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# BioPerl module for Bio::Search::Result::WABAResult |
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# |
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# Please direct questions and support issues to |
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# |
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# Cared for by Jason Stajich |
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# |
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# Copyright Jason Stajich |
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# |
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# You may distribute this module under the same terms as perl itself |
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# POD documentation - main docs before the code |
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=head1 NAME |
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Bio::Search::Result::WABAResult - Result object for WABA alignment output |
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=head1 SYNOPSIS |
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# use this object exactly as you would a GenericResult |
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# the only extra method is query_database which is the |
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# name of the file where the query sequence came from |
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=head1 DESCRIPTION |
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This object is for WABA result output, there is little difference |
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between this object and a GenericResult save the addition of one |
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method query_database. Expect many of the fields for GenericResult to |
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be empty however as WABA was not intended to provide a lot of extra |
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information other than the alignment. |
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=head1 FEEDBACK |
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=head2 Mailing Lists |
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User feedback is an integral part of the evolution of this and other |
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Bioperl modules. Send your comments and suggestions preferably to |
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the Bioperl mailing list. Your participation is much appreciated. |
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bioperl-l@bioperl.org - General discussion |
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http://bioperl.org/wiki/Mailing_lists - About the mailing lists |
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=head2 Support |
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Please direct usage questions or support issues to the mailing list: |
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I |
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rather than to the module maintainer directly. Many experienced and |
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reponsive experts will be able look at the problem and quickly |
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address it. Please include a thorough description of the problem |
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with code and data examples if at all possible. |
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=head2 Reporting Bugs |
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Report bugs to the Bioperl bug tracking system to help us keep track |
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of the bugs and their resolution. Bug reports can be submitted via the |
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web: |
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https://github.com/bioperl/bioperl-live/issues |
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=head1 AUTHOR - Jason Stajich |
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Email jason@bioperl.org |
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=head1 APPENDIX |
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The rest of the documentation details each of the object methods. |
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Internal methods are usually preceded with a _ |
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=cut |
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# Let the code begin... |
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package Bio::Search::Result::WABAResult; |
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use strict; |
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use base qw(Bio::Search::Result::GenericResult); |
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=head2 new |
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Title : new |
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Usage : my $obj = Bio::Search::Result::WABAResult->new(); |
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Function: Builds a new Bio::Search::Result::WABAResult object |
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Returns : Bio::Search::Result::WABAResult |
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Args : -query_database => "name of the database where the query came from" |
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=cut |
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sub new { |
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my($class,@args) = @_; |
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my $self = $class->SUPER::new(@args); |
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my ($db) = $self->_rearrange([qw(QUERY_DATABASE)], @args); |
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defined $db && $self->query_database($db); |
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return $self; |
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} |
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=head2 query_database |
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Title : query_database |
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Usage : $obj->query_database($newval) |
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Function: Data field for the database filename where the |
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query sequence came from |
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Returns : value of query_database |
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Args : newvalue (optional) |
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=cut |
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sub query_database{ |
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my ($self,$value) = @_; |
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if( defined $value) { |
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$self->{'query_database'} = $value; |
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} |
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return $self->{'query_database'}; |
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} |
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=head2 All other methods are inherited from Bio::Search::Result::GenericResult |
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See the L for complete |
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documentation of the rest of the methods that are available for this |
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module. |
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=cut |
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1; |