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 ()

Detailed Description

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

Definition at line 29 of file ArchiveStableId.pm.

Member Function Documentation

◆ adaptor()

public Bio::EnsEMBL::ArchiveStableId::adaptor ( )

Undocumented method

Code:

click to view

◆ assembly()

public Bio::EnsEMBL::ArchiveStableId::assembly ( )

Undocumented method

Code:

click to view

◆ current_version()

public Boolean Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ db_name()

public Bio::EnsEMBL::ArchiveStableId::db_name ( )

Undocumented method

Code:

click to view

◆ get_all_associated_archived()

public Listref Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ get_all_gene_archive_ids()

public Listref Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ get_all_predecessors()

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

Code:

click to view

◆ get_all_successors()

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

Code:

click to view

◆ get_all_transcript_archive_ids()

public Listref Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ get_all_translation_archive_ids()

public Listref Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ get_event()

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

Code:

click to view

◆ get_history_tree()

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     :

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

Code:

click to view

◆ get_latest_incarnation()

public Bio::EnsEMBL::ArchiveStableId Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ get_peptide()

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

Code:

click to view

◆ is_current()

public Boolean Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ is_latest()

public Boolean Bio::EnsEMBL::ArchiveStableId::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

Code:

click to view

◆ new()

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

Code:

click to view

◆ new_fast()

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

Code:

click to view

◆ release()

public Bio::EnsEMBL::ArchiveStableId::release ( )

Undocumented method

Code:

click to view

◆ stable_id()

public Bio::EnsEMBL::ArchiveStableId::stable_id ( )

Undocumented method

Code:

click to view

◆ successors()

public Bio::EnsEMBL::ArchiveStableId::successors ( )

Undocumented method

Code:

click to view

◆ type()

public Bio::EnsEMBL::ArchiveStableId::type ( )

Undocumented method

Code:

click to view

◆ version()

public Bio::EnsEMBL::ArchiveStableId::version ( )

Undocumented method

Code:

click to view

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

ensembl/modules/Bio/EnsEMBL/ArchiveStableId.pm

Public Member Functions

Detailed Description

Description

See-also

Member Function Documentation

◆ adaptor()

◆ assembly()

◆ current_version()

◆ db_name()

◆ get_all_associated_archived()

◆ get_all_gene_archive_ids()

◆ get_all_predecessors()

◆ get_all_successors()

◆ get_all_transcript_archive_ids()

◆ get_all_translation_archive_ids()

◆ get_event()

◆ get_history_tree()

◆ get_latest_incarnation()

◆ get_peptide()

◆ is_current()

◆ is_latest()

◆ new()

◆ new_fast()

◆ release()

◆ stable_id()

◆ successors()

◆ type()

◆ version()