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

List of all members.


Class Summary

Synopsis

$dafa = $compara_dbadaptor-\>get_DnaAlignFeatureAdaptor;
@align_features = @{$dafa-\>fetch_by_Slice_species($slice, $qy_species)};

Description

Retrieves alignments from a compara database in the form of DnaDnaAlignFeatures
 

Definition at line 21 of file DnaAlignFeatureAdaptor.pm.

Available Methods

protected _columns ()
protected _convert_GenomicAlignBlocks_into_DnaDnaAlignFeatures ()
protected _default_where_clause ()
protected _final_clause ()
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 void deleteObj ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_dbID_list ()
public An fetch_all_by_Slice ()
public An fetch_all_by_species_region ()
public Bio::EnsEMBL::Feature fetch_by_dbID ()
public Listref generic_fetch ()
public get_dumped_data ()
public Array interpolate_best_location ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public void new ()
public DBI::StatementHandle prepare ()
public Int species_id ()

Method Documentation

protected Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor::_convert_GenomicAlignBlocks_into_DnaDnaAlignFeatures ( )

Undocumented method

Code:
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public void Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor::deleteObj ( )
  Arg [1]    : none
  Example    : none
  Description: Called automatically by DBConnection during object destruction
               phase. Clears the cache to avoid memory leaks.
  Returntype : none
  Exceptions : none
  Caller     : none
 
Code:
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  Arg [1]    : none
  Example    : none
  Description: Called automatically by DBConnection during object destruction
               phase. Clears the cache to avoid memory leaks.
  Returntype : none
  Exceptions : none
  Caller     : none
 

/**

public An Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor::fetch_all_by_Slice ( )
 Arg [1]    : Bio::EnsEMBL::Slice
 Arg [2]    : string $qy_species
              The query species to retrieve alignments against
 Arg [3]    : string $qy_assembly
 Arg [4]    : string $$alignment_type
              The type of alignments to be retrieved
              e.g. WGA or WGA_HCR
 Example    : $gaa->fetch_all_by_Slice($slice, "Mus musculus","WGA");
 Description: find matches of query_species in the region of a slice of a
              subject species
 Returntype : an array reference of Bio::EnsEMBL::DnaDnaAlignFeature objects
 Exceptions : none
 Caller     : general
 
Code:
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public An Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor::fetch_all_by_species_region ( )
 Arg [1]    : string $cs_species
              e.g. "Homo sapiens"
 Arg [2]    : string $cs_assembly (can be undef)
              e.g. "NCBI_31" if undef assembly_default will be taken
 Arg [3]    : string $qy_species
              e.g. "Mus musculus"
 Arg [4]    : string $qy_assembly (can be undef)
              e.g. "MGSC_3", if undef assembly_default will be taken
 Arg [5]    : string $chromosome_name
              the name of the chromosome to retrieve alignments from (e.g. 'X')
 Arg [6]    : int start
 Arg [7]    : int end
 Arg [8]    : string $alignment_type
              The type of alignments to be retrieved
              e.g. WGA or WGA_HCR
 Example    : $gaa->fetch_all_by_species_region("Homo sapiens", "NCBI_31",
						"Mus musculus", "MGSC_3",
                                                "X", 250_000, 750_000,"WGA");
 Description: Retrieves alignments between the consensus and query species
              from a specified region of the consensus genome.
 Returntype : an array reference of Bio::EnsEMBL::DnaDnaAlignFeature objects
 Exceptions : returns a ref to an empty list if requested DnaFrag or MethodLinkSpeciesSet
              are not in the compara DB.
 Caller     : general
 
Code:
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public Array Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor::interpolate_best_location ( )
  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Arg [2]    : string $species
               e.g. "Mus musculus"
  Arg [3]    : string $alignment_type
               e.g. "BLASTZ_NET"
  Arg [4]    : string $seq_region_name
               e.g. "6-COX"
  Example    :
  Description:
  Returntype : array with 3 elements
  Exceptions :
  Caller     :
 
Code:
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public void Bio::EnsEMBL::Compara::DBSQL::DnaAlignFeatureAdaptor::new ( )
  Arg [1]    : list of args to super class constructor
  Example    : $dafa = new Bio::EnsEMBL::Compara::Genomi
  Description: Creates a new DnaAlignFeatureAdaptor.  The superclass
               constructor is extended to initialise an internal cache.  This
               class should be instantiated through the get method on the
               DBAdaptor rather than calling this method directory.
  Returntype : none
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.


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