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

List of all members.


Class Summary

Synopsis

  use Bio::EnsEMBL::Registry;

  my $reg = "Bio::EnsEMBL::Registry";

  $reg-\>load_registry_from_db(-host=\>"ensembldb.ensembl.org", -user=\>"anonymous");

  my $dnafrag_adaptor = $reg-\>get_adaptor("Multi", "compara", "DnaFrag");

  $dnafrag_adaptor-\>store($dnafrag);
  
  $dnafrag = $dnafrag_adaptor-\>fetch_by_dbID(905406);
  $dnafrag = $dnafrag_adaptor-\>fetch_by_GenomeDB_and_name($human_genome_db, 'X');
  $dnafrags = $dnafrag_adaptor-\>fetch_all_by_GenomeDB_region(
                                $human_genome_db, 'chromosome')

  $dnafrag = $dnafrag_adaptor-\>fetch_by_Slice($slice);
  $all_dnafrags = $dnafrag_adaptor-\>fetch_all();

Description

This module is intended to access data in the dnafrag table. The dnafrag table stores information on the toplevel sequences such as the name, coordinate system, length and species.
 

Definition at line 35 of file DnaFragAdaptor.pm.

Available Methods

protected List _columns ()
protected _default_where_clause ()
protected _final_clause ()
protected _left_join ()
protected _list_dbIDs ()
protected Listref _objs_from_sth ()
protected _straight_join ()
protected List _tables ()
public Listref bind_param_generic_fetch ()
public
Bio::EnsEMBL::DBSQL::DBAdaptor 
db ()
public
Bio::EnsEMBL::DBSQL::DBConnection 
dbc ()
public dump_data ()
public Listref fetch_all ()
public Listref fetch_all_by_dbID_list ()
public Listref fetch_all_by_GenomeDB_region ()
public
Bio::EnsEMBL::Compara::DnaFrag 
fetch_by_dbID ()
public
Bio::EnsEMBL::Compara::DnaFrag 
fetch_by_GenomeDB_and_name ()
public
Bio::EnsEMBL::Compara::DnaFrag 
fetch_by_Slice ()
public Listref generic_fetch ()
public get_dumped_data ()
public is_already_stored ()
public Boolean is_multispecies ()
public Scalar last_insert_id ()
public
Bio::EnsEMBL::DBSQL::BaseAdaptor 
new ()
public DBI::StatementHandle prepare ()
public Int species_id ()
public Int store ()
public store_if_needed ()
public Int update ()

Method Documentation

protected List Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::_columns ( )
  Args       : none
  Example    : $columns = $self->_columns()
  Description: a list of [tablename, alias] pairs for use with generic_fetch
  Returntype : list of [tablename, alias] pairs
  Exceptions : none
  Caller     : BaseAdaptor::generic_fetch
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected Listref Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::_objs_from_sth ( )
  Args[1]    : DBI::row_hashref $hashref containing key-value pairs
  Example    : my $dna_frags = $self->_objs_from_sth($sth);
  Description: convert DBI row hash reference into a 
               Bio::EnsEMBL::Compara::DnaFrag object
  Returntype : listref of Bio::EnsEMBL::Compara::DnaFrag objects
  Exceptions : throw if $sth is not supplied
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected List Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::_tables ( )
  Args       : none
  Example    : $tables = $self->_tables()
  Description: a list of [tablename, alias] pairs for use with generic_fetch
  Returntype : list of [tablename, alias] pairs
  Exceptions : none
  Caller     : BaseAdaptor::generic_fetch
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::fetch_all ( )
  Arg         : none
  Example     : my $all_dnafrags = $dnafrag_adaptor->fetch_all();
  Description : fetches all Bio::EnsEMBL::Compara::DnaFrag objects for this
                compara database
  Returntype  : listref of all Bio::EnsEMBL::Compara::DnaFrag objects
  Exceptions  : none
  Caller      : general
  Status      : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Listref Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::fetch_all_by_GenomeDB_region ( )
  Arg [1]    : Bio::EnsEMBL::Compara::DBSQL::GenomeDB
  Arg [2]    : (optional) string $coord_system_name
  Arg [3]    : (optional) string $name
  Example    : my $human_chr_dnafrags = $dnafrag_adaptor->
                   fetch_all_by_GenomeDB_region(
                     $human_genome_db, 'chromosome')
  Description: Returns the Bio::EnsEMBL::Compara::DnaFrag object corresponding to the
               Bio::EnsEMBL::Compara::GenomeDB and region given.
  Returntype : listref of Bio::EnsEMBL::Compara::DnaFrag objects
  Exceptions : throw unless $genome_db is a Bio::EnsEMBL::Compara::GenomeDB
  Caller     : 
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DnaFrag Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::fetch_by_dbID ( )
  Arg [1]    : integer $db_id
  Example    : my $dnafrag = $dnafrag_adaptor->fetch_by_dbID(905406);
  Description: Returns the Bio::EnsEMBL::Compara::DnaFrag object corresponding to the database internal identifier
  Returntype : Bio::EnsEMBL::Compara::DnaFrag
  Exceptions : throw if $dbid is not supplied. 
  Caller     : general
  Status     : Stable
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Bio::EnsEMBL::Compara::DnaFrag Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::fetch_by_GenomeDB_and_name ( )
  Arg [1]    : integer $genome_db_id

