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

List of all members.


Class Summary

Definition at line 9 of file BlastZ.pm.

Available Methods

protected _write_output ()
public Bio::EnsEMBL::Analysis analysis ()
public catch ()
public void check_if_exit_cleanly ()
public compact_cigar_line ()
public configure_defaults ()
public configure_runnable ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
data_dbc ()
public dataflow_output_id ()
public
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor 
db ()
public db_DnaFragChunkSet ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public Int debug ()
public delete_fasta_dumps_but_these ()
public void deprecate ()
public DESTROY ()
public do_transactions ()
public dump_loc ()
public dumpChunkSetToWorkdir ()
public dumpChunkToWorkdir ()
public void fetch_input ()
public get_params ()
public go_figure_dbc ()
public void info ()
public input_id ()
public
Bio::EnsEMBL::Hive::AnalysisJob 
input_job ()
public max_alignments ()
public method_link_type ()
public new ()
public options ()
public Array output ()
public param ()
public param_defaults ()
public param_substitute ()
public parameters ()
public print_simple_align ()
public Bio::EnsEMBL::Hive::Queen queen ()
public query_DnaFragChunkSet ()
public run ()
public Arrayref runnable ()
public Array stack_trace ()
public String stack_trace_dump ()
public store_featurePair_as_genomicAlignBlock ()
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

protected Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::_write_output ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::compact_cigar_line ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::BlastZ::configure_defaults ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::BlastZ::configure_runnable ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner.

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::db_DnaFragChunkSet ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::delete_fasta_dumps_but_these ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::do_transactions ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::dump_loc ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::dumpChunkSetToWorkdir ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::dumpChunkToWorkdir ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::get_params ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::max_alignments ( ) [inherited]

Undocumented method

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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::method_link_type ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::options ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::print_simple_align ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::query_DnaFragChunkSet ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::run ( ) [inherited]

Undocumented method

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

public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::store_featurePair_as_genomicAlignBlock ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::Production::GenomicAlignBlock::PairAligner::write_output ( ) [inherited]

Undocumented method

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


The documentation for this class was generated from the following file:
  • Bio/EnsEMBL/Compara/Production/GenomicAlignBlock/BlastZ.pm