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1 #---------------------------------------------------------------
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2 # $Id: AnalysisParserI.pm,v 1.7 2002/12/01 00:05:19 jason Exp $
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3 #
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4 # BioPerl module Bio::AnalysisParserI
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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 # Derived from Bio::SeqAnalysisParserI by Jason Stajich, Hilmar Lapp.
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9 #
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10 # You may distribute this module under the same terms as perl itself
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11 #---------------------------------------------------------------
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12
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13 =head1 NAME
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14
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15 Bio::AnalysisParserI - Generic analysis output parser interface
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16
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17 =head1 SYNOPSIS
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18
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19 # get a AnalysisParserI somehow.
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20 # Eventually, there may be an Bio::Factory::AnalysisParserFactory.
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21 # For now a SearchIO object, an implementation of AnalysisParserI, can be created
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22 # directly, as in the following:
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23 my $parser = Bio::SearchIO->new(
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24 '-file' => 'inputfile',
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25 '-format' => 'blast');
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26
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27 while( my $result = $parser->next_result() ) {
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28 print "Result: ", $result->analysis_method,
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29 ", Query: ", $result->query_name, "\n";
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30
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31 while( my $feature = $result->next_feature() ) {
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32 print "Feature from ", $feature->start, " to ",
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33 $feature->end, "\n";
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34 }
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35 }
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36
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37 =head1 DESCRIPTION
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38
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39 AnalysisParserI is a interface for describing generic analysis
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40 result parsers. This module makes no assumption about the nature of
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41 analysis being parsed, only that zero or more result sets can be
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42 obtained from the input source.
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43
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44 This module was derived from Bio::SeqAnalysisParserI, the differences being
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45
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46 =over 4
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47
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48 =item 1. next_feature() was replaced with next_result().
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49
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50 Instead of flattening a stream containing potentially multiple
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51 analysis results into a single set of features, AnalysisParserI
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52 segments the stream in terms of analysis result sets
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53 (Bio::AnalysisResultI objects). Each AnalysisResultI can then be
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54 queried for its features (if any) as well as other information
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55 about the result
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56
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57 =item 2. AnalysisParserI is a pure interface.
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58
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59 It does not inherit from Bio::Root::RootI and does not provide a new()
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60 method. Implementations are free to choose how to implement it.
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61
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62 =back
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63
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64 =head2 Rationale (copied from Bio::SeqAnalysisParserI)
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65
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66 The concept behind this interface is to have a generic interface in sequence
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67 annotation pipelines (as used e.g. in high-throughput automated
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68 sequence annotation). This interface enables plug-and-play for new analysis
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69 methods and their corresponding parsers without the necessity for modifying
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70 the core of the annotation pipeline. In this concept the annotation pipeline
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71 has to rely on only a list of methods for which to process the results, and a
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72 factory from which it can obtain the corresponding parser implementing this
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73 interface.
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74
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75 =head2 TODO
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76
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77 Create Bio::Factory::AnalysisParserFactoryI and
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78 Bio::Factory::AnalysisParserFactory for interface and an implementation.
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79 Note that this factory could return Bio::SearchIO-derived objects.
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80
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81 =head1 FEEDBACK
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82
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83 =head2 Mailing Lists
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84
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85 User feedback is an integral part of the evolution of this
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86 and other Bioperl modules. Send your comments and suggestions preferably
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87 to one of the Bioperl mailing lists.
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88 Your participation is much appreciated.
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89
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90 bioperl-l@bioperl.org - General discussion
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91 http://bio.perl.org/MailList.html - About the mailing lists
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92
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93 =head2 Reporting Bugs
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94
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95 Report bugs to the Bioperl bug tracking system to help us keep track
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96 the bugs and their resolution.
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97 Bug reports can be submitted via email or the web:
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98
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99 bioperl-bugs@bio.perl.org
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100 http://bugzilla.bioperl.org/
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101
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102 =head1 AUTHOR - Steve Chervitz, Jason Stajich, Hilmar Lapp
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103
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104 Email sac@bioperl.org
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105
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106 Authors of Bio::SeqAnalysisParserI on which this module is based:
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107 Email jason@bioperl.org
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108 Email hlapp@gmx.net
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109
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110 =head1 COPYRIGHT
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111
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112 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
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113
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114 =head1 DISCLAIMER
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115
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116 This software is provided "as is" without warranty of any kind.
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117
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118 =head1 APPENDIX
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119
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120 The rest of the documentation details each of the object methods.
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121 Internal methods are usually preceded with a _
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122
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123 =cut
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124
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125 package Bio::AnalysisParserI;
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126 use strict;
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127 use vars qw(@ISA);
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128
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129 use Bio::Root::RootI;
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130
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131 @ISA = qw(Bio::Root::RootI);
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132
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133 =head2 next_result
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134
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135 Title : next_result
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136 Usage : $result = $obj->next_result();
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137 Function: Returns the next result available from the input, or
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138 undef if there are no more results.
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139 Example :
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140 Returns : A Bio::Search::Result::ResultI implementing object,
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141 or undef if there are no more results.
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142 Args : none
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143
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144 =cut
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145
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146 sub next_result {
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147 my ($self);
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148 $self->throw_not_implemented;
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149 }
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150
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151
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152
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153 =head2 result_factory
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154
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155 Title : result_factory
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156 Usage : $res_fact = $obj->result_factory; (get)
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157 : $obj->result_factory( $factory ); (set)
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158 Function: Sets/Gets a factory object to create result objects for this AnalysisParser.
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159 Returns : Bio::Factory::ResultFactoryI object
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160 Args : Bio::Factory::ResultFactoryI object (when setting)
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161 Comments: A AnalysisParserI implementation should provide a default result factory.
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162 obtainable by the default_result_factory_class() method.
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163
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164 =cut
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165
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166 sub result_factory {
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167 my $self = shift;
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168 $self->throw_not_implemented;
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169 }
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170
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171 =head2 default_result_factory_class
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172
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173 Title : default_result_factory_class
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174 Usage : $res_factory = $obj->default_result_factory_class()->new( @args )
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175 Function: Returns the name of the default class to be used for creating
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176 Bio::AnalysisResultI objects.
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177 Example :
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178 Returns : A string containing the name of a class that implements
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179 the Bio::Factory::ResultFactoryI interface.
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180 Args : none
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181
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182 =cut
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183
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184 sub default_result_factory_class {
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185 my $self = shift;
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186 # TODO: Uncomment this when Jason's SearchIO code conforms
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187 # $self->throw_not_implemented;
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188 }
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189
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190 1;
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191 __END__
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192
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193 NOTE: My ten-month old son Russell added the following line.
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194 It doesn't look like it will compile so I'm putting it here:
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195 mt6 j7qa
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