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1 #-----------------------------------------------------------------
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2 # $Id: AnalysisResultI.pm,v 1.5 2002/10/22 07:38:24 lapp Exp $
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3 #
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4 # BioPerl module Bio::AnalysisResultI
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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::Tools::AnalysisResult by Hilmar Lapp <hlapp@gmx.net>
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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 # POD documentation - main docs before the code
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14
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15 =head1 NAME
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16
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17 Bio::AnalysisResultI - Interface for analysis result objects
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18
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19 =head1 SYNOPSIS
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20
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21 Bio::AnalysisResultI defines an interface that must be implemented by
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22 a subclass. So you cannot create Bio::AnalysisResultI objects,
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23 only objects that inherit from Bio::AnalysisResultI.
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24
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25 =head1 DESCRIPTION
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26
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27 The AnalysisResultI module provides an interface for modules
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28 encapsulating the result of an analysis that was carried out with a
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29 query sequence and an optional subject dataset.
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30
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31 The notion of an analysis represented by this base class is that of a unary or
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32 binary operator, taking either one query or a query and a subject and producing
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33 a result. The query is e.g. a sequence, and a subject is either a sequence,
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34 too, or a database of sequences.
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35
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36 This interface defines methods to access analysis result data and does
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37 not impose any contraints on how the analysis result data is acquired.
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38
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39 Note that this module does not provide support for B<running> an analysis.
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40 Rather, it is positioned in the subsequent parsing step (concerned with
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41 turning raw results into BioPerl objects).
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42
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43 =head1 FEEDBACK
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44
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45 =head2 Mailing Lists
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46
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47 User feedback is an integral part of the evolution of this and other
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48 Bioperl modules. Send your comments and suggestions preferably to one
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49 of the Bioperl mailing lists. Your participation is much appreciated.
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50
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51 bioperl-l@bioperl.org - General discussion
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52 http://bio.perl.org/MailList.html - About the mailing lists
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53
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54 =head2 Reporting Bugs
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55
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56 Report bugs to the Bioperl bug tracking system to help us keep track
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57 the bugs and their resolution. Bug reports can be submitted via email
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58 or the web:
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59
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60 bioperl-bugs@bio.perl.org
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61 http://bugzilla.bioperl.org/
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62
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63 =head1 AUTHOR - Steve Chervitz, Hilmar Lapp
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64
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65 Email sac@bioperl.org
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66 Email hlapp@gmx.net (author of Bio::Tools::AnalysisResult on which this module is based)
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67
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68 =head1 COPYRIGHT
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69
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70 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
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71
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72 =head1 DISCLAIMER
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73
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74 This software is provided "as is" without warranty of any kind.
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75
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76 =head1 APPENDIX
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77
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78 The rest of the documentation details each of the object
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79 methods. Internal methods are usually preceded with a _
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80
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81 =cut
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82
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83
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84 # Let the code begin...
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85
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86
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87 package Bio::AnalysisResultI;
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88 use strict;
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89 use vars qw(@ISA);
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90
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91 use Bio::Root::RootI;
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92
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93 @ISA = qw( Bio::Root::RootI );
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94
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95
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96 =head2 analysis_query
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97
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98 Usage : $query_obj = $result->analysis_query();
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99 Purpose : Get a Bio::PrimarySeqI-compatible object representing the entity
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100 on which the analysis was performed. Lacks sequence information.
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101 Argument : n/a
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102 Returns : A Bio::PrimarySeqI-compatible object without sequence information.
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103 The sequence will have display_id, description, moltype, and length data.
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104
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105 =cut
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106
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107 #---------------------
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108 sub analysis_query {
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109 #---------------------
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110 my ($self) = @_;
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111 $self->throw_not_implemented;
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112 }
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113
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114
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115 =head2 analysis_subject
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116
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117 Usage : $obj = $result->analyis_subject();
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118 Purpose : Get the subject of the analysis against which it was
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119 performed. For similarity searches it will probably be a database,
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120 and for sequence feature predictions (exons, promoters, etc) it
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121 may be a collection of models or homologous sequences that were
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122 used, or undefined.
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123 Returns : An object of a type the depends on the implementation
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124 May also return undef for analyses that don\'t involve subjects.
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125 Argument : n/a
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126 Comments : Implementation of this method is optional.
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127 AnalysisResultI provides a default behavior of returning undef.
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128
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129 =cut
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130
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131 #---------------
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132 sub analysis_subject {
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133 #---------------
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134 my ($self) = @_;
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135 return undef;
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136 }
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137
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138 =head2 analysis_subject_version
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139
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140 Usage : $vers = $result->analyis_subject_version();
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141 Purpose : Get the version string of the subject of the analysis.
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142 Returns : String or undef for analyses that don\'t involve subjects.
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143 Argument : n/a
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144 Comments : Implementation of this method is optional.
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145 AnalysisResultI provides a default behavior of returning undef.
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146
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147 =cut
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148
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149 #---------------
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150 sub analysis_subject_version {
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151 #---------------
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152 my ($self) = @_;
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153 return undef;
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154 }
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155
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156
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157 =head2 analysis_date
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158
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159 Usage : $date = $result->analysis_date();
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160 Purpose : Get the date on which the analysis was performed.
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161 Returns : String
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162 Argument : n/a
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163
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164 =cut
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165
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166 #---------------------
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167 sub analysis_date {
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168 #---------------------
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169 my ($self) = @_;
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170 $self->throw_not_implemented;
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171 }
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172
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173 =head2 analysis_method
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174
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175 Usage : $meth = $result->analysis_method();
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176 Purpose : Get the name of the sequence analysis method that was used
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177 to produce this result (BLASTP, FASTA, etc.). May also be the
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178 actual name of a program.
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179 Returns : String
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180 Argument : n/a
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181
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182 =cut
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183
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184 #-------------
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185 sub analysis_method {
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186 #-------------
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187 my ($self) = @_;
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188 $self->throw_not_implemented;
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189 }
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190
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191 =head2 analysis_method_version
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192
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193 Usage : $vers = $result->analysis_method_version();
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194 Purpose : Get the version string of the analysis program.
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195 : (e.g., 1.4.9MP, 2.0a19MP-WashU).
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196 Returns : String
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197 Argument : n/a
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198
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199 =cut
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200
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201 #---------------------
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202 sub analysis_method_version {
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203 #---------------------
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204 my ($self) = @_;
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205 $self->throw_not_implemented;
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206 }
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207
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208 =head2 next_feature
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209
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210 Title : next_feature
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211 Usage : $seqfeature = $obj->next_feature();
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212 Function: Returns the next feature available in the analysis result, or
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213 undef if there are no more features.
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214 Example :
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215 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
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216 more features.
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217 Args : none
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218
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219 =cut
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220
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221 #---------------------
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222 sub next_feature {
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223 #---------------------
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224 my ($self);
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225 $self->throw_not_implemented;
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226 }
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227
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228
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229 1;
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