  • or - Bio::EnsEMBL::Compara::DBSQL::GenomeDB Arg [2] : string $name Example : my $dnafrag = $dnafrag_adaptor->fetch_by_GenomeDB_and_name($human_genome_db, 'X'); Example : my $dnafrag = $dnafrag_adaptor->fetch_by_GenomeDB_and_name(1, 'X'); Description: Returns the Bio::EnsEMBL::Compara::DnaFrag object corresponding to the Bio::EnsEMBL::Compara::GenomeDB and name given. $genome_db can be a valid $genome_db_id instead. Returntype : Bio::EnsEMBL::Compara::DnaFrag Exceptions : throw when genome_db_id cannot be retrieved Exceptions : warns and returns undef when no DnaFrag matches the query Caller : $dnafrag_adaptor->fetch_by_GenomeDB_and_name Status : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DnaFrag Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::fetch_by_Slice ( )
  Arg [1]    : Bio::EnsEMBL::Slice $slice
  Example    : $dnafrag = $dnafrag_adaptor->fetch_by_Slice($slice);
  Description: Retrieves the DnaFrag corresponding to this
               Bio::EnsEMBL::Slice object
  Returntype : Bio::EnsEMBL::Compara::DnaFrag
  Exceptions : thrown if $slice is not a Bio::EnsEMBL::Slice
  Caller     : general
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::is_already_stored ( )
 Title   : is_already_stored
 Usage   : $self->is_already_stored($dnafrag)
 Function: checks if already stored by querying database
 Example :
 Returns : $dnafrag->dbID if stored and 0 if not stored
 Args    : Bio::EnsEMBL::Compara::DnaFrag object
 Status  : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::store ( )
 Arg [1]     : Bio::EnsEMBL::Compara::DnaFrag $new_dnafrag
 Example     : $dnafrag_adaptor->store($new_dnafrag)
 Description : Stores a Bio::EnsEMBL::Compara::DnaFrag object
               in the DB-
 ReturnType  : integer new_dnafrag_id
 Exceptions  : throw if $new_dnafrag is not a
               Bio::EnsEMBL::Compara::DnaFrag object
 Exceptions  : does not store anything if $new_dnafrag->adaptor is
               already defined and is equal to this adaptor
 Exceptions  : throw if $new_dnafrag->genome_db is not defined or has
               no dbID.
 Exceptions  : throw if $new_dnafrag has no name
 Caller      : $object->methodname
  Status     : Stable
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::store_if_needed ( )
 Title   : store_if_needed
 Usage   : $self->store_if_needed($dnafrag)
 Function: store instance in the defined database if NOT
           already present.
 Example :
 Returns : $dnafrag->dbID
 Args    : Bio::EnsEMBL::Compara::DnaFrag object
 Status  : Stable
 
Code:
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public Int Bio::EnsEMBL::Compara::DBSQL::DnaFragAdaptor::update ( )
 Title   : update
 Usage   : $self->update($dnafrag)
 Function: look for this dnafrag in the database, using the genome_db_id,
           the coordinate_system_name and the name of the
           Bio::EnsEMBL::Compara::DnaFrag object. If there is already an
           entry in the database for this dnafrag, it does do anything. If
           the length is different, it updates it. If there is not any entry
           for this, it stores it.
 Example :
 Returns : int $dnafrag->dbID
 Args    : Bio::EnsEMBL::Compara::DnaFrag object
 Status  : Stable
 
Code:
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The documentation for this class was generated from the following file: