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Bio::EnsEMBL::ArchiveStableId Class Reference
Inheritance diagram for Bio::EnsEMBL::ArchiveStableId:

List of all members.


Class Summary

Synopsis

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.
 

Definition at line 28 of file ArchiveStableId.pm.

Available Methods

protected _rearrange ()
public adaptor ()
public assembly ()
public Boolean current_version ()
public db_name ()
public Listref get_all_associated_archived ()
public Listref get_all_gene_archive_ids ()
public Listref get_all_predecessors ()
public Listref get_all_successors ()
public Listref get_all_transcript_archive_ids ()
public Listref get_all_translation_archive_ids ()
public
Bio::EnsEMBL::StableIdHistoryTree 
get_history_tree ()
public
Bio::EnsEMBL::ArchiveStableId 
get_latest_incarnation ()
public String get_peptide ()
public Boolean is_current ()
public Boolean is_latest ()
public
Bio::EnsEMBL::ArchiveStableId 
new ()
public
Bio::EnsEMBL::ArchiveStableId 
new_fast ()
public release ()
public stable_id ()
public stack_trace ()
public stack_trace_dump ()
public successors ()
public throw ()
public type ()
public verbose ()
public version ()
public warn ()

Method Documentation

protected Bio::EnsEMBL::Root::_rearrange ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::ArchiveStableId::adaptor ( )

Undocumented method

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

Undocumented method

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

Undocumented method

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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
 
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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
 
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public Listref Bio::EnsEMBL::ArchiveStableId::get_all_predecessors ( )
  Args        : none
  Example     : 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
 
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public Listref Bio::EnsEMBL::ArchiveStableId::get_all_successors ( )
  Args        : none
  Example     : 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
 
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public Listref Bio::EnsEMBL::ArchiveStableId::get_all_transcript_archive_ids ( )
  Example     : none
  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
 
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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
 
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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
 
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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
 
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public String Bio::EnsEMBL::ArchiveStableId::get_peptide ( )
  Example     : none
  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
 
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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
 
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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
 
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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 
  Example         : none
  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
 
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Reimplemented from Bio::EnsEMBL::Root.

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 
  Example     : none
  Description : faster version of above constructor
  Returntype  : Bio::EnsEMBL::ArchiveStableId
  Exceptions  : none
  Caller      : general, Bio::EnsEMBL::DBSQL::ArchiveStableIdAdaptor
  Status      : At Risk
              : under development
 
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public Bio::EnsEMBL::ArchiveStableId::release ( )

Undocumented method

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

Undocumented method

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public Bio::EnsEMBL::Root::stack_trace ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::Root::stack_trace_dump ( ) [inherited]
Deprecated:
 
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public Bio::EnsEMBL::ArchiveStableId::successors ( )

Undocumented method

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public Bio::EnsEMBL::Root::throw ( ) [inherited]
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public Bio::EnsEMBL::ArchiveStableId::type ( )

Undocumented method

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public Bio::EnsEMBL::Root::verbose ( ) [inherited]
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public Bio::EnsEMBL::ArchiveStableId::version ( )

Undocumented method

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public Bio::EnsEMBL::Root::warn ( ) [inherited]
Deprecated:
 
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The documentation for this class was generated from the following file: