Raw content of Bio::Search::Result::WABAResult # $Id: WABAResult.pm,v 1.2 2002/10/22 07:45:18 lapp Exp $ # # BioPerl module for Bio::Search::Result::WABAResult # # Cared for by Jason Stajich <jason@bioperl.org> # # Copyright Jason Stajich # # You may distribute this module under the same terms as perl itself # POD documentation - main docs before the code =head1 NAME Bio::Search::Result::WABAResult - Result object for WABA alignment output =head1 SYNOPSIS # use this object exactly as you would a GenericResult # the only extra method is query_database which is the # name of the file where the query sequence came from =head1 DESCRIPTION This object is for WABA result output, there is little difference between this object and a GenericResult save the addition of one method query_database. Expect many of the fields for GenericResult to be empty however as WABA was not intended to provide a lot of extra information other than the alignment. =head1 FEEDBACK =head2 Mailing Lists User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated. bioperl-l@bioperl.org - General discussion http://bioperl.org/MailList.shtml - About the mailing lists =head2 Reporting Bugs Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web: bioperl-bugs@bioperl.org http://bugzilla.bioperl.org/ =head1 AUTHOR - Jason Stajich Email jason@bioperl.org Describe contact details here =head1 CONTRIBUTORS Additional contributors names and emails here =head1 APPENDIX The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _ =cut # Let the code begin... package Bio::Search::Result::WABAResult; use vars qw(@ISA); use strict; use Bio::Search::Result::GenericResult; @ISA = qw( Bio::Search::Result::GenericResult ); =head2 new Title : new Usage : my $obj = new Bio::Search::Result::WABAResult(); Function: Builds a new Bio::Search::Result::WABAResult object Returns : Bio::Search::Result::WABAResult Args : -query_database => "name of the database where the query came from" =cut sub new { my($class,@args) = @_; my $self = $class->SUPER::new(@args); my ($db) = $self->_rearrange([qw(QUERY_DATABASE)], @args); defined $db && $self->query_database($db); return $self; } =head2 query_database Title : query_database Usage : $obj->query_database($newval) Function: Data field for the database filename where the query sequence came from Returns : value of query_database Args : newvalue (optional) =cut sub query_database{ my ($self,$value) = @_; if( defined $value) { $self->{'query_database'} = $value; } return $self->{'query_database'}; } =head2 All other methods are inherited from Bio::Search::Result::GenericResult See the L<Bio::Search::Result::GenericResult> for complete documentation of the rest of the methods that are available for this module. =cut 1;