Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::IdMapping::StableIdGenerator::PristionchusPacificus Class Reference
Inheritance diagram for Bio::EnsEMBL::IdMapping::StableIdGenerator::PristionchusPacificus:

List of all members.


Class Summary

Definition at line 5 of file PristionchusPacificus.pm.

Available Methods

public
Bio::EnsEMBL::IdMapping::Cache 
cache ()
public String calculate_version ()
public
Bio::EnsEMBL::Utils::ConfParser 
conf ()
public Int dump_table_to_file ()
public SQLStatement fetch_value_from_db ()
public Boolean file_exists ()
public Filehandle get_filehandle ()
public increment_stable_id ()
public String initial_stable_id ()
public is_valid ()
public Bio::EnsEMBL::Utils::Logger logger ()
public $this new ()
public Int upload_file_into_table ()

Method Documentation

public Bio::EnsEMBL::IdMapping::Cache Bio::EnsEMBL::IdMapping::BaseObject::cache ( ) [inherited]
  Arg[1]      : (optional) Bio::EnsEMBL::IdMapping::Cache - the cache to set
  Example     : $object->cache->read_from_file('source');
  Description : Getter/setter for cache object
  Return type : Bio::EnsEMBL::IdMapping::Cache
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development
 
Code:
click to view
public String Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric::calculate_version ( ) [inherited]
  Arg[1]      : Bio::EnsEMBL::IdMapping::TinyFeature $s_obj - source object
  Arg[2]      : Bio::EnsEMBL::IdMapping::TinyFeature $t_obj - target object
  Example     : my $version = $generator->calculate_version($source_gene,
                  $target_gene);
                $target_gene->version($version);
  Description : Determines the version for a mapped stable Id. For Ensembl
                genes, the rules for incrementing the version number are:

  • exons: if exon sequence changed
  • transcript: if spliced exon sequence changed
  • translation: if transcript changed
  • gene: if any of its transcript changed Return type : String - the version to be used Exceptions : thrown on wrong argument Caller : Bio::EnsEMBL::IdMapping::StableIdMapper::map_stable_ids() Status : At Risk : under development
 
Code:
click to view
public Bio::EnsEMBL::Utils::ConfParser Bio::EnsEMBL::IdMapping::BaseObject::conf ( ) [inherited]
  Arg[1]      : (optional) Bio::EnsEMBL::Utils::ConfParser - the configuration
                to set
  Example     : my $basedir = $object->conf->param('basedir');
  Description : Getter/setter for configuration object
  Return type : Bio::EnsEMBL::Utils::ConfParser
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development
 
Code:
click to view
public Int Bio::EnsEMBL::IdMapping::BaseObject::dump_table_to_file ( ) [inherited]
  Arg[1]      : String $dbtype - db type (source|target)
  Arg[2]      : String $table - name of table to dump
  Arg[3]      : String $filename - name of dump file
  Arg[4]      : Boolean $check_existing - turn on test for existing dump
  Example     : my $rows_dumped = $object->dump_table_to_file('source',
                  'stable_id_event', 'stable_id_event_existing.txt');
  Description : Dumps the contents of a db table to a tab-delimited file. The
                dump file will be written to a subdirectory called 'tables'
                under the basedir from your configuration.
  Return type : Int - the number of rows dumped
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public SQLStatement Bio::EnsEMBL::IdMapping::BaseObject::fetch_value_from_db ( ) [inherited]
  Arg[1]      : DBI::db $dbh - a DBI database handle
  Arg[2]      : String $sql - SQL statement to execute
  Example     : my $num_genes = $object->fetch_value_from_db($dbh,
                  'SELECT count(*) FROM gene');
  Description : Executes an SQL statement on a db handle and returns the first
                column of the first row returned. Useful for queries returning a
                single value, like table counts.
  Return type : Return type of SQL statement
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Boolean Bio::EnsEMBL::IdMapping::BaseObject::file_exists ( ) [inherited]
  Arg[1]      : String $filename - filename to test
  Arg[2]      : Boolean $path_append - turn on pre-pending of basedir
  Example     : unless ($object->file_exists('gene_mappings.ser', 1)) {
                  $object->do_gene_mapping;
                }
  Description : Tests if a file exists and has non-zero size.
  Return type : Boolean
  Exceptions  : none
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Filehandle Bio::EnsEMBL::IdMapping::BaseObject::get_filehandle ( ) [inherited]
  Arg[1]      : String $filename - filename for filehandle
  Arg[2]      : String $path_append - append subdirectory name to basedir
  Arg[3]      : String $mode - filehandle mode (<|>|>>)
  Example     : my $fh = $object->get_filehandle('mapping_stats.txt', 'stats',
                  '>');
                print $fh "Stats:\\n";
  Description : Returns a filehandle to a file for reading or writing. The file
                is qualified with the basedir defined in the configuration and
                an optional subdirectory name.
  Return type : filehandle
  Exceptions  : thrown on missing filename
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::IdMapping::StableIdGenerator::PristionchusPacificus::increment_stable_id ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric.

