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

List of all members.


Class Summary

Synopsis

  Please, consider using the Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor instead.

=head2 Get the adaptor from the Registry

  use Bio::EnsEMBL::Registry;

  my $reg = "Bio::EnsEMBL::Registry";
  $reg-\>load_registry_from_db(
      -host =\> "ensembldb.ensembl.org",
      -user =\> "anonymous");

  my $genomic_align_adaptor = $reg-\>get_adaptor(
      "Multi", "compara", "GenomicAlign");

=head2 Store method

  $genomic_align_adaptor-\>store($synteny_region);

=head2 Fetching methods

  my $genomic_align = $genomic_align_adaptor-\>fetch_by_dbID(1);

  my $genomic_aligns = $genomic_align_adaptor-\>
      fetch_by_GenomicAlignBlock($genomic_align_block);

  my $genomic_aligns = $genomic_align_adaptor-\>
      fetch_by_genomic_align_block_id(1001);

=head2 Other methods

  $genomic_align_adaptor-\>delete_by_genomic_align_block_id(1001);

  $genomic_align = $genomic_align_adaptor-\>
      retrieve_all_direct_attributes($genomic_align);

  $genomic_align_adaptor-\>use_autoincrement(0);

Description

This module is intended to access data in the genomic_align table. In most cases, you want to use
the Bio::EnsEMBL::Compara::DBSQL::GenomicAlignBlockAdaptor instead.
Each alignment is represented by Bio::EnsEMBL::Compara::GenomicAlignBlock. Each GenomicAlignBlock
contains several Bio::EnsEMBL::Compara::GenomicAlign, one per sequence included in the alignment.
The GenomicAlign contains information about the coordinates of the sequence and the sequence of
gaps, information needed to rebuild the aligned sequence. By combining all the aligned sequences
of the GenomicAlignBlock, it is possible to get the orignal alignment back.
 

Definition at line 62 of file GenomicAlignAdaptor.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 void delete_by_genomic_align_block_id ()
public dump_data ()
public fetch_all ()
public Listref fetch_all_by_dbID_list ()
public Ref fetch_all_by_genomic_align_block_id ()
public Ref fetch_all_by_GenomicAlignBlock ()
public Ref fetch_all_by_node_id ()
public
Bio::EnsEMBL::Compara::GenomicAlign 
fetch_by_dbID ()
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
Bio::EnsEMBL::Compara::GenomicAlign 
retrieve_all_direct_attributes ()
public Int species_id ()
public void store ()
public Int use_autoincrement ()

Method Documentation

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::delete_by_genomic_align_block_id ( )
  Arg  1     : integer $genomic_align_block_id
  Example    : $gen_ali_blk_adaptor->delete_by_genomic_align_block_id(352158763);
  Description: It removes the matching GenomicAlign objects from the database
  Returntype : none
  Exceptions : none
  Caller     : general
  Status     : Stable
 
Code:
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public Ref Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::fetch_all_by_genomic_align_block_id ( )
  Arg  1     : integer $genomic_align_block_id
  Example    : my $genomic_aligns =
                    $genomic_align_adaptor->fetch_all_by_genomic_align_block_id(23134);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlign objects
  Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : Returns a ref. to an empty array if there are no matching entries
  Exceptions : Thrown if $genomic_align_block is neither a number 
  Caller     : object::methodname
  Status     : Stable
 
Code:
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public Ref Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::fetch_all_by_GenomicAlignBlock ( )
  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlignBlock object with a valid dbID
  Example    : my $genomic_aligns =
                    $genomic_align_adaptor->fetch_all_by_GenomicAlignBlock($genomic_align_block);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlign objects
  Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : Returns a ref. to an empty array if there are no matching entries
  Exceptions : Thrown if $genomic_align_block is not a
               Bio::EnsEMBL::Compara::GenomicAlignBlock object
  Caller     : object::methodname
  Status     : Stable
 
Code:
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public Ref Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::fetch_all_by_node_id ( )
  Arg  1     : integer $node_id
  Example    : my $genomic_aligns =
                    $genomic_align_adaptor->fetch_all_by_node_id(5530002705680);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlign objects
  Returntype : ref. to an array of Bio::EnsEMBL::Compara::GenomicAlign objects
  Exceptions : Returns a ref. to an empty array if there are no matching entries
  Exceptions : Thrown if $node_id is not a number 
  Caller     : object::methodname
  Status     : At risk
 
Code:
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public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::fetch_by_dbID ( )
  Arg  1     : integer $dbID
  Example    : my $genomic_align = $genomic_align_adaptor->fetch_by_dbID(23134);
  Description: Retrieve the corresponding
               Bio::EnsEMBL::Compara::GenomicAlign object
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : Returns undef if no matching entry is found in the database.
  Caller     : object::methodname
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::new ( )
  Arg [1]    : list of args to super class constructor
  Example    : $ga_a = new Bio::EnsEMBL::Compara::GenomicAlignAdaptor($dbobj);
  Description: Creates a new GenomicAlignAdaptor. 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:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::GenomicAlign Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::retrieve_all_direct_attributes ( )
  Arg  1     : Bio::EnsEMBL::Compara::GenomicAlign $genomic_align
  Example    : $genomic_align_adaptor->retrieve_all_direct_attributes($genomic_align)
  Description: Retrieve the all the direct attibutes corresponding to the dbID of the
               Bio::EnsEMBL::Compara::GenomicAlign object. It is used after lazy fetching
               of the object for populating it when required.
  Returntype : Bio::EnsEMBL::Compara::GenomicAlign object
  Exceptions : 
  Caller     : none
  Status     : Stable
 
Code:
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public void Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::store ( )
  Arg  1     : listref  Bio::EnsEMBL::Compara::GenomicAlign $ga 
               The things you want to store
  Example    : none
  Description: It stores the given GA in the database. Attached
               objects are not stored. Make sure you store them first.
  Returntype : none
  Exceptions : throw if the linked Bio::EnsEMBL::Compara::DnaFrag object or
               the linked Bio::EnsEMBL::Compara::GenomicAlignBlock or
               the linked Bio::EnsEMBL::Compara::MethodLinkSpeciesSet
               are not in the database
  Caller     : $object->methodname
  Status     : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DBSQL::GenomicAlignAdaptor::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:
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The documentation for this class was generated from the following file: