LICENSE

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

     http://www.apache.org/licenses/LICENSE-2.0

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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

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

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

cpanm Bio::EnsEMBL

perl -MCPAN -e shell
install Bio::EnsEMBL