Available Methods
Bio::EnsEMBL::MetaData::GenomeAssemblyInfo Class Reference
Inheritance diagram for Bio::EnsEMBL::MetaData::GenomeAssemblyInfo:

List of all members.

Class Summary

Synopsis

      my $assembly_info =
        Bio::EnsEMBL::MetaData::GenomeAssemblyInfo->new(
                                              -ASSEMBLY_NAME      => $assembly_name,
                                              -ASSEMBLY_ACCESSION => $assembly_accession,
                                              -ASSEMBLY_LEVEL     => $assembly_level,
                                              -ORGANISM           => $organism
        );

Description

Object encapsulating information about a particular assembly. Release-independent.

See-also

Bio::EnsEMBL::MetaData::BaseInfo Bio::EnsEMBL::MetaData::GenomeOrganismInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeAssemblyInfoAdaptor

Definition at line 29 of file GenomeAssemblyInfo.pm.

Available Methods

protected void _load_child ()
protected void _preload ()
protected _unload ()
public
Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor 		adaptor ()
public String assembly_accession ()
public String assembly_level ()
public assembly_name ()
public Int base_count ()
public Int count_hash_lengths ()
public count_hash_values ()
public DbID dbID ()
public String display_name ()
public Bool is_reference ()
public String name ()
public new ()
public
Bio::EnsEMBL::MetaData::GenomeOrganismInfo 		organism ()
public Arrayref sequences ()
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:
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protected void Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::_preload ( ) 
  Description: Ensure all children are loaded (used for hash transformation)
  Returntype : none
  Exceptions : none
  Caller     : Internal
  Status     : Stable
Code:
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  Description: Remove all children (used after hash transformation to ensure object is minimised)
  Returntype : none
  Exceptions : none
  Caller     : dump_metadata.pl
  Status     : Stable

/**

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

protected Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::_unload ( )

Undocumented method

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

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

public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::assembly_accession ( ) 
  Arg        : (optional) assembly_accession to set
  Description: Gets/sets INSDC accession for assembly
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::assembly_level ( ) 
  Arg        : (optional) assembly_level to set
  Description: Gets/sets highest level of assembly (chromosome, supercontig etc.)
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::assembly_name ( )

Undocumented method

Code:
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public Int Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::base_count ( ) 
  Arg        : (optional) base_count to set
  Description: Gets/sets total number of bases in assembled genome
  Returntype : integer
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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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:
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Reimplemented in Bio::EnsEMBL::MetaData::GenomeInfo.

public Bio::EnsEMBL::MetaData::BaseInfo::count_hash_values ( ) [inherited]

Undocumented method

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

public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::display_name ( ) 
  Description: Gets display_name
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bool Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::is_reference ( ) 
  Description: Gets whether this is a reference for the species
  Returntype : bool
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::name ( ) 
  Description: Gets name for genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::new ( )

Undocumented method

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

public Bio::EnsEMBL::MetaData::GenomeOrganismInfo Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::organism ( ) 
  Arg        : (optional) organism object to set
  Description: Gets/sets organism to which genome belongs
  Returntype : Bio::EnsEMBL::MetaData::GenomeOrganismInfo
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Arrayref Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::sequences ( ) 
  Arg        : (optional) arrayref of sequences to set
  Description: Gets/sets array of hashrefs describing sequences from the assembly. Elements are hashrefs with name and acc as keys
  Returntype : Arrayref
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::serotype ( ) 
  Description: Gets serotype
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::species_taxonomy_id ( ) 
  Description: Gets NCBI taxonomy ID for species to which this organism belongs
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::strain ( ) 
  Description: Gets strain of genome
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public String Bio::EnsEMBL::MetaData::GenomeAssemblyInfo::taxonomy_id ( ) 
  Description: Gets NCBI taxonomy ID
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
Code:
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public Bio::EnsEMBL::MetaData::BaseInfo::to_hash ( ) [inherited]

Undocumented method

Code:
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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::GenomeAssemblyInfo::to_string ( )

Undocumented method

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