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Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor:

List of all members.


Class Summary

Synopsis

Definition at line 14 of file AnchorAlignAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected _final_clause ()
protected Listref _generic_fetch ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public fetch_all ()
public Hashref fetch_all_anchor_ids_by_test_mlssid_and_genome_db_ids ()
public Arrayref fetch_all_anchors_by_dnafrag_id_and_test_mlssid ()
public Arrayref fetch_all_anchors_by_genome_db_id_and_mlssid ()
public Hashref fetch_all_anchors_with_zero_strand ()
public Hashref fetch_all_by_anchor_id_and_mlss_id ()
public Listref fetch_all_by_dbID_list ()
public Listref fetch_all_by_MethodLinkSpeciesSet ()
public Arrayref fetch_all_dnafrag_ids ()
public void fetch_all_filtered_anchors ()
public fetch_anchors_by_genomedb_id ()
public
Bio::EnsEMBL::Compara::Production::AnchorAlign 
fetch_by_dbID ()
public Hashref fetch_dnafrag_and_genome_db_ids_by_test_mlssid ()
public fetch_dnafrag_id ()
public Listref generic_fetch ()
public get_dumped_data ()
public get_target_file ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public void store ()
public store_exonerate_hits ()
public void update_failed_anchor ()
public update_zero_strand_anchors ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::_columns ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::_default_where_clause ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::_final_clause ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Listref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::_generic_fetch ( )
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
  Arg [2]    : (optional) string $logic_name
               the logic_name of the analysis of the features to obtain
  Example    : $fts = $a->_generic_fetch('contig_id in (1234, 1235)', 'Swall');
  Description: Performs a database fetch and returns feature objects in
               contig coordinates.
  Returntype : listref of Bio::EnsEMBL::Production::DnaFragChunk in contig coordinates
  Exceptions : none
  Caller     : internal
 
Code:
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protected Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::_objs_from_sth ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::_tables ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Hashref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_anchor_ids_by_test_mlssid_and_genome_db_ids ( )
  Arg[1]     : method_link_species_set_id, string
  Arg[2]     : genome_db_ids, arrray_ref
  Arg[3]     : anchor_id, string
  Example    : my $anchor = $anchor_align_adaptor->fetch_all_by_anchor_id_and_mlss_id($self->input_anchor_id,$self->method_link_species_set_id);
  Description: returns hashref of cols. from anchor_align table using anchor_align_id as unique hash key
  Returntype : hashref 
  Exceptions : none
  Caller     : general
 
Code:
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public Arrayref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_anchors_by_dnafrag_id_and_test_mlssid ( )
  Arg[1]     : dnafrag_id, string
  Example    : 
  Description: 
  Returntype : arrayref 
  Exceptions : none
  Caller     : general
 
Code:
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public Arrayref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_anchors_by_genome_db_id_and_mlssid ( )
  Arg[0]     : genome_db_id, string
  Arg[1]     : mlssid, string
  Example    : 
  Description: 
  Returntype : arrayref 
  Exceptions : none
  Caller     : general
 
Code:
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public Hashref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_anchors_with_zero_strand ( )
  Arg[1]     : genome_db_ids, array_reff
  Arg[2]     : method_link_species_set_id, string
  Example    : my $anchor = $anchor_align_adaptor->fetch_all_anchors_with_zero_strand($self->genome_db_ids, $self->test_method_link_species_set_id);
  Description: returns arrayref of anchor_id's. from anchor_align table
  Returntype : hashref 
  Exceptions : none
  Caller     : general
 
Code:
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public Hashref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_by_anchor_id_and_mlss_id ( )
  Arg[1]     : anchor_id, string
  Arg[2]     : method_link_species_set_id, string
  Example    : my $anchor = $anchor_align_adaptor->fetch_all_by_anchor_id_and_mlss_id($self->input_anchor_id,$self->method_link_species_set_id);
  Description: returns hashref of cols. from anchor_align table using anchor_align_id as unique hash key
  Returntype : hashref 
  Exceptions : none
  Caller     : general
 
Code:
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public Listref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_by_MethodLinkSpeciesSet ( )
  Arg [1]    : Bio::EnsEMBL::Compara::MethodLinkSpeciesSet $mlss
  Example    :
  Description: Returns all the AnchorAlign obejcts for this MethodLinkSpeciesSet
  Returntype : listref of Bio::EnsEMBL::Compara::Production::AnchorAlign objects
  Exceptions :
  Caller     : general
 
Code:
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public Arrayref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_dnafrag_ids ( )
  Arg[1]     : listref of genome_db_ids 
  Example    : 
  Description: 
  Returntype : arrayref 
  Exceptions : none
  Caller     : general
 
Code:
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public void Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_all_filtered_anchors ( )
  Args       : none
  Example    : 
  Description: 
  Returntype : none
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_anchors_by_genomedb_id ( )
  Arg[1]     : 
  Arg[2]     :
  Example    : 
  Description: 
  Returntype : 
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::Production::AnchorAlign Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_by_dbID ( )
  Arg [1]    : int $dbID
  Example    :
  Description: Returns the AnchorAlign obejcts with this anchor_align_id
  Returntype : Bio::EnsEMBL::Compara::Production::AnchorAlign object
  Exceptions :
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Hashref Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_dnafrag_and_genome_db_ids_by_test_mlssid ( )
  Arg[1]     : method_link_species_set_id, string
  Arg[2]     : genome_db_ids, arrray_ref
  Example    : my $anchor = $anchor_align_adaptor->fetch_all_by_anchor_id_and_mlss_id($self->input_anchor_id,$self->method_link_species_set_id);
  Description: returns hashref of cols. from anchor_align table using anchor_align_id as unique hash key
  Returntype : hashref 
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::fetch_dnafrag_id ( )
  Arg[1]     : 
  Arg[2]     :
  Example    : 
  Description: 
  Returntype : 
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::get_target_file ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::store ( )
  Arg[1]     : one or many DnaFragChunk objects
  Example    : $adaptor->store($chunk);
  Description: stores DnaFragChunk objects into compara database
  Returntype : none
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::store_exonerate_hits ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::update_failed_anchor ( )
  Arg[1]     : anchor_id, hashref 
  Arg[2]     : current analysis_id, string
  Example    : $anchor_align_adaptor->update_failed_anchor($self->input_anchor_id, $self->input_analysis_id);
  Description: updates anchor_status field, setting it to the current analysis_id, if the anchor fails the filters associated with the analysis_id
  Returntype : none
  Exceptions : none
  Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::AnchorAlignAdaptor::update_zero_strand_anchors ( )
  Arg[1]     : anchor_ids, arrayref
  Arg[2]     : analysis_id, string
  Arg[3]     : method_link_species_set_id, string
  Example    : 
  Description: 
  Returntype : 
  Exceptions : none
  Caller     : general
 
Code:
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The documentation for this class was generated from the following file: