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Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable Class Reference

Inherits Bio::EnsEMBL::Hive::Process.

Inherited by Bio::EnsEMBL::Compara::Production::EPOanchors::ChunkRefDnafrags, Bio::EnsEMBL::Compara::Production::EPOanchors::FindStrand, Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::ChunkDnafrags, Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::DumpRepeats, Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::FindRepeatGabs, Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::HMMsearch, Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::LoadConsEles, Bio::EnsEMBL::Compara::Production::EPOanchors::HMMer::SplitCeIds, Bio::EnsEMBL::Compara::Production::EPOanchors::ParseEnredo, Bio::EnsEMBL::Compara::Production::EPOanchors::SetGenomeDBLocator, Bio::EnsEMBL::Compara::Production::EPOanchors::UpdateMaxAlignmentLength, Bio::EnsEMBL::Compara::RunnableDB::DumpMemberSequencesIntoFasta, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Compress, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::CreateChrJobs, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::CreateOtherJobs, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::CreateSuperJobs, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::DumpMultiAlign, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Emf2Maf, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::InitJobs, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::MD5SUM, Bio::EnsEMBL::Compara::RunnableDB::DumpMultiAlign::Readme, Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::CreateDefaultPairwiseMlss, Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::ImportAlignment, Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::LowCoverageGenomeAlignment, Bio::EnsEMBL::Compara::RunnableDB::EpoLowCoverage::SetNeighbourNodes, Bio::EnsEMBL::Compara::RunnableDB::Families::BlastAndParseDistances, Bio::EnsEMBL::Compara::RunnableDB::Families::ConsensifyAfamily, Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtEntries, Bio::EnsEMBL::Compara::RunnableDB::Families::LoadUniProtIndex, Bio::EnsEMBL::Compara::RunnableDB::Families::MafftAfamily, Bio::EnsEMBL::Compara::RunnableDB::Families::ParseMCLintoFamilies, Bio::EnsEMBL::Compara::RunnableDB::FindCoreRegionLength, Bio::EnsEMBL::Compara::RunnableDB::FindPartialGenesOnTree, Bio::EnsEMBL::Compara::RunnableDB::FindSingleGenesOnTree, Bio::EnsEMBL::Compara::RunnableDB::FindSplitGenesOnTree, Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllHomologiesOrthoXML, Bio::EnsEMBL::Compara::RunnableDB::GeneTrees::DumpAllTreesOrthoXML, Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::Gerp, Bio::EnsEMBL::Compara::RunnableDB::GenomicAlignBlock::UpdateMaxAlignmentLength, Bio::EnsEMBL::Compara::RunnableDB::HealthCheck, Bio::EnsEMBL::Compara::RunnableDB::HomologyGroupingFactory, Bio::EnsEMBL::Compara::RunnableDB::LoadMembers, Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB, Bio::EnsEMBL::Compara::RunnableDB::MakeSpeciesTree, Bio::EnsEMBL::Compara::RunnableDB::MemberDisplayLabelUpdater, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastAndParsePAF, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::BlastFactory, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::CheckReuseDB, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpMercatorFiles, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::DumpSubsetIntoFasta, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Mercator, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::MercatorFileFactory, Bio::EnsEMBL::Compara::RunnableDB::MercatorPecan::Pecan, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFEAnalysis, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFESpeciesTree, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::CAFETable, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::GeneStoreNCMembers, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::GenomePrepareNCMembers, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Infernal, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::Ktreedist, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCFastTrees, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicAlignment, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCGenomicTree, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCOrthoTree, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCRecoverEPO, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCRecoverSearch, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCSecStructTree, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::NCTreeBestMMerge, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::PrepareSecStructModels, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMClassify, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::RFAMLoadModels, Bio::EnsEMBL::Compara::RunnableDB::ncRNAtrees::SecStructModelTree, Bio::EnsEMBL::Compara::RunnableDB::ObjectFactory, Bio::EnsEMBL::Compara::RunnableDB::Ortheus, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::AlignmentProcessing, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ChunkAndGroupDna, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreateAlignmentChainsJobs, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreateAlignmentNetsJobs, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreateFilterDuplicatesJobs, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::CreatePairAlignerJobs, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::DumpDnaCollection, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::FilterDuplicates, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportChains, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ImportNets, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::PairAligner, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::PairAlignerConfig, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::ParsePairAlignerConf, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::RemoveAlignmentDataInconsistencies, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::SetInternalIds, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::StoreSequence, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscChainFactory, Bio::EnsEMBL::Compara::RunnableDB::PairAligner::UcscToEnsemblMapping, Bio::EnsEMBL::Compara::RunnableDB::PeptideMemberGroupingFactory, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BlastpWithReuse, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::BuildHMM, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::CheckGenomedbReusability, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::DumpSubsetCreateBlastDB, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FlowMemberSeq, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FromScratch::CheckGenomeReuse, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::FromScratch::StoreMembersSequence, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::GroupGenomesUnderTaxa, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HclusterParseOutput, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HclusterPrepare, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Homology_dNdS, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::HomologyGroupingFactory, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MCoffee, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::MLSSIDFactory, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::NJTREE_PHYML, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OrthoTree, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OtherParalogs, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::OverallGroupsetQC, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::PerGenomeGroupsetQC, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::QuickTreeBreak, Bio::EnsEMBL::Compara::RunnableDB::ProteinTrees::Threshold_on_dS, Bio::EnsEMBL::Compara::RunnableDB::StableIdMapper, and Bio::EnsEMBL::Compara::RunnableDB::TreefamXrefMapper.

List of all members.


Class Summary

Synopsis

        # from within a Compara Runnable:
    my $FamilyAdaptor = $self-\>compara_dba()-\>get_FamilyAdaptor();

    my $ExternalFooFeatureAdaptor = $self-\>compara_dba($self-\>param('external_source'))-\>get_FooFeatureAdaptor();

Description

All Compara RunnableDBs *should* inherit from this module in order to work with module parameters and compara_dba in a neat way.
It inherits the parameter parsing functionality from Bio::EnsEMBL::Hive::Process
and provides a convenience method for creating the compara_dba from almost anything that can provide connection parameters.
Please refer to Bio::EnsEMBL::Hive::Process documentation to understand the basics of the RunnableDB interface.
 

Definition at line 27 of file BaseRunnable.pm.

Available Methods

public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
public compara_dba ()
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 go_figure_compara_dba ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public new ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
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 Int verbose ()
public warning ()
public worker ()
public worker_temp_directory ()
public write_output ()

Method Documentation

public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::compara_dba ( )
    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
 
Code:
click to view
public Bio::EnsEMBL::Compara::RunnableDB::BaseRunnable::go_figure_compara_dba ( )
    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.
 
Code:
click to view

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