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Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf:

List of all members.


Class Summary

Synopsis

If master_db defined then use populate_new_database which needs either mlss_id or a list of species provided from the conf_file. Use conf_file when adding multiple pairwise analyses. If have only one pairwise, then define mlss_id in the master.

If master_db is not defined, must populate the compara database from either core databases defined in conf_file or in default_options (core_dbs). Create genome_dbs, the genome_db_id is defined in the conf_file but not in the default_options. Create mlss_ids.

ERROR:
If no master_db, no conf_file and no core_dbs.

Description

Parse configuration file
 

Definition at line 25 of file ParsePairAlignerConf.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public Bio::EnsEMBL::DBSQL::DBAdaptor::extract_assembly_name ()
public Bio::EnsEMBL::DBSQL::DBAdaptor::locator ()
public catch ()
public void check_if_exit_cleanly ()
public compara_dba ()
public create_chain_dataflows ()
public create_net_dataflows ()
public create_pair_aligner_dataflows ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public void deprecate ()
public DESTROY ()
public fetch_input ()
public find_config ()
public get_chain_configs ()
public get_chunking ()
public get_default_chunking ()
public get_dna_collection ()
public get_locator ()
public get_net_configs ()
public get_pair_aligner ()
public get_species ()
public go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public load_registry_dbs ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public parse_conf ()
public parse_defaults ()
public populate_database_from_core_db ()
public print_conf ()
public print_pair_aligner ()
public Bio::EnsEMBL::Hive::Queen queen ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public void throw ()
public Depend try ()
public update_dnafrags ()
public update_genome_db ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_masking_options ()
public write_mlss_entry ()
public write_output ()
public write_parameters_to_meta ()

Method Documentation

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::Bio::EnsEMBL::DBSQL::DBAdaptor::extract_assembly_name ( )
public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::Bio::EnsEMBL::DBSQL::DBAdaptor::locator ( )
public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::compara_dba ( ) [inherited]
    Description: this is an intelligent setter/getter of a Compara DBA. Resorts to magic in order to figure out how to connect.
    Example 1:   my $family_adaptor = $self->compara_dba()->get_FamilyAdaptor();    # implicit initialization and hashing
    Example 2:   my $external_foo_adaptor = $self->compara_dba( $self->param('db_conn') )->get_FooAdaptor();    # explicit initialization and hashing
 
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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::create_chain_dataflows ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::create_net_dataflows ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::create_pair_aligner_dataflows ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::fetch_input ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::find_config ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_chain_configs ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_chunking ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_default_chunking ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_dna_collection ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_locator ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_net_configs ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_pair_aligner ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::get_species ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::go_figure_compara_dba ( ) [inherited]
    Description: this is a method that tries lots of different ways to find connection parameters
                 from a given object/hash and returns a Compara DBA. Does not hash anything, just does the detective magic.
 
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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::load_registry_dbs ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::parse_conf ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::parse_defaults ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::populate_database_from_core_db ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::print_conf ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::print_pair_aligner ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::run ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::update_dnafrags ( )
  Arg[1]      : Bio::EnsEMBL::Compara::DBSQL::DBAdaptor $compara_dba
  Arg[2]      : Bio::EnsEMBL::Compara::GenomeDB $genome_db
  Arg[3]      : Bio::EnsEMBL::DBSQL::DBAdaptor $species_dba
  Description : This method fetches all the dnafrag in the compara DB
                corresponding to the $genome_db. It also gets the list
                of top_level seq_regions from the species core DB and
                updates the list of dnafrags in the compara DB.
  Returns     : -none-
  Exceptions  :
 
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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::update_genome_db ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::write_masking_options ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::write_mlss_entry ( )

Undocumented method

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public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::write_output ( )

Undocumented method

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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf::write_parameters_to_meta ( )

Undocumented method

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