public String Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric::initial_stable_id ( ) [inherited]
  Arg[1]      : String $type - an entity type (gene|transcript|translation|exon)
  Example     : my $new_stable_id = $generator->initial_stable_id('gene');
  Description : Determine the initial stable Id to use for new assignments. This
                method is called once at the beginning of stable Id mapping.
  Return type : String - a stable Id of appropriate type
  Exceptions  : none
  Caller      : Bio::EnsEMBL::IdMapping::StableIdMapper::map_stable_ids()
  Status      : At Risk
              : under development
 
Code:
click to view
public Bio::EnsEMBL::IdMapping::StableIdGenerator::PristionchusPacificus::is_valid ( )

Undocumented method

Code:
click to view

Reimplemented from Bio::EnsEMBL::IdMapping::StableIdGenerator::EnsemblGeneric.

public Bio::EnsEMBL::Utils::Logger Bio::EnsEMBL::IdMapping::BaseObject::logger ( ) [inherited]
  Arg[1]      : (optional) Bio::EnsEMBL::Utils::Logger - the logger to set
  Example     : $object->logger->info("Starting ID mapping.\\n");
  Description : Getter/setter for logger object
  Return type : Bio::EnsEMBL::Utils::Logger
  Exceptions  : none
  Caller      : constructor
  Status      : At Risk
              : under development
 
Code:
click to view
public $this Bio::EnsEMBL::IdMapping::BaseObject::new ( ) [inherited]
  Arg [LOGGER]: Bio::EnsEMBL::Utils::Logger $logger - a logger object
  Arg [CONF]  : Bio::EnsEMBL::Utils::ConfParser $conf - a configuration object
  Arg [CACHE] : Bio::EnsEMBL::IdMapping::Cache $cache - a cache object
  Example     : my $object = Bio::EnsEMBL::IdMapping::BaseObjectSubclass->new(
                  -LOGGER => $logger,
                  -CONF   => $conf,
                  -CACHE  => $cache
                );
  Description : Constructor
  Return type : implementing subclass type
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view

Reimplemented in Bio::EnsEMBL::IdMapping::StableIdMapper.

public Int Bio::EnsEMBL::IdMapping::BaseObject::upload_file_into_table ( ) [inherited]
  Arg[1]      : String $dbtype - db type (source|target)
  Arg[2]      : String $table - name of table to upload the data to
  Arg[3]      : String $filename - name of dump file
  Arg[4]      : Boolean $no_check_empty - don't check if table is empty
  Example     : my $rows_uploaded = $object->upload_file_into_table('target',
                  'stable_id_event', 'stable_id_event_new.txt');
  Description : Uploads a tab-delimited data file into a db table. The data file
                will be taken from a subdirectory 'tables' under your configured
                basedir. If the db table isn't empty and $no_check_empty isn't
                set, no data is uploaded (and a warning is issued).
  Return type : Int - the number of rows uploaded
  Exceptions  : thrown on wrong or missing arguments
  Caller      : general
  Status      : At Risk
              : under development
 
Code:
click to view

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