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

List of all members.


Class Summary

Synopsis

  $peptideAlignFeatureAdaptor = $db_adaptor-\>get_PeptideAlignFeatureAdaptor;
  $peptideAlignFeatureAdaptor = $peptideAlignFeatureObj-\>adaptor;

Description

  Module to encapsulate all db access for persistent class PeptideAlignFeature
  There should be just one per application and database connection.
 

Definition at line 22 of file PeptideAlignFeatureAdaptor.pm.

Available Methods

protected _columns ()
protected _create_PAF_from_BaseAlignFeature ()
protected _default_where_clause ()
protected _final_clause ()
protected _generic_fetch ()
protected _left_join ()
protected _list_dbIDs ()
protected _objs_from_sth ()
protected _recursive_find_brh_pafs_for_member_genome_db ()
protected _store_PAFS ()
protected _straight_join ()
protected _tables ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public displayHSP ()
public displayHSP_short ()
public dump_data ()
public Array fetch_all ()
public fetch_all_besthit_by_qgenome_db_id ()
public fetch_all_besthit_by_qgenome_db_id_hgenome_db_id ()
public Listref fetch_all_by_dbID_list ()
public fetch_all_by_hgenome_db_id ()
public Array fetch_all_by_hmember_id ()
public Array fetch_all_by_hmember_id_qgenome_db_id ()
public fetch_all_by_qgenome_db_id ()
public fetch_all_by_qgenome_db_id_hgenome_db_id ()
public Array fetch_all_by_qmember_id ()
public Array fetch_all_by_qmember_id_hgenome_db_id ()
public Array fetch_all_by_qmember_id_hmember_id ()
public Array fetch_all_RH_by_member ()
public Array fetch_all_RH_by_member_genomedb ()
public Array fetch_BRH_by_member_genomedb ()
public Array fetch_BRH_web_for_member_genome_db ()
public
Bio::EnsEMBL::Compara::PeptideAlignFeature 
fetch_by_dbID ()
public Array fetch_by_dbIDs ()
public
Bio::EnsEMBL::Compara::PeptideAlignFeature 
fetch_selfhit_by_qmember_id ()
public final_clause ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
new ()
public pafs_equal ()
public DBI::StatementHandle prepare ()
public sort_by_score_evalue_and_pid ()
public Int species_id ()
public store ()

Method Documentation

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

Undocumented method

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

protected Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::_create_PAF_from_BaseAlignFeature ( )

Undocumented method

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

Undocumented method

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

protected Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::_generic_fetch ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::_objs_from_sth ( )

Undocumented method

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

protected Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::_recursive_find_brh_pafs_for_member_genome_db ( )

Undocumented method

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protected Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::_store_PAFS ( )

Undocumented method

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

Undocumented method

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

public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::displayHSP ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::displayHSP_short ( )

Undocumented method

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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all ( )
  Arg        : None
  Example    : @pafs = @{$adaptor->fetch_all};
  Description: fetch all peptide align features.  Not generally useful since it
               can return millions of objects.
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions :
  Caller     :
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_besthit_by_qgenome_db_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_besthit_by_qgenome_db_id_hgenome_db_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_hgenome_db_id ( )

Undocumented method

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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_hmember_id ( )
  Arg [1]    : int $member->dbID
               the database id for a peptide member
  Example    : $pafs = $adaptor->fetch_all_by_hmember_id($member->dbID);
  Description: Returns all PeptideAlignFeatures from all query species
               where the hit peptide member is know.
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_hmember_id_qgenome_db_id ( )
  Arg [1]    : int $hit_member->dbID
               the database id for a peptide member
  Arg [2]    : int $query_genome_db->dbID
               the database id for a genome_db
  Example    : $pafs = $adaptor->fetch_all_by_hmember_id_qgenome_db_id(
                    $member->dbID, $genome_db->dbID);
  Description: Returns all PeptideAlignFeatures for a given hit member and
               query species specified via a genome_db_id
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions : thrown if either member->dbID or genome_db->dbID is not defined
  Caller     : general
 
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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_qgenome_db_id ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_qgenome_db_id_hgenome_db_id ( )

Undocumented method

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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_qmember_id ( )
  Arg [1]    : int $member->dbID
               the database id for a peptide member
  Example    : $pafs = $adaptor->fetch_all_by_qmember_id($member->dbID);
  Description: Returns all PeptideAlignFeatures from all target species
               where the query peptide member is know.
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions : thrown if $id is not defined
  Caller     : general
 
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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_qmember_id_hgenome_db_id ( )
  Arg [1]    : int $query_member->dbID
               the database id for a peptide member
  Arg [2]    : int $hit_genome_db->dbID
               the database id for a genome_db
  Example    : $pafs = $adaptor->fetch_all_by_qmember_id_hgenome_db_id(
                    $member->dbID, $genome_db->dbID);
  Description: Returns all PeptideAlignFeatures for a given query member and
               target hit species specified via a genome_db_id
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions : thrown if either member->dbID or genome_db->dbID is not defined
  Caller     : general
 
