package MS::Reader::MzIdentML::DBSequence; use strict; use warnings; use parent qw/MS::Reader::MzIdentML::SequenceItem/; sub id { return $_[0]->{id} } sub acc { return $_[0]->{accession} } sub search_db { return $_[0]->{searchDatabase_ref} } 1; __END__ =pod =encoding UTF-8 =head1 NAME MS::Reader::MzIdentML::DBSequence - mzIdentML database sequence object =head1 SYNOPSIS my $pro = $search->fetch_dbsequence_by_id('FooBarProtein'); say $pro->id; say $pro->acc; say $pro->search_db; =head1 DESCRIPTION C<MS::Reader::MzIdentML::DBSequence> is a class representing an mzIdentML search database sequence (typically a protein). =head1 METHODS =head2 id =head2 acc my $id = $pro->id; my $acc = $pro->acc; Return the ID and accession of the sequence, respectively =head2 search_db my $db_id = $seq->search_db; Returns the identifier of the search database that the sequence belongs to. This can be used to link to the database used. Currently the database is not implemented as a class, so an understanding of the data structure is needed to extract this information. =head1 CAVEATS AND BUGS The API is in alpha stage and is not guaranteed to be stable. Please reports bugs or feature requests through the issue tracker at L<https://github.com/jvolkening/p5-MS/issues>. =head1 AUTHOR Jeremy Volkening <jdv@base2bio.com> =head1 COPYRIGHT AND LICENSE Copyright 2015-2016 Jeremy Volkening This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>. =cut