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Bio-EnsEMBL-112.0_56
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LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::ArchiveStableId

DESCRIPTION

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.

SEE ALSO

Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor Bio::EnsEMBL::StableIdEvent Bio::EnsEMBL::StableIdHistoryTree

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

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

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     : my $history_tree = $archive_id->get_history_tree;
Description : Returns the history tree of this ArchiveStableId
Return type : Bio::EnsEMBL::StableIdHistoryTree
Exceptions  : none
Caller      : general
Status      : At Risk
            : under development

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

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

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

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

get_all_associated_archived

Example     : my ($arch_gene, $arch_tr, $arch_tl, $pep_seq) =
                @{ $arch_id->get_all_associated_archived };
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

get_all_gene_archive_ids

Example     : my @archived_genes = @{ $arch_id->get_all_gene_archive_ids };
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

get_all_transcript_archive_ids

Example     : my @archived_transcripts =
                @{ $arch_id->get_all_transcript_archive_ids };
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

get_all_translation_archive_ids

Example     : my @archived_peptides =
                @{ $arch_id->get_all_translation_archive_ids };
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

current_version

Example     : if (my $v = $arch_id->current_version) {
                print "Current version of this stable ID ", $v, "\n";
              } else {
                print "This stable ID is not in the current db.\n";
              }
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

is_current

Example     : if ($arch_id->is_current) {
                print $arch_id->version, " is the current version of this
                  stable ID.\n";
              }
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

get_latest_incarnation

Example     : my $latest = $arch_id->get_latest_incarnation;
              print "Latest version of ".$arch_id->stable_id." is ".
                $latest->version."\n";
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

is_latest

Arg[1]      : (optional) Boolean $is_latest
Example     : if ($arch_id->is_latest) {
                print "Version ".$arch_id->version." is the latest version 
                  of ".$arch_id->stable_id."\n";
              }
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