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1 # $Id: WABAResult.pm,v 1.2 2002/10/22 07:45:18 lapp Exp $
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2 #
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3 # BioPerl module for Bio::Search::Result::WABAResult
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4 #
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5 # Cared for by Jason Stajich <jason@bioperl.org>
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6 #
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7 # Copyright Jason Stajich
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8 #
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9 # You may distribute this module under the same terms as perl itself
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10
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11 # POD documentation - main docs before the code
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12
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13 =head1 NAME
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14
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15 Bio::Search::Result::WABAResult - Result object for WABA alignment output
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16
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17 =head1 SYNOPSIS
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18
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19 # use this object exactly as you would a GenericResult
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20 # the only extra method is query_database which is the
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21 # name of the file where the query sequence came from
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22
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23 =head1 DESCRIPTION
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24
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25 This object is for WABA result output, there is little difference
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26 between this object and a GenericResult save the addition of one
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27 method query_database. Expect many of the fields for GenericResult to
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28 be empty however as WABA was not intended to provide a lot of extra
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29 information other than the alignment.
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30
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31 =head1 FEEDBACK
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32
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33 =head2 Mailing Lists
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34
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35 User feedback is an integral part of the evolution of this and other
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36 Bioperl modules. Send your comments and suggestions preferably to
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37 the Bioperl mailing list. Your participation is much appreciated.
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38
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39 bioperl-l@bioperl.org - General discussion
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40 http://bioperl.org/MailList.shtml - About the mailing lists
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41
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42 =head2 Reporting Bugs
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43
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44 Report bugs to the Bioperl bug tracking system to help us keep track
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45 of the bugs and their resolution. Bug reports can be submitted via
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46 email or the web:
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47
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48 bioperl-bugs@bioperl.org
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49 http://bugzilla.bioperl.org/
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50
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51 =head1 AUTHOR - Jason Stajich
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52
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53 Email jason@bioperl.org
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54
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55 Describe contact details here
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56
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57 =head1 CONTRIBUTORS
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58
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59 Additional contributors names and emails here
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60
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61 =head1 APPENDIX
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62
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63 The rest of the documentation details each of the object methods.
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64 Internal methods are usually preceded with a _
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65
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66 =cut
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67
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68
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69 # Let the code begin...
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70
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71
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72 package Bio::Search::Result::WABAResult;
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73 use vars qw(@ISA);
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74 use strict;
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75
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76 use Bio::Search::Result::GenericResult;
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77
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78 @ISA = qw( Bio::Search::Result::GenericResult );
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79
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80 =head2 new
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81
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82 Title : new
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83 Usage : my $obj = new Bio::Search::Result::WABAResult();
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84 Function: Builds a new Bio::Search::Result::WABAResult object
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85 Returns : Bio::Search::Result::WABAResult
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86 Args : -query_database => "name of the database where the query came from"
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87
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88
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89 =cut
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90
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91 sub new {
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92 my($class,@args) = @_;
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93
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94 my $self = $class->SUPER::new(@args);
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95 my ($db) = $self->_rearrange([qw(QUERY_DATABASE)], @args);
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96 defined $db && $self->query_database($db);
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97 return $self;
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98 }
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99
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100 =head2 query_database
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101
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102 Title : query_database
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103 Usage : $obj->query_database($newval)
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104 Function: Data field for the database filename where the
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105 query sequence came from
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106 Returns : value of query_database
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107 Args : newvalue (optional)
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108
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109
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110 =cut
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111
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112 sub query_database{
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113 my ($self,$value) = @_;
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114 if( defined $value) {
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115 $self->{'query_database'} = $value;
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116 }
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117 return $self->{'query_database'};
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118 }
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119
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120
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121 =head2 All other methods are inherited from Bio::Search::Result::GenericResult
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122
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123 See the L<Bio::Search::Result::GenericResult> for complete
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124 documentation of the rest of the methods that are available for this
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125 module.
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126
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127 =cut
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128
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129 1;
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