Bio::EnsEMBL::MetaData::GenomeOrganismInfo Class Reference

Inheritance diagram for Bio::EnsEMBL::MetaData::GenomeOrganismInfo:

List of all members.

---

Class Summary

Synopsis

      my $info =
        Bio::EnsEMBL::MetaData::GenomeOrganismInfo->new(
        -DISPLAY_NAME=>$display_name, -NAME=>$name, -STRAIN=>$strain, -SEROTYPE=>$serotype, -IS_REFERENCE=>$is_reference
      );

Description

Object encapsulating information about the organism to which a particular genome belongs

See-also

Bio::EnsEMBL::MetaData::BaseInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeOrganismInfoAdaptor

Definition at line 24 of file GenomeOrganismInfo.pm.

Available Methods
protected void	_load_child ()
protected void	_preload ()
protected	_unload ()
public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor	adaptor ()
public Arrayref	aliases ()
public Int	count_hash_lengths ()
public	count_hash_values ()
public DbID	dbID ()
public String	display_name ()
public String	is_reference ()
public	name ()
public	new ()
public Arrayref	publications ()
public String	serotype ()
public String	species_taxonomy_id ()
public String	strain ()
public String	taxonomy_id ()
public	to_hash ()
public	to_string ()

---

Method Documentation

protected void Bio::EnsEMBL::MetaData::BaseInfo::_load_child

(

)

[inherited]

  Description: Lazy load method for loading children from database if not initialised
  Arg        : Key to find child data in object hash
  Arg        : Method for loading child data from adaptor()
  Returntype : none
  Exceptions : none
  Caller     : Internal
  Status     : Stable
 

Code:

protected void Bio::EnsEMBL::MetaData::BaseInfo::_preload

(

)

[inherited]

  Description: Ensure all children are loaded (used for hash transformation)
  Returntype : none
  Exceptions : none
  Caller     : Internal
  Status     : Stable
 

Code:

  Description: Remove all children (used after hash transformation to ensure object is minimised)
  Returntype : none
  Exceptions : none
  Caller     : dump_metadata.pl
  Status     : Stable
 

/**

Reimplemented in Bio::EnsEMBL::MetaData::GenomeAssemblyInfo, and Bio::EnsEMBL::MetaData::GenomeInfo.

protected Bio::EnsEMBL::MetaData::BaseInfo::_unload

(

)

[inherited]

Undocumented method

Code:

Reimplemented in Bio::EnsEMBL::MetaData::GenomeAssemblyInfo, and Bio::EnsEMBL::MetaData::GenomeInfo.

public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::MetaData::BaseInfo::adaptor

(

)

[inherited]

  Arg        : (optional) adaptor to set set
  Description: Gets/sets GenomeInfoAdaptor
  Returntype : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor
  Exceptions : none
  Caller     : Internal
  Status     : Stable
 

Code:

Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public Arrayref Bio::EnsEMBL::MetaData::GenomeOrganismInfo::aliases

(

)

  Arg        : (optional) arrayref of aliases to set
  Description: Gets/sets aliases by which the genome is also known 
  Returntype : Arrayref of aliases
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Int Bio::EnsEMBL::MetaData::BaseInfo::count_hash_lengths

(

)

[inherited]

  Description: Sums sizes of arrays found in hash as values
  Arg		 : hashref
  Returntype : integer
  Exceptions : none
  Caller     : internal
  Status     : Stable
 

Code:

Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public Bio::EnsEMBL::MetaData::BaseInfo::count_hash_values

(

)

[inherited]

Undocumented method

Code:

Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public DbID Bio::EnsEMBL::MetaData::BaseInfo::dbID

(

)

[inherited]

  Arg        : (optional) dbID to set set
  Description: Gets/sets internal genome_id used as database primary key
  Returntype : dbID string
  Exceptions : none
  Caller     : Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor
  Status     : Stable
 

Code:

Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public String Bio::EnsEMBL::MetaData::GenomeOrganismInfo::display_name

(

)

  Arg        : (optional) display_name to set
  Description: Gets/sets display_name 
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public String Bio::EnsEMBL::MetaData::GenomeOrganismInfo::is_reference

(

)

  Arg        : (optional) whether organism is reference
  Description: Gets/sets whether this organism is the reference for its species
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Bio::EnsEMBL::MetaData::GenomeOrganismInfo::name

(

)

Undocumented method

Code:

public Bio::EnsEMBL::MetaData::GenomeOrganismInfo::new

(

)

Undocumented method

Code:

Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.

public Arrayref Bio::EnsEMBL::MetaData::GenomeOrganismInfo::publications

(

)

  Arg        : (optional) arrayref of pubmed IDs to set
  Description: Gets/sets PubMed IDs for publications associated with the genome
  Returntype : Arrayref of PubMed IDs
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public String Bio::EnsEMBL::MetaData::GenomeOrganismInfo::serotype

(

)

  Arg        : (optional) serotype to set
  Description: Gets/sets serotype
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public String Bio::EnsEMBL::MetaData::GenomeOrganismInfo::species_taxonomy_id

(

)

  Arg        : (optional) taxonomy_id to set
  Description: Gets/sets NCBI taxonomy ID of species to which this belongs
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public String Bio::EnsEMBL::MetaData::GenomeOrganismInfo::strain

(

)

  Arg        : (optional) strain to set
  Description: Gets/sets strain of genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public String Bio::EnsEMBL::MetaData::GenomeOrganismInfo::taxonomy_id

(

)

  Arg        : (optional) taxonomy_id to set
  Description: Gets/sets NCBI taxonomy ID
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Bio::EnsEMBL::MetaData::BaseInfo::to_hash

(

)

[inherited]

Undocumented method

Code:

Reimplemented in Bio::EnsEMBL::MetaData::DatabaseInfo, Bio::EnsEMBL::MetaData::DataReleaseInfo, Bio::EnsEMBL::MetaData::EventInfo, Bio::EnsEMBL::MetaData::GenomeComparaInfo, and Bio::EnsEMBL::MetaData::GenomeInfo.

public Bio::EnsEMBL::MetaData::GenomeOrganismInfo::to_string

(

)

Undocumented method

Code:

---

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

• Bio/EnsEMBL/MetaData/GenomeOrganismInfo.pm