Raw content of Bio::EnsEMBL::Map::DBSQL::DitagAdaptor
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=cut
=head1 NAME
Bio::EnsEMBL::Map::DBSQL::DitagAdaptor
=head1 SYNOPSIS
my $ditagadaptor = $db->get_DitagAdaptor();
my @ditags = @{ $ditagadaptor->fetch_by_type("ZZ11") };
=head1 DESCRIPTION
Provides database interaction for the Bio::EnsEMBL::Map::Ditag object
=head1 METHODS
=cut
package Bio::EnsEMBL::Map::DBSQL::DitagAdaptor;
use strict;
use vars ('@ISA');
use Bio::EnsEMBL::Map::Ditag;
use Bio::EnsEMBL::DBSQL::BaseAdaptor;
use Bio::EnsEMBL::Utils::Exception qw( throw warning );
@ISA = qw(Bio::EnsEMBL::DBSQL::BaseAdaptor);
=head2 fetch_all_by_name
Arg [1] : ditag name
Example : $tag = $ditag_adaptor->fetch_by_name("U3");
Description: Retrieves ditags from the database using the name
Returntype : listref of Bio::EnsEMBL::Map::Ditag
Caller : general
=cut
sub fetch_all_by_name {
my ($self, $tagname) = @_;
if(!$tagname){
throw "must be called with a name of a ditag.";
}
my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
FROM ditag d
WHERE d.name = ?");
$sth->execute($tagname);
my $result = $self->_fetch($sth);
return $result;
}
=head2 fetch_by_dbID
Arg [1] : ditag type
Example : @all_tags = @{$ditag_adaptor->fetch_by_dbID(1003)};
Description: Retrieve ditags with a certain id from the database
Returntype : Bio::EnsEMBL::Map::Ditag
Caller : general
=cut
sub fetch_by_dbID {
my ($self, $tagid) = @_;
if(!$tagid){
throw "must be called with the type of a ditag.";
}
my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
FROM ditag d
WHERE d.ditag_id = ?");
$sth->execute($tagid);
my $result = $self->_fetch($sth);
return $result->[0];
}
=head2 fetch_all_by_type
Arg [1] : ditag type
Example : @all_tags = @{$ditag_adaptor->fetch_by_type("SME005")};
Description: Retrieves all ditags of a certain type from the database
Returntype : listref of Bio::EnsEMBL::Map::Ditag
Caller : general
=cut
sub fetch_all_by_type {
my ($self, $tagtype) = @_;
if(!$tagtype){
throw "must be called with the type of a ditag.";
}
my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
FROM ditag d
WHERE d.type = ?");
$sth->execute($tagtype);
my $result = $self->_fetch($sth);
return $result;
}
=head2 fetch_by_name_and_type
Arg [1] : ditag name
Arg [2] : ditag type
Example : $tag = $ditag_adaptor->fetch_by_name_and_type("U3", "SME005");
Description: Retrieves ditags from the database using name/type combination
which should be non-ambiguous
Returntype : Bio::EnsEMBL::Map::Ditag
Caller : general
=cut
sub fetch_by_name_and_type {
my ($self, $tagname, $tagtype) = @_;
if(!$tagname or !$tagtype){
throw "must be called with a name and type of a ditag.";
}
my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
FROM ditag d
WHERE d.name = ? and d.type = ?");
$sth->execute($tagname, $tagtype);
my $result = $self->_fetch($sth);
return $result->[0];
}
=head2 fetch_all
Args : none
Example : @all_tags = @{$ditag_adaptor->fetch_all};
Description: Retrieves all ditags from the database
Returntype : listref of Bio::EnsEMBL::Map::Ditag
Caller : general
=cut
sub fetch_all {
my ($self) = @_;
my $sth = $self->prepare("SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence
FROM ditag d");
$sth->execute;
my $result = $self->_fetch($sth);
return $result;
}
=head2 fetch_all_with_limit
Arg [1] : ditag type
Arg [2] : row limit
Arg [3] : row offset
Description: fetch_by_type with row limit and offset
Returntype : listref of Bio::EnsEMBL::Map::Ditag
Caller : general
=cut
sub fetch_all_with_limit {
my ($self, $tagtype, $limit, $offset) = @_;
my @ditags = ();
my $sql = "SELECT d.ditag_id, d.name, d.type, d.tag_count, d.sequence ".
"FROM ditag d ".
"WHERE d.type = ? LIMIT ? OFFSET ?;";
my $sth = $self->db->dbc->prepare($sql);
$sth->execute($tagtype, $limit, $offset);
my $result = $self->_fetch($sth);
return $result;
}
=head2 _fetch
Arg [1] : statement handler object
Description: generic sql-fetch function for the ditag fetch methods
Returntype : listref of Bio::EnsEMBL::Map::Ditag
Caller : private
=cut
sub _fetch {
my ($self, $sth) = @_;
my($tag_id, $name, $type, $count, $sequence);
my @tags;
$sth->bind_columns(\$tag_id, \$name, \$type, \$count, \$sequence);
while($sth->fetch) {
push @tags, Bio::EnsEMBL::Map::Ditag->new (
-dbID => $tag_id,
-name => $name,
-type => $type,
-tag_count => $count,
-sequence => $sequence,
-adaptor => $self,
);
}
return \@tags;
}
=head2 store
Arg [1] : Bio::EnsEMBL::Map::Ditag
Example : $ditag_adaptor->store(\@ditags);
Description: Stores a single ditag or
a list of ditags in this database.
Returntype : none
Caller : general
=cut
sub store {
my ($self, $ditags) = @_;
if(ref $ditags eq 'ARRAY'){
if(scalar(@$ditags) == 0){
throw("Must call store with ditag or list ref of ditags");
}
}
elsif($ditags){
my @ditags;
push @ditags, $ditags;
$ditags = \@ditags;
}
else{
throw("Must call store with ditag or list ref of ditags not ".$ditags);
}
my $db = $self->db() or throw "Couldn t get database connection.";
TAG:
foreach my $ditag (@$ditags) {
if ( !ref $ditag || !$ditag->isa("Bio::EnsEMBL::Map::Ditag") ) {
throw( "Object must be an Ensembl Ditag, " . "not a [" . ref($ditag) . "]" );
}
if ( $ditag->is_stored($db) ) {
warning( "Ditag [" . $ditag->dbID . "] is already stored in this database." );
next TAG;
}
#check if tag with same name/type already exists
my $sth = $self->prepare( "SELECT COUNT(*) FROM ditag
WHERE name = ? AND type = ?" );
$sth->execute($ditag->name, $ditag->type);
if($sth->fetchrow() > 0){
warning( "Ditag with name/type ".$ditag->name." / ".$ditag->type.
" is already stored in this database.\n".
"Use update_ditag() instead.");
next TAG;
}
if ( $ditag->dbID ) {
my $sth = $self->prepare( "INSERT INTO ditag( ditag_id , name, type, tag_count, sequence ) ".
"VALUES( ?,?,?,?,? )" );
$sth->bind_param(1,$ditag->dbID,SQL_INTEGER);
$sth->bind_param(2,$ditag->name,SQL_VARCHAR);
$sth->bind_param(3,$ditag->type,SQL_VARCHAR);
$sth->bind_param(4,$ditag->tag_count,SQL_VARCHAR);
$sth->bind_param(5,$ditag->sequence,SQL_VARCHAR);
$sth->execute();
} else {
my $sth = $self->prepare( "INSERT INTO ditag( name, type, tag_count, sequence ) ".
"VALUES( ?,?,?,? )" );
$sth->bind_param(1,$ditag->name,SQL_VARCHAR);
$sth->bind_param(2,$ditag->type,SQL_VARCHAR);
$sth->bind_param(3,$ditag->tag_count,SQL_VARCHAR);
$sth->bind_param(4,$ditag->sequence,SQL_VARCHAR);
$sth->execute();
my $dbID = $sth->{'mysql_insertid'};
$ditag->dbID($dbID);
$ditag->adaptor($self);
}
}
return 1;
}
=head2 print_creation
Arg [1] : ditag probe name
Arg [2] : ditag type
Arg [3] : ditag count
Arg [4] : ditag sequence
Arg [5] : (optional) ditag dbID
Description: convenience method to produce SQL insert statements
to speed up the creation of new ditags
Returntype : string
=cut
sub print_creation {
my ($self, $probe_name, $type, $count, $sequence, $dbid) = @_;
my $string;
if($dbid){
$string = "INSERT INTO ditag( ditag_id, name, type, tag_count, sequence ) ".
"VALUES($dbid, '".$probe_name."', '".$type."', ".$count."'".$sequence."');\n";
}
else {
$string = "INSERT INTO ditag( name, type, tag_count, sequence ) ".
"VALUES('".$probe_name."', '".$type."', ".$count.", '".$sequence."');\n";
}
return $string;
}
=head2 update_ditag
Arg [1] : ditag to update
Description: update an existing ditag with new values
Returntype : true on success
=cut
sub update_ditag {
my ($self, $ditag) = @_;
my $sth = $self->prepare( "UPDATE ditag SET name=?, type=?, tag_count=?, sequence=? where ditag_id=?;" );
my $result =$sth->execute(
$ditag->name,
$ditag->type,
$ditag->tag_count,
$ditag->sequence,
$ditag->dbID,
);
return $result;
}
=head2 list_dbIDs
Args : None
Example : my @feature_ids = @{$da->list_dbIDs()};
Description: Gets an array of internal IDs for all Ditag objects in
the current database.
Returntype : List of ints
Exceptions : None
=cut
sub list_dbIDs {
my ($self, $ordered) = shift;
return $self->_list_dbIDs('ditag');
}
1;
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