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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_by_qmember_id_hmember_id ( )
  Arg [1]    : int $query_member->dbID
               the database id for a peptide member
  Arg [2]    : int $hit_member->dbID
               the database id for a peptide member
  Example    : $pafs = $adaptor->fetch_all_by_qmember_id_hmember_id($qmember_id, $hmember_id);
  Description: Returns all PeptideAlignFeatures for a given query member and
               hit member.  If pair did not align, array will be empty.
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions : thrown if either member_id is not defined
  Caller     : general
 
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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_RH_by_member ( )
  Overview   : This an experimental method and not currently used in production
  Arg [1]    : member_id of query peptide member
  Example    : $feat = $adaptor->fetch_by_dbID($musBlastAnal, $ratBlastAnal);
  Description: Returns all the PeptideAlignFeatures that reciprocal hit all genomes
  Returntype : array of Bio::EnsEMBL::Compara::PeptideAlignFeature objects by reference
  Exceptions : thrown if $id is not defined
  Caller     : general
 
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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_all_RH_by_member_genomedb ( )
  Overview   : This an experimental method and not currently used in production
  Arg [1]    : member_id of query peptide member
  Arg [2]    : genome_db_id of hit species
  Example    : $feat = $adaptor->fetch_by_dbID($musBlastAnal, $ratBlastAnal);
  Description: Returns all the PeptideAlignFeatures that reciprocal hit the qmember_id
               onto the hit_genome_db_id
  Returntype : array of Bio::EnsEMBL::Compara::PeptideAlignFeature objects by reference
  Exceptions : thrown if $id is not defined
  Caller     : general
 
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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_BRH_by_member_genomedb ( )
  Arg [1]    : member_id of query peptide member
  Arg [2]    : genome_db_id of hit species
  Example    : $paf = $adaptor->fetch_BRH_by_member_genomedb(31957, 3);
  Description: Returns the PeptideAlignFeature created from the database
               This is the old algorithm for pulling BRHs (compara release 20-23)
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions : none
  Caller     : general
 
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public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_BRH_web_for_member_genome_db ( )
  Overview   : This is the new (compara_24) algorithm method for finding UBRH and MBRH
               homologies.  
  Arg [1]    : member_id of query peptide member
  Arg [2]    : genome_db_id of hit species
  Description: Returns all the 'best' PeptideAlignFeatures starting with qmember_id
               hitting onto the hit_genome_db_id via recursive search
  Returntype : array of Bio::EnsEMBL::Compara::PeptideAlignFeature objects by reference
               or undef if nothing found
  Exceptions : none
  Caller     : general
 
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public Bio::EnsEMBL::Compara::PeptideAlignFeature Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_by_dbID ( )
  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
  Example    : $paf = $adaptor->fetch_by_dbID(1234);
  Description: Returns the PeptideAlignFeature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::Compara::PeptideAlignFeature
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Array Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_by_dbIDs ( )
  Arg [1...] : int $id (multiple)
               the unique database identifier for the feature to be obtained
  Example    : $pafs = $adaptor->fetch_by_dbID(paf1_id, $paf2_id, $paf3_id);
  Description: Returns the PeptideAlignFeature created from the database defined by the
               the id $id.
  Returntype : array reference of Bio::EnsEMBL::Compara::PeptideAlignFeature objects
  Exceptions : thrown if $id is not defined
  Caller     : general
 
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public Bio::EnsEMBL::Compara::PeptideAlignFeature Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::fetch_selfhit_by_qmember_id ( )
  Arg [1]    : int $member->dbID
               the database id for a peptide member
  Example    : $paf = $adaptor->fetch_selfhit_by_qmember_id($member->dbID);
  Description: Returns the selfhit PeptideAlignFeature defined by the id $id.
  Returntype : Bio::EnsEMBL::Compara::PeptideAlignFeature
  Exceptions : thrown if $id is not defined
  Caller     : general
 
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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::final_clause ( )
  Arg [1]    : <string> SQL clause
  Example    : $adaptor->final_clause("ORDER BY paf.qmember_id LIMIT 10");
               $pafs = $adaptor->fetch_all;
               $adaptor->final_clause("");
  Description: getter/setter method for specifying an extension to the SQL prior to
               a fetch operation.  Useful final clauses are either 'ORDER BY' or 'LIMIT'
  Returntype : <string>
  Caller     : general
 
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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::pafs_equal ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::sort_by_score_evalue_and_pid ( )

Undocumented method

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public Bio::EnsEMBL::Compara::DBSQL::PeptideAlignFeatureAdaptor::store ( )

Undocumented method

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