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

List of all members.


Class Summary

Description

  This object represents a family coming from a database of protein families.
 

Synopsis

  use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;

  my $db = new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(-user   =\> 'myusername',
                               -dbname =\> 'myfamily_db',
                               -host   =\> 'myhost');

  my $fa = $db-\>get_FamilyAdaptor;
  my $fam = $fa-\>fetch_by_stable_id('ENSF000013034');

  my $ma = $db-\>get_MemberAdaptor;
  my $member = $ma-\>fetch_by_source_stable_id('Uniprot/SWISSPROT', 'YSV4_CAEEL')};
  my @fam = @{$fa-\>fetch_all_by_Member($member)};

  @fam = @{$fa-\>fetch_by_description_with_wildcards('interleukin',1)};
  @fam = @{$fa-\>fetch_all};

Description

This module is an entry point into a database of protein families,
clustering SWISSPROT/TREMBL and ensembl protein sets using the TRIBE MCL algorithm.
The clustering neatly follows the SWISSPROT DE-lines, which are 
taken as the description of the whole family.
The objects can be read from and write to a family database.
For more info, see ensembl-doc/family.txt
 

Definition at line 44 of file FamilyAdaptor.pm.

Available Methods

protected _columns ()
protected _default_where_clause ()
protected String _final_clause ()
protected A _join ()
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 An fetch_all_by_Member ()
public fetch_all_by_Member_method_link_type ()
public fetch_all_by_method_link_type ()
public Bio::EnsEMBL::SeqFeature fetch_by_dbID ()
public An fetch_by_description_with_wildcards ()
public fetch_by_Member_source_stable_id ()
public Bio::EnsEMBL::SeqFeature fetch_by_stable_id ()
public Arrayref generic_fetch ()
public get_dumped_data ()
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_relation ()
public update_relation ()

Method Documentation

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

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor.

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

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor.

protected String Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::_final_clause ( ) [inherited]
  Arg [1]    : none
  Example    : none
  Description: May be overriden to provide an additional clause to the end
               of the SQL query used to fetch feature records.
               This is useful to add a required ORDER BY clause to the
               query for example.
  Returntype : string
  Exceptions : none
  Caller     : generic_fetch
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

protected A Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::_join ( ) [inherited]
  Arg [1]    : none
  Example    : none
  Description: Can be overridden by a subclass to specify any left joins
               which should occur. The table name specigfied in the join
               must still be present in the return values of
  Returntype : a {'tablename' => 'join condition'} pair
  Exceptions : none
  Caller     : general
 
Code:
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protected Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor::_objs_from_sth ( )

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor.

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

Undocumented method

Code:
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Reimplemented from Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor.

public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_all ( ) [inherited]

Undocumented method

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

public An Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor::fetch_all_by_Member ( )
 Arg [1]    : Bio::EnsEMBL::Compara::Member $member
 Example    : $families = $FamilyAdaptor->fetch_all_by_Member($member);
 Description: find the families to which the given member belongs to
 Returntype : an array reference of Bio::EnsEMBL::Compara::Family objects
              (could be empty or contain more than one Family in the case of ENSEMBLGENE only)
 Exceptions : when missing arguments
 Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor::fetch_all_by_Member_method_link_type ( )

Undocumented method

public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_all_by_method_link_type ( ) [inherited]

Undocumented method

public Bio::EnsEMBL::SeqFeature Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_by_dbID ( ) [inherited]
  Arg [1]    : int $id
               the unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234);
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::SeqFeature
  Exceptions : thrown if $id is not defined
  Caller     : general
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public An Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor::fetch_by_description_with_wildcards ( )
 Arg [1]    : string $description
 Arg [2]    : int $wildcard (optional)
              if set to 1, wildcards are added and the search is a slower LIKE search
 Example    : $fams = $FamilyAdaptor->fetch_by_description_with_wildcards('REDUCTASE',1);
 Description: simplistic substring searching on the description to get the families
              matching the description. (The search is currently case-insensitive;
              this may change if SPTR changes to case-preservation)
 Returntype : an array reference of Bio::EnsEMBL::Compara::Family objects
 Exceptions : none
 Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor::fetch_by_Member_source_stable_id ( )

Undocumented method

Code:
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public Bio::EnsEMBL::SeqFeature Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::fetch_by_stable_id ( ) [inherited]
  Arg [1]    : string $stable_id
               the unique database identifier for the feature to be obtained
  Example    : $feat = $adaptor->fetch_by_dbID(1234);
  Description: Returns the feature created from the database defined by the
               the id $id.
  Returntype : Bio::EnsEMBL::SeqFeature
  Exceptions : thrown if $stable_id is not defined
  Caller     : general
 
Code:
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public Arrayref Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::generic_fetch ( ) [inherited]
  Arg [1]    : (optional) string $constraint
               An SQL query constraint (i.e. part of the WHERE clause)
               e.g. "fm.family_id = $family_id"
  Arg [2]    : (optional) arrayref $join
               the arrayref $join should contain arrayrefs of this form
               [['family_member', 'fm'],
                # the table to join with synonym (mandatory) as an arrayref
                'm.member_id = fm.member_id',
                # the join condition (mandatory)
                [qw(fm.family_id fm.member_id fm.cigar_line)]]
                # any additional columns that the join could imply (optional)
                # as an arrayref 
  Example    : $arrayref = $a->generic_fetch($constraint, $join);
  Description: Performs a database fetch and returns BaseRelation-inherited objects
  Returntype : arrayref of Bio::EnsEMBL::Compara::BaseRelation-inherited objects
  Exceptions : none
  Caller     : various adaptors' specific fetch_ subroutines
 
Code:
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Reimplemented from Bio::EnsEMBL::DBSQL::BaseAdaptor.

public Int Bio::EnsEMBL::Compara::DBSQL::FamilyAdaptor::store ( )
 Arg [1]    : Bio::EnsEMBL::Compara::Family $fam
 Example    : $FamilyAdaptor->store($fam)
 Description: Stores a family object into a family  database
 Returntype : int 
              been the database family identifier, if family stored correctly
 Exceptions : when isa if Arg [1] is not Bio::EnsEMBL::Compara::Family
 Caller     : general
 
Code:
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public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::store_relation ( ) [inherited]

Undocumented method

Code:
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public Bio::EnsEMBL::Compara::DBSQL::BaseRelationAdaptor::update_relation ( ) [inherited]

Undocumented method

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