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1 #-----------------------------------------------------------------
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2 # $Id: SearchWriterI.pm,v 1.7 2002/12/01 00:05:01 jason Exp $
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3 #
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4 # BioPerl module Bio::SearchIO::SearchWriterI
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5 #
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6 # Cared for by Steve Chervitz <sac@bioperl.org>
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7 #
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8 # You may distribute this module under the same terms as perl itself
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9 #-----------------------------------------------------------------
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10
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11 =head1 NAME
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12
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13 Bio::SearchIO::SearchWriterI - Interface for outputting parsed Search results
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14
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15 =head1 SYNOPSIS
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16
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17 Bio::SearchIO::SearchWriterI objects cannot be instantiated since this
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18 module defines a pure interface.
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19
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20 Given an object that implements the Bio::SearchIO::SearchWriterI interface,
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21 you can do the following things with it:
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22
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23 print $writer->to_string( $result_obj, @args );
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24
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25 =head1 DESCRIPTION
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26
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27 This module defines abstract methods that all subclasses must implement
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28 to be used for outputting results from B<Bio::Search::Result::ResultI>
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29 objects.
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30
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31 =head1 AUTHOR
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32
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33 Steve Chervitz E<lt>sac@bioperl.orgE<gt>
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34
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35 =head1 DISCLAIMER
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36
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37 This software is provided "as is" without warranty of any kind.
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38
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39 =head1 APPENDIX
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40
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41 The rest of the documentation details each of the object methods.
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42
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43 =cut
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44
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45 package Bio::SearchIO::SearchWriterI;
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46
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47 use Bio::Root::RootI;
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48
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49 @ISA = qw( Bio::Root::RootI );
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50
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51 =head2 to_string
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52
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53 Purpose : Produces data for each Search::Result::ResultI in a string.
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54 : This is an abstract method. For some useful implementations,
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55 : see ResultTableWriter.pm, HitTableWriter.pm,
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56 : and HSPTableWriter.pm.
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57 Usage : print $writer->to_string( $result_obj, @args );
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58 Argument : $result_obj = A Bio::Search::Result::ResultI object
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59 : @args = any additional arguments used by your implementation.
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60 Returns : String containing data for each search Result or any of its
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61 : sub-objects (Hits and HSPs).
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62 Throws : n/a
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63
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64 =cut
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65
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66 sub to_string {
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67 my ($self, $result, @args) = @_;
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68 $self->throw_not_implemented;
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69 }
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70
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71 =head2 end_report
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72
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73 Title : end_report
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74 Usage : $self->end_report()
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75 Function: The method to call when ending a report, this is
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76 mostly for cleanup for formats which require you to
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77 have something at the end of the document (</BODY></HTML>)
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78 for HTML
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79 Returns : string
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80 Args : none
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81
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82
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83 =cut
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84
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85 sub end_report {
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86 my $self = shift;
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87 return '';
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88 }
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89
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90 =head2 filter
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91
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92 Title : filter
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93 Usage : $writer->filter('hsp', \&hsp_filter);
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94 Function: Filter out either at HSP,Hit,or Result level
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95 Returns : none
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96 Args : string => data type,
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97 CODE reference
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98
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99
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100 =cut
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101
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102 # yes this is an implementation in the interface,
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103 # yes it assumes that the underlying class is hash-based
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104 # yes that might not be a good idea, but until people
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105 # start extending the SearchWriterI interface I think
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106 # this is an okay way to go
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107
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108 sub filter {
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109 my ($self,$method,$code) = @_;
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110 return undef unless $method;
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111 $method = uc($method);
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112 if( $method ne 'HSP' &&
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113 $method ne 'HIT' &&
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114 $method ne 'RESULT' ) {
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115 $self->warn("Unknown method $method");
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116 return undef;
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117 }
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118 if( $code ) {
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119 $self->throw("Must provide a valid code reference") unless ref($code) =~ /CODE/;
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120 $self->{$method} = $code;
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121 }
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122 return $self->{$method};
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123 }
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124
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125 1;
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126
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127
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