Inheritance diagram for Bio::EnsEMBL::MetaData::GenomeComparaInfo:
my $compara_info =
Bio::EnsEMBL::MetaData::GenomeComparaInfo->new(
-DBNAME => $compara->dbc()->dbname(),
-DIVISION => $division,
-METHOD => $method,
-SET_NAME => $set_name,
-GENOMES => [$genome1, $genome2],
-RELEASE => $release);
Object encapsulating information about a particular compara analysis and the genomes it involves
Bio::EnsEMBL::MetaData::BaseInfo Bio::EnsEMBL::MetaData::GenomeInfo Bio::EnsEMBL::MetaData::DBSQL::GenomeComparaInfoAdaptor
Definition at line 29 of file GenomeComparaInfo.pm.
Available Methods | |
| protected void | _load_child () |
| protected void | _preload () |
| protected | _unload () |
| public Bio::EnsEMBL::MetaData::DBSQL::GenomeInfoAdaptor | adaptor () |
| public Int | count_hash_lengths () |
| public | count_hash_values () |
| public DbID | dbID () |
| public | dbname () |
| public String | division () |
| public Arrayref | genomes () |
| public Boolean | is_dna_compara () |
| public | is_pan_compara () |
| public Boolean | is_peptide_compara () |
| public Boolean | is_synteny () |
| public String | method () |
| public | new () |
| public String | set_name () |
| public Hashref | to_hash () |
| public String | to_string () |
| 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 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] |
| 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 Bio::EnsEMBL::MetaData::GenomeComparaInfo::dbname | ( | ) |
Undocumented method
Code:
| public String Bio::EnsEMBL::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::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::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::MetaData::GenomeComparaInfo::is_pan_compara | ( | ) |
Undocumented method
Code:
| public Boolean Bio::EnsEMBL::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::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::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::MetaData::GenomeComparaInfo::new | ( | ) |
| public String Bio::EnsEMBL::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::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:
Reimplemented from Bio::EnsEMBL::MetaData::BaseInfo.
| public String Bio::EnsEMBL::MetaData::GenomeComparaInfo::to_string | ( | ) |
Description: Render as plain string Returntype : string Exceptions : none Caller : general Status : Stable
Code: