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Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds:

List of all members.


Class Summary

Synopsis

Description

This module makes the internal ids unique by setting auto_increment to start at method_link_species_set_id * 10**10. This will do this on the following tables: genomic_align_block, genomic_align, genomic_align_group, genomic_align_tree
 

Definition at line 21 of file SetInternalIds.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
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 void fetch_input ()
public genome_db_ids ()
public get_params ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public method_link_species_set_id ()
public method_link_type ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public Bio::EnsEMBL::Hive::Queen queen ()
public void run ()
public Arrayref runnable ()
public setInternalIds ()
public Array stack_trace ()
public String stack_trace_dump ()
public strict_hash_format ()
public tables ()
public void throw ()
public Depend try ()
public Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public Boolean write_output ()

Method Documentation

public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::fetch_input ( )
    Title   :   fetch_input
    Usage   :   $self->fetch_input
    Function:   Fetches input data for gerp from the database
    Returns :   none
    Args    :   none
 
Code:
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Reimplemented from Bio::EnsEMBL::Hive::Process.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::genome_db_ids ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::get_params ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::method_link_species_set_id ( )

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::method_link_type ( )

Undocumented method

public void Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::run ( )
    Title   :   run
    Usage   :   $self->run
    Function:   Run gerp
    Returns :   none
    Args    :   none
 
Code:
click to view

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

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::setInternalIds ( )

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::tables ( )

Undocumented method

Code:
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public Boolean Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::SetInternalIds::write_output ( )
    Title   :   write_output
    Usage   :   $self->write_output
    Function:   Write results to the database
    Returns :   1
    Args    :   none
 
Code:
click to view

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


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