Inheritance diagram for Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor:

Public Member Functions
public ArrayRef	fetch_all ()

public Bio::EnsEMBL::AltAlleleGroup	fetch_by_dbID ()

public Bio::EnsEMBL::AltAlleleGroup	fetch_by_gene_id ()

public Array	fetch_all_by_gene_id ()

public Int	store ()

public Int	update ()

public	remove ()

protected	_tables ()

Public Member Functions inherited from Bio::EnsEMBL::DBSQL::BaseAdaptor
public Bio::EnsEMBL::DBSQL::BaseAdaptor	new ()

public DBI::StatementHandle	prepare ()

public Bio::EnsEMBL::DBSQL::DBAdaptor	db ()

public Bio::EnsEMBL::DBSQL::DBConnection	dbc ()

public Boolean	is_multispecies ()

public Int	species_id ()

protected	_list_dbIDs ()

protected	_straight_join ()

protected	_can_straight_join ()

public Listref	bind_param_generic_fetch ()

protected	_bind_param_generic_fetch ()

public String	generate_in_constraint ()

public Listref	generic_fetch ()

public Int	generic_count ()

protected	_generate_sql ()

public Bio::EnsEMBL::Feature	fetch_by_dbID ()

protected	_uncached_fetch_by_dbID ()

public Listref	fetch_all_by_dbID_list ()

protected	_uncached_fetch_all_by_dbID_list ()

protected ArrayRef	_uncached_fetch_all_by_id_list ()

public	fetch_all ()

public Scalar	last_insert_id ()

public	insert_ignore_clause ()

protected Bio::EnsEMBL::DBSQL::Support::BaseCache	_id_cache ()

protected Boolean	_no_id_cache ()

public Boolean	ignore_cache_override ()

public Int	schema_version ()

protected	_tables ()

protected	_columns ()

protected	_default_where_clause ()

protected	_left_join ()

protected	_final_clause ()

protected	_objs_from_sth ()

protected	_build_id_cache ()

protected	_logic_name_to_constraint ()

Detailed Description

Synopsis

use Bio::EnsEMBL::AltAlleleGroup;
use Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor;
 
my $aag_adaptor = Bio::EnsEMBL::Registry->get_DBAdaptor("Human","core","AltAlleleGroup");
 
# For a known Gene, find the reference alternative allele
my $aag = $aag_adaptor->fetch_by_gene_id($gene->dbID);
my $reference_gene = $aag->get_ref_Gene;
 
# Get a list of AltAlleleGroups
my $list = $aag_adaptor->fetch_all_('IS_REPRESENTATIVE');
$list = $aag_adaptor->fetch_all();
 
my $dbID = $aag_adaptor->store($aag);
 
$aag = $aag_adaptor->fetch_by_dbID($dbID);
$aag_adaptor->remove($aag);

Description

  The AltAlleleGroupAdaptor provides CRUD for AltAlleleGroup objects. It allows
  groups of alleles to be retrieved by group and gene ids.

Definition at line 36 of file AltAlleleGroupAdaptor.pm.

Member Function Documentation

◆ _tables()

protected Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::_tables ( )

Undocumented method

Code:

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◆ fetch_all()

public ArrayRef Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_all ( )

  Arg[1]      : (optional) String - type of group
                Restrict group fetches to just one type. Technically it selects 
                out mixed-annotation groups where a single member contains that type.
  Description : Fetches all the alt-allele groups, creates objects to represent
                them and returns them in a list. Specifying a group type 
                identifies all groups containing a member of this type. It 
                does not filter out the other members

                Multispecies support is triggered by the is_multispecies flag
                and species_id of the DBAdaptor.
  Returntype  : ArrayRef of Bio::EnsEMBL::AltAlleleGroup

Code:

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sub fetch_all {
    my $self = shift;
    my $type = shift;
 
    $type = uc($type) if ($type);
    
    my @group_list = ();
    my @members;
    
    my $species_id;
    my $get_all_sql;
    if ($self->db->is_multispecies()) {
        # multispecies databases must be restricted in their treatment
        $species_id = $self->db->species_id;
        
        if ($type) {
            $get_all_sql = q(
                SELECT DISTINCT alt_allele_group_id
                FROM alt_allele        a
                JOIN gene              g  ON g.gene_id         = a.gene_id
                JOIN seq_region        s  ON s.seq_region_id   = g.seq_region_id
                JOIN coord_system      c  ON c.coord_system_id = s.coord_system_id
                JOIN alt_allele_attrib b  ON a.alt_allele_id   = b.alt_allele_id
                WHERE c.species_id = ? AND b.attrib = ?
            );
        } else {
            $get_all_sql = q(
                SELECT DISTINCT alt_allele_group_id
                FROM alt_allele a
                JOIN gene              g  ON g.gene_id         = a.gene_id
                JOIN seq_region        s  ON s.seq_region_id   = g.seq_region_id
                JOIN coord_system      c  ON c.coord_system_id = s.coord_system_id
                WHERE c.species_id = ?
            );
        }
    } else {
        if ($type) {
            $get_all_sql = q(SELECT DISTINCT alt_allele_group_id 
                FROM alt_allele a, alt_allele_attrib b
                WHERE a.alt_allele_id = b.alt_allele_id
                AND b.attrib = ?);
        } else {
            $get_all_sql = q(SELECT DISTINCT alt_allele_group_id FROM alt_allele);
        }
       
    }
    
    my $sth = $self->prepare($get_all_sql);
    
    my $x = 1;
    if ($self->db->is_multispecies()) {
        $sth->bind_param($x,$species_id, SQL_INTEGER);
        $x++;
    }
    
    $sth->bind_param($x,$type, SQL_VARCHAR) if ($type);
    eval { $sth->execute() };
    if ($@) {
        throw("Query error in AltAlleleGroupAdaptor: $@");
    }
    
    
    my $group_id;    
    $sth->bind_col(1, \$group_id );
    
    while ( $sth->fetch() ) {
        my $aag = $self->fetch_by_dbID($group_id);
        push @group_list, $aag;
    }
    $sth->finish;
    return \@group_list;
}

◆ fetch_all_by_gene_id()

public Array Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_all_by_gene_id ( )

  Arg[1]      : Integer Gene ID of the member to query by
  Description : Returns an array of one or more AltAlleleGroups,
                which each contain the specified gene member                
  Returntype  : Array of Bio::EnsEMBL::AltAlleleGroup objects

Code:

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◆ fetch_by_dbID()

public Bio::EnsEMBL::AltAlleleGroup Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_by_dbID ( )

  Arg[1]      : AltAlleleGroup dbID.
  Description : Creates and returns an AltAlleleGroup for the given group id

  Returntype  : Bio::EnsEMBL::AltAlleleGroup

Code:

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◆ fetch_by_gene_id()

public Bio::EnsEMBL::AltAlleleGroup Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::fetch_by_gene_id ( )

  Arg[1]      : Integer Gene ID of the member to query by
  Description : Returns an AltAlleleGroup which contains
                the specified gene member                
  Returntype  : Bio::EnsEMBL::AltAlleleGroup

Code:

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◆ remove()

public Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::remove ( )

  Arg [1]    : The AltAlleleGroup to remove.
  Arg [2]    : Boolean indicates if the entry in alt_allele_group should be retained or remove. Defaults to removing the entry
  Example    :

$aaga->remove($alt_allele_group);

  Description: This removes an AltAlleleGroup from all tables of the database. 
  Exceptions : None

Code:

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◆ store()

public Int Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::store ( )

  Arg[1]     : Bio::EnsEMBL::AltAlleleGroup
  Description: Used for persisting new groups to the database.
               It updates the dbID of the object handed to it to match the
               database.
  Returntype : Integer Alt Allele Group id

Code:

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sub store {
    my $self = shift;
    my $allele_group = shift;
 
    assert_ref($allele_group, 'Bio::EnsEMBL::AltAlleleGroup', 'allele_group');
    if ($allele_group->size < 2) {
        warning('At least 2 genes must be provided to construct alternative alleles. Ignoring.');
        return;
    }
    
    my $helper = $self->dbc()->sql_helper();
    my $dbID = $allele_group->dbID;
    
    my $new_group_sql = 'INSERT INTO alt_allele_group (alt_allele_group_id) VALUES (?)';
    my $existing_group_sql = 'SELECT count(*) FROM alt_allele_group WHERE alt_allele_group_id = ?';
 
    my $already_exists = $helper->execute_single_result(-SQL => $existing_group_sql, -PARAMS => [[$dbID, SQL_INTEGER]]);
    
    # If the ID is not already there then we need to add one
    if($already_exists == 0) {
        $helper->execute_update(-SQL => $new_group_sql, -CALLBACK => sub {
            my ($sth, $dbh, $rv) = @_;
            if($rv) {
                my $id = $dbh->last_insert_id(undef, undef, 'alt_allele_group', 'alt_allele_group_id');
                $dbID = $id;
            }
            return;
        });
    }
    
    my $sth = $self->prepare("INSERT INTO alt_allele (alt_allele_id, alt_allele_group_id, gene_id) VALUES (?,?,?)");
    my $attrib_sth = $self->prepare("INSERT INTO alt_allele_attrib (alt_allele_id,attrib) VALUES (?,?)");
    my $check_exists_sth = $self->prepare("SELECT alt_allele_id FROM alt_allele WHERE gene_id = ?");
 
    foreach my $allele (@{ $allele_group->get_all_members() }) {
        my $gene_id = $allele->[0];
        my %flags = %{$allele->[1]};
        my $allele_id;
 
# Check if gene is not already stored
# Return allele_id if it is
        $check_exists_sth->bind_param(1, $gene_id, SQL_INTEGER);
        $check_exists_sth->execute();
        $check_exists_sth->bind_col(1, \$allele_id);
        if ($check_exists_sth->fetch() ) {
          return $allele_id;
        }
        
        $sth->bind_param(1, undef, SQL_INTEGER);
        $sth->bind_param(2, $dbID, SQL_INTEGER);
        $sth->bind_param(3, $gene_id, SQL_INTEGER);
        my $altered_rows = $sth->execute();
        if ($altered_rows > 0) {
            $allele_id = $self->last_insert_id(); # all alleles get added to the same alt_allele_id group
        } else {
            throw("Creation of new alt_allele failed: $@");
        }
        
            
        foreach my $flag (keys %flags) {
            $attrib_sth->bind_param(1, $allele_id);
            $attrib_sth->bind_param(2, $flag);
            $attrib_sth->execute();
        }
    }
    if ($@) {throw ("Problem inserting new AltAlleleGroup into database: $@");}
    $sth->finish;
    $attrib_sth->finish;
    $check_exists_sth->finish;
    
    $allele_group->dbID($dbID);
    
    return $dbID;
}

◆ update()

public Int Bio::EnsEMBL::DBSQL::AltAlleleGroupAdaptor::update ( )

  Arg [1]    : AltAlleleGroup 
  Description: Removes the existing DB record of an AltAlleleGroup and stores 
               the altered version.
  Returntype : Integer - the return value of the store method, viz. whether the
               insert was successful.

Code:

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

ensembl/modules/Bio/EnsEMBL/DBSQL/AltAlleleGroupAdaptor.pm

Public Member Functions

Detailed Description

Synopsis

Description

Member Function Documentation

◆ _tables()

◆ fetch_all()

◆ fetch_all_by_gene_id()

◆ fetch_by_dbID()

◆ fetch_by_gene_id()

◆ remove()

◆ store()

◆ update()