Archive Ensembl HomeArchive Ensembl Home
Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor Class Reference
Inheritance diagram for Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor:

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor; 
  my $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor (
      -host =\> $host,
      -user =\> $dbuser,
      -pass =\> $dbpass,
      -port =\> $port,
      -dbname =\> $dbname,
      -conf_file =\> $conf_file);
  
  my $genomic_align_group_adaptor = $db-\>get_GenomicAlignGroupAdaptor();

  $genomic_align_group_adaptor-\>store($genomic_align_group);

  $genomic_align_groups = $genomic_align_group_adaptor-\>fetch_all_by_GenomicAlign($genomic_align);
  $genomic_align_groups = $genomic_align_group_adaptor-\>fetch_all_by_genomic_align_id(11223);

  $genomic_align_group = $genomic_align_group_adaptor-\>fetch_by_GenomicAlign($genomic_align);
  $genomic_align_group = $genomic_align_group_adaptor-\>fetch_by_genomic_align_id(11223);

Description

This class is intended to access data in genomic_align_group table
 

Definition at line 38 of file GenomicAlignGroupAdaptor.pm.

Available Methods

protected _columns ()
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 dump_data ()
public fetch_all ()
public Listref fetch_all_by_dbID_list ()
public
Bio::EnsEMBL::Compara::GenomicAlignGroup 
fetch_by_dbID ()
public
Bio::EnsEMBL::Compara::GenomicAlignGroup 
fetch_by_genomic_align_id ()
public
Bio::EnsEMBL::Compara::GenomicAlignGroup 
fetch_by_GenomicAlign ()
public Listref generic_fetch ()
public get_dumped_data ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public void new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public
Bio::EnsEMBL::Compara::GenomicAlignGroup 
store ()
public Int use_autoincrement ()

Method Documentation

public Bio::EnsEMBL::Compara::GenomicAlignGroup Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor::fetch_by_dbID ( )
  Arg  1     : integer node_id
  Example    : my $genomic_align_group =
                  $genomic_align_group_adaptor->fetch_by_dbID(12413)
  Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
               to the given node_id.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
  Exceptions : none
  Caller     : object::methodname
  Status     : Stable
 
Code:
click to view

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

public Bio::EnsEMBL::Compara::GenomicAlignGroup Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor::fetch_by_genomic_align_id ( )
  Arg  1     : integer $genomic_align_id
  Example    : my $genomic_align_group =
                  $genomic_align_group_adaptor->fetch_by_genomic_align_id(
                          12322)
  Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
               to the given Bio::EnsEMBL::Compara::GenomicAlign defined by the
               $genomic_align_id
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
  Exceptions : none
  Caller     : object::methodname
  Status     : Stable
 
Code:
click to view
public Bio::EnsEMBL::Compara::GenomicAlignGroup Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor::fetch_by_GenomicAlign ( )
  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
  Example    : my $genomic_align_group =
                  $genomic_align_group_adaptor->fetch_by_GenomicAlign(
                          $genomic_align)
  Description: Returns a Bio::EnsEMBL::Compara::GenomicAlignGroup corresponding
               to the given Bio::EnsEMBL::Compara::GenomicAlign and group_type.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup
  Exceptions : none
  Caller     : object::methodname
  Status     : Stable
 
Code:
click to view
public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor::new ( )
  Arg [1]    : list of args to super class constructor
  Example    : $gag_a = new Bio::EnsEMBL::Compara::GenomicAlignGroupAdaptor($dbobj);
  Description: Creates a new GenomicAlignGroupAdaptor. This
               class should be instantiated through the get method on the 
               DBAdaptor rather than calling this method directly.
  Returntype : none
  Exceptions : none
  Caller     : Bio::EnsEMBL::DBSQL::DBConnection
  Status     : Stable
 
Code:
click to view

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

public Bio::EnsEMBL::Compara::GenomicAlignGroup Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor::store ( )
  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlignGroup
               The things you want to store
  Example    : $gen_ali_grp_adaptor->store($genomic_align_group);
  Description: It stores the given GenomicAlginGroup in the database
  Returntype : Bio::EnsEMBL::Compara::GenomicAlignGroup object
  Exceptions : not stored linked Bio::EnsEMBL::Compara::GenomicAlign objects throw.
  Caller     : general
  Status     : Stable
 
Code:
click to view
public Int Bio::EnsEMBL::Compara::DBSQL::GenomicAlignGroupAdaptor::use_autoincrement ( )
  [Arg  1]   : (optional)int value
  Example    : $genomic_align_adaptor->use_autoincrement(0);
  Description: Getter/setter for the _use_autoincrement flag. This flag
               is used when storing new objects with no dbID in the
               database. If the flag is ON (default), the adaptor will
               let the DB set the dbID using the AUTO_INCREMENT ability.
               If you unset the flag, then the adaptor will look for the
               first available dbID after 10^10 times the
               method_link_species_set_id.
  Returntype : integer
  Exceptions : 
  Caller     : none
  Status     : Stable
 
Code:
click to view

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