Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo Class Reference

Public Member Functions
public	new ()
public	dbname ()
public String	method ()
public String	set_name ()
public String	division ()
public Arrayref	genomes ()
public	is_pan_compara ()
public Boolean	is_peptide_compara ()
public Boolean	is_dna_compara ()
public Boolean	is_synteny ()
public Hashref	to_hash ()
public	to_string ()
public	dbID ()
public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor	adaptor ()

Detailed Description

Synopsis

my $compara_info =
  Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo->new(
                             -DBNAME   => $compara->dbc()->dbname(),
                             -DIVISION => $division,
                             -METHOD   => $method,
                             -SET_NAME => $set_name,
                             -GENOMES  => [$genome1, $genome2]);

Description

Object encapsulating information about a particular compara analysis and the genomes it involves

Member Function Documentation

public Bio::EnsEMBL::Utils::MetaData::DBSQL::GenomeInfoAdaptor Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::adaptor

(

)

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

Code:

public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::dbID

(

)

Undocumented method

Code:

public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::dbname

(

)

Undocumented method

Code:

public String Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::division

(

)

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

Code:

public Arrayref Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::genomes

(

)

  Arg        : (optional) genomes to set
  Description: Gets/sets arrayref of genomes 
  Returntype : arrayref
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Boolean Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::is_dna_compara

(

)

  Arg        : (optional) 1/0 to set 
  Description: Boolean-style method, returns 1 if analysis is part of a DNA compara, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::is_pan_compara

(

)

Undocumented method

Code:

public Boolean Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::is_peptide_compara

(

)

  Arg        : (optional) 1/0 to set 
  Description: Boolean-style method, returns 1 if analysis is part of a peptide compara, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Boolean Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::is_synteny

(

)

  Arg        : (optional) 1/0 to set 
  Description: Boolean-style method, returns 1 if analysis is part of a synteny compara, 0 if not
  Returntype : 1 or 0
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public String Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::method

(

)

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

Code:

public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::new

(

)

Undocumented method

Code:

public String Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::set_name

(

)

  Arg        : (optional) species set name to set
  Description: Gets/sets name of species set used in compara analysis
  Returntype : string
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Hashref Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::to_hash

(

)

  Description: Render compara as plain hash suitable for export as JSON/XML
  Returntype : Hashref
  Exceptions : none
  Caller     : general
  Status     : Stable
 

Code:

public Bio::EnsEMBL::Utils::MetaData::GenomeComparaInfo::to_string

(

)

Undocumented method

Code:

---

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

• modules/Bio/EnsEMBL/Utils/MetaData/GenomeComparaInfo.pm