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Bio-EnsEMBL-113.0.0
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/ Bio::EnsEMBL::Map::DBSQL::DitagAdaptor

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Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

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NAME

Bio::EnsEMBL::Map::DBSQL::DitagAdaptor

SYNOPSIS

my $ditagadaptor = $db->get_DitagAdaptor();
my @ditags       = @{ $ditagadaptor->fetch_by_type("ZZ11") };

DESCRIPTION

Provides database interaction for the Bio::EnsEMBL::Map::Ditag object

METHODS

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

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

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

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

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

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

_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

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
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

update_ditag

Arg [1]    : ditag to update
Description: update an existing ditag with new values
Returntype : true on success

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