara::GenomeDB object
 Exeption  : thrown if argument is not a Bio::EnsEMBL::Compara::GenomeDB
             object
 Caller    : $object->genome_db
 Status    : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFrag::genome_db_id ( )
 Arg [1]   : int $genome_db_id
 Example   : $genome_db_id = $dnafrag->genome_db_id()
 Example   : $dnafrag->genome_db_id(123)
 Function  : get/set genome_db_id attribute. If no argument is given and the genome_db_id
             is not defined, it tries to get the data from other sources like the
             corresponding Bio::EnsEMBL::Compara::GenomeDB object. Use 0 as argument to
             clear this attribute.
 Returns   : integer
 Exeption  : none
 Caller    : $object->genome_db_id
 Status    : Stable
 
Code:
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public Bool Bio::EnsEMBL::Compara::DnaFrag::is_reference ( )
 Arg [1]   : bool $is_reference
 Example   : $is_reference = $dnafrag->is_reference()
 Example   : $dnafrag->is_reference(1)
 Function  : get/set is_reference attribute. The default value
             is 1 (TRUE).
 Returns   : bool
 Exeption  : none
 Caller    : $object->is_reference
 Status    : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFrag::length ( )
 Arg [1]   : int $length
 Example   : $length = $dnafrag->length()
 Example   : $dnafrag->length(256)
 Function  : get/set length attribute. Use 0 as argument to reset this attribute.
 Returns   : integer
 Exeption  : none
 Caller    : $object->length
 Status    : Stable
 
Code:
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public String Bio::EnsEMBL::Compara::DnaFrag::name ( )
 Arg [1]   : string $name
 Example   : $name = $dnafrag->name()
 Example   : $dnafrag->name("19")
 Function  : get/set name attribute. Use "" as argument to reset this attribute.
 Returns   : string
 Exeption  : none
 Caller    : $object->name
 Status    : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DnaFrag Bio::EnsEMBL::Compara::DnaFrag::new ( )
  Arg [-DBID] : (opt.) int $dbID (the database internal ID for this object)
  Arg [-ADAPTOR]
              : (opt.) Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor $adaptor
                (the adaptor for connecting to the database)
  Arg [-LENGTH]:(opt.) int $length (the length of this dnafrag)
  Arg [-NAME]:  (opt.) string $name (the name of this dnafrag)
  Arg [-GENOME_DB]
               :(opt.) Bio::EnsEMBL::Compara::GenomeDB $genome_db (the 
                genome_db object representing the species of this dnafrag)
  Arg [-GENOME_DB_ID]
               :(opt.) int $genome_db_id (the database internal for the 
                 genome_db)
  Arg [-COORD_SYSTEM_NAME]
               :(opt.) string $coord_system_name (the name of the toplevel
                 coordinate system of the dnafrag eg 'chromosome', 'scaffold')
  Example : my $dnafrag = new Bio::EnsEMBL::Compara::DnaFrag(
                      -length 247249719,
                      -name "1",
                      -genome_db $genome_db,
                      -coord_system_name "chromosome");
  Example : my $dnafrag = new Bio::EnsEMBL::Compara::DnaFrag(
                      -length 247249719,
                      -name "1",
                      -genome_db_id 22,
                      -coord_system_name "chromosome");
  Description: Creates a new DnaFrag object
  Returntype : Bio::EnsEMBL::Compara::DnaFrag
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DnaFrag::new_fast ( )
  Arg [1]    : hash reference $hashref
  Example    : none
  Description: This is an ultra fast constructor which requires knowledge of
               the objects internals to be used.
  Returntype :
  Exceptions : none
  Caller     :
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Slice Bio::EnsEMBL::Compara::DnaFrag::slice ( )
 Arg 1      : -none-
 Example    : $slice = $dnafrag->slice;
 Description: Returns the Bio::EnsEMBL::Slice object corresponding to this
              Bio::EnsEMBL::Compara::DnaFrag object.
 Returntype : Bio::EnsEMBL::Slice object
 Exceptions : warns when the corresponding Bio::EnsEMBL::Compara::GenomeDB,
              coord_system_name, name or Bio::EnsEMBL::DBSQL::DBAdaptor
              cannot be retrieved and returns undef.
 Caller     : $object->methodname
 Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DnaFrag::start ( )
 
Deprecated:
! All Bio::EnsEMBL::Compara::DnaFrag objects start in 1
  Arg [1]    : int
  Example    : $dnafrag->start(1);
  Description: Getter/Setter for the start attribute
  Returntype : int
  Exceptions : thrown when trying to set a starting position different from 1
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: