1 #-----------------------------------------------------------------
4 # BioPerl module Bio::AnalysisResultI
6 # Cared for by Steve Chervitz <sac@bioperl.org>
8 # Derived from Bio::Tools::AnalysisResult by Hilmar Lapp <hlapp@gmx.net>
10 # You may distribute this module under the same terms as perl itself
11 #-----------------------------------------------------------------
13 # POD documentation - main docs before the code
17 Bio::AnalysisResultI - Interface for analysis result objects
21 Bio::AnalysisResultI defines an interface that must be implemented by
22 a subclass. So you cannot create Bio::AnalysisResultI objects,
23 only objects that inherit from Bio::AnalysisResultI.
27 The AnalysisResultI module provides an interface for modules
28 encapsulating the result of an analysis that was carried out with a
29 query sequence and an optional subject dataset.
31 The notion of an analysis represented by this base class is that of a unary or
32 binary operator, taking either one query or a query and a subject and producing
33 a result. The query is e.g. a sequence, and a subject is either a sequence,
34 too, or a database of sequences.
36 This interface defines methods to access analysis result data and does
37 not impose any contraints on how the analysis result data is acquired.
39 Note that this module does not provide support for B<running> an analysis.
40 Rather, it is positioned in the subsequent parsing step (concerned with
41 turning raw results into BioPerl objects).
47 User feedback is an integral part of the evolution of this and other
48 Bioperl modules. Send your comments and suggestions preferably to one
49 of the Bioperl mailing lists. Your participation is much appreciated.
51 bioperl-l@bioperl.org - General discussion
52 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
56 Report bugs to the Bioperl bug tracking system to help us keep track
57 the bugs and their resolution. Bug reports can be submitted via the web:
59 http://bugzilla.open-bio.org/
61 =head1 AUTHOR - Steve Chervitz, Hilmar Lapp
64 Email hlapp@gmx.net (author of Bio::Tools::AnalysisResult on which this module is based)
68 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
72 This software is provided "as is" without warranty of any kind.
76 The rest of the documentation details each of the object
77 methods. Internal methods are usually preceded with a _
82 # Let the code begin...
85 package Bio
::AnalysisResultI
;
89 use base
qw(Bio::Root::RootI);
94 Usage : $query_obj = $result->analysis_query();
95 Purpose : Get a Bio::PrimarySeqI-compatible object representing the entity
96 on which the analysis was performed. Lacks sequence information.
98 Returns : A Bio::PrimarySeqI-compatible object without sequence information.
99 The sequence will have display_id, description, moltype, and length data.
103 #---------------------
105 #---------------------
107 $self->throw_not_implemented;
111 =head2 analysis_subject
113 Usage : $obj = $result->analyis_subject();
114 Purpose : Get the subject of the analysis against which it was
115 performed. For similarity searches it will probably be a database,
116 and for sequence feature predictions (exons, promoters, etc) it
117 may be a collection of models or homologous sequences that were
119 Returns : An object of a type the depends on the implementation
120 May also return undef for analyses that don\'t involve subjects.
122 Comments : Implementation of this method is optional.
123 AnalysisResultI provides a default behavior of returning undef.
128 sub analysis_subject
{
134 =head2 analysis_subject_version
136 Usage : $vers = $result->analyis_subject_version();
137 Purpose : Get the version string of the subject of the analysis.
138 Returns : String or undef for analyses that don\'t involve subjects.
140 Comments : Implementation of this method is optional.
141 AnalysisResultI provides a default behavior of returning undef.
146 sub analysis_subject_version
{
155 Usage : $date = $result->analysis_date();
156 Purpose : Get the date on which the analysis was performed.
162 #---------------------
164 #---------------------
166 $self->throw_not_implemented;
169 =head2 analysis_method
171 Usage : $meth = $result->analysis_method();
172 Purpose : Get the name of the sequence analysis method that was used
173 to produce this result (BLASTP, FASTA, etc.). May also be the
174 actual name of a program.
181 sub analysis_method
{
184 $self->throw_not_implemented;
187 =head2 analysis_method_version
189 Usage : $vers = $result->analysis_method_version();
190 Purpose : Get the version string of the analysis program.
191 : (e.g., 1.4.9MP, 2.0a19MP-WashU).
197 #---------------------
198 sub analysis_method_version
{
199 #---------------------
201 $self->throw_not_implemented;
207 Usage : $seqfeature = $obj->next_feature();
208 Function: Returns the