ensembl-hive
2.6
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Public Member Functions | |
public Bio::EnsEMBL::ArchiveStableId | new () |
public Bio::EnsEMBL::ArchiveStableId | new_fast () |
public Bio::EnsEMBL::StableIdHistoryTree | get_history_tree () |
public Listref | get_event () |
public Listref | get_all_predecessors () |
public Listref | get_all_successors () |
public String | get_peptide () |
public Listref | get_all_associated_archived () |
public Listref | get_all_gene_archive_ids () |
public Listref | get_all_transcript_archive_ids () |
public Listref | get_all_translation_archive_ids () |
public Boolean | current_version () |
public Boolean | is_current () |
public Bio::EnsEMBL::ArchiveStableId | get_latest_incarnation () |
public Boolean | is_latest () |
public | stable_id () |
public | version () |
public | db_name () |
public | release () |
public | assembly () |
public | type () |
public | adaptor () |
public | successors () |
ArchiveStableId objects are the main workunit for retrieving stable id archived information from EnsEMBL core database. Attributes: type: Gene, Transcript, Translation, Exon, other, undef stable_id: eg. ENSG00000000001 version: e.g. 1 db_name: eg. homo_sapiens_core_12_31 release: e.g. 35 assembly: e.g. NCBI35 successors: listref of Bio::EnsEMBL::ArchiveStableIds adaptor: Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor Status: At Risk. This module is in development.
Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor Bio::EnsEMBL::StableIdEvent Bio::EnsEMBL::StableIdHistoryTree
Definition at line 29 of file ArchiveStableId.pm.
public Bio::EnsEMBL::ArchiveStableId::adaptor | ( | ) |
Undocumented method
public Bio::EnsEMBL::ArchiveStableId::assembly | ( | ) |
Undocumented method
public Boolean Bio::EnsEMBL::ArchiveStableId::current_version | ( | ) |
Example :
Description : Lazy-loads the current version of stable ID Return type : Boolean (TRUE is current version found, else FALSE) Exceptions : none Caller : general Status : At Risk : under development
public Bio::EnsEMBL::ArchiveStableId::db_name | ( | ) |
Undocumented method
public Listref Bio::EnsEMBL::ArchiveStableId::get_all_associated_archived | ( | ) |
Example :
Description : Fetches associated archived stable IDs from the db for this ArchiveStableId (version is taken into account). Return type : Listref of ArchiveStableId archived gene ArchiveStableId archived transcript (optional) ArchiveStableId archived translation (optional) peptide sequence Caller : webcode, general Status : At Risk : under development
public Listref Bio::EnsEMBL::ArchiveStableId::get_all_gene_archive_ids | ( | ) |
Example :
Description : Returns gene ArchiveStableIds associated with this ArchiveStableId. If this is a gene, it returns itself. Returntype : listref of Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general Status : At Risk : under development
public Listref Bio::EnsEMBL::ArchiveStableId::get_all_predecessors | ( | ) |
Args : none Description : Retrieve a list of ArchiveStableIds that were mapped to this one. Returntype : listref of Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general Status : At Risk : under development
public Listref Bio::EnsEMBL::ArchiveStableId::get_all_successors | ( | ) |
Args : none Description : Retrieve a list of ArchiveStableIds that this one was mapped to. Returntype : listref Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general Status : At Risk : under development
public Listref Bio::EnsEMBL::ArchiveStableId::get_all_transcript_archive_ids | ( | ) |
Example :
Description : Returns transcript ArchiveStableIds associated with this ArchiveStableId. If this is a transcript, it returns itself. Returntype : listref of Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general Status : At Risk : under development
public Listref Bio::EnsEMBL::ArchiveStableId::get_all_translation_archive_ids | ( | ) |
Example :
Description : Returns translation ArchiveStableIds associated with this ArchiveStableId. If this is a translation, it returns itself. Returntype : listref of Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general Status : At Risk : under development
public Listref Bio::EnsEMBL::ArchiveStableId::get_event | ( | ) |
Args : stable_id Description : Retrieve a specific event for this archive and a given stable id Returntype : listref of Bio::EnsEMBL::StableIdEvent Exceptions : none Caller : general Status : At Risk : under development
public Bio::EnsEMBL::StableIdHistoryTree Bio::EnsEMBL::ArchiveStableId::get_history_tree | ( | ) |
Arg[1] : (optional) Int $num_high_scorers number of mappings per stable ID allowed when filtering Arg[2] : (optional) Int $max_rows maximum number of stable IDs in history tree (used for filtering) Example :
Description : Returns the history tree of this ArchiveStableId Return type : Bio::EnsEMBL::StableIdHistoryTree Exceptions : none Caller : general Status : At Risk : under development
public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::ArchiveStableId::get_latest_incarnation | ( | ) |
Example :
Description : Returns the ArchiveStableId representing the latest version of this stable ID. Returns itself if this already is the latest version, otherwise fetches it from the db. Return type : Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general Status : At Risk : under development
public String Bio::EnsEMBL::ArchiveStableId::get_peptide | ( | ) |
Description : Retrieves the peptide string for this ArchiveStableId. Returntype : String, or undef if this is not a Translation or cant be found in the database. Exceptions : none Caller : general Status : At Risk : under development
public Boolean Bio::EnsEMBL::ArchiveStableId::is_current | ( | ) |
Example :
Description : Determines if the version of this object is the current version of this stable ID. Note that this method doesn't lazy-load the current version of an ArchiveStableId; if you want to be sure, use current_version() instead. Return type : Boolean (TRUE if it is current, else FALSE) Exceptions : none Caller : general Status : At Risk : under development
public Boolean Bio::EnsEMBL::ArchiveStableId::is_latest | ( | ) |
Arg[1] : (optional) Boolean $is_latest Example :
Description : Indicates whether this is the latest version of this stable ID. Can also be used as a setter if we know this is the latest version. Return type : Boolean (TRUE if yes, FALSE if no) Exceptions : none Caller : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor->fetch_by_stable_id, general Status : At Risk : under development
public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::ArchiveStableId::new | ( | ) |
Arg [STABLE_ID] : String $stable_id Arg [VERSION] : Int $version Arg [CURRENT_VERSION]: Int $current_version Arg [DB_NAME] : String $db_name Arg [RELEASE] : String $release Arg [ASSEMBLY_NAME] : String $assembly Arg [TYPE] : String $type - "Gene", "Transcript", "Translation", "Exon" Arg [ADAPTOR] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor Description : standard constructor with named arguments to create ArchiveStableId Returntype : Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general, Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor Status : At Risk : under development
public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::ArchiveStableId::new_fast | ( | ) |
Arg [1] : String $stable_id Arg [2] : Int $version Arg [3] : String $db_name Arg [4] : String $release Arg [5] : String $assembly Arg [6] : String $type - "Gene", "Transcript", "Translation", "Exon" Arg [7] : Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor $adaptor Arg [8] : Int $current_version Description : faster version of above constructor Returntype : Bio::EnsEMBL::ArchiveStableId Exceptions : none Caller : general, Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor Status : At Risk : under development
public Bio::EnsEMBL::ArchiveStableId::release | ( | ) |
Undocumented method
public Bio::EnsEMBL::ArchiveStableId::stable_id | ( | ) |
Undocumented method
public Bio::EnsEMBL::ArchiveStableId::successors | ( | ) |
Undocumented method
public Bio::EnsEMBL::ArchiveStableId::type | ( | ) |
Undocumented method
public Bio::EnsEMBL::ArchiveStableId::version | ( | ) |
Undocumented method