lib/Bio/Search/Result/WABAResult.pm

   1 #
   2 # BioPerl module for Bio::Search::Result::WABAResult
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::Search::Result::WABAResult - Result object for WABA alignment output
  17
  18 =head1 SYNOPSIS
  19
  20 # use this object exactly as you would a GenericResult
  21 # the only extra method is query_database which is the
  22 # name of the file where the query sequence came from
  23
  24 =head1 DESCRIPTION
  25
  26 This object is for WABA result output, there is little difference
  27 between this object and a GenericResult save the addition of one
  28 method query_database.  Expect many of the fields for GenericResult to
  29 be empty however as WABA was not intended to provide a lot of extra
  30 information other than the alignment.
  31
  32 =head1 FEEDBACK
  33
  34 =head2 Mailing Lists
  35
  36 User feedback is an integral part of the evolution of this and other
  37 Bioperl modules. Send your comments and suggestions preferably to
  38 the Bioperl mailing list.  Your participation is much appreciated.
  39
  40   bioperl-l@bioperl.org                  - General discussion
  41   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  42
  43 =head2 Support
  44
  45 Please direct usage questions or support issues to the mailing list:
  46
  47 I<bioperl-l@bioperl.org>
  48
  49 rather than to the module maintainer directly. Many experienced and
  50 reponsive experts will be able look at the problem and quickly
  51 address it. Please include a thorough description of the problem
  52 with code and data examples if at all possible.
  53
  54 =head2 Reporting Bugs
  55
  56 Report bugs to the Bioperl bug tracking system to help us keep track
  57 of the bugs and their resolution. Bug reports can be submitted via the
  58 web:
  59
  60   https://github.com/bioperl/bioperl-live/issues
  61
  62 =head1 AUTHOR - Jason Stajich
  63
  64 Email jason@bioperl.org
  65
  66 =head1 APPENDIX
  67
  68 The rest of the documentation details each of the object methods.
  69 Internal methods are usually preceded with a _
  70
  71 =cut
  72
  73
  74 # Let the code begin...
  75
  76
  77 package Bio::Search::Result::WABAResult;
  78 use strict;
  79
  80
  81 use base qw(Bio::Search::Result::GenericResult);
  82
  83 =head2 new
  84
  85  Title   : new
  86  Usage   : my $obj = Bio::Search::Result::WABAResult->new();
  87  Function: Builds a new Bio::Search::Result::WABAResult object
  88  Returns : Bio::Search::Result::WABAResult
  89  Args    : -query_database => "name of the database where the query came from"
  90
  91
  92 =cut
  93
  94 sub new {
  95   my($class,@args) = @_;
  96
  97   my $self = $class->SUPER::new(@args);
  98   my ($db) = $self->_rearrange([qw(QUERY_DATABASE)], @args);
  99   defined $db && $self->query_database($db);
 100   return $self;
 101 }
 102
 103 =head2 query_database
 104
 105  Title   : query_database
 106  Usage   : $obj->query_database($newval)
 107  Function: Data field for the database filename where the
 108            query sequence came from
 109  Returns : value of query_database
 110  Args    : newvalue (optional)
 111
 112
 113 =cut
 114
 115 sub query_database{
 116     my ($self,$value) = @_;
 117     if( defined $value) {
 118         $self->{'query_database'} = $value;
 119     }
 120     return $self->{'query_database'};
 121 }
 122
 123
 124 =head2 All other methods are inherited from Bio::Search::Result::GenericResult
 125
 126 See the L<Bio::Search::Result::GenericResult> for complete
 127 documentation of the rest of the methods that are available for this
 128 module.
 129
 130 =cut
 131
 132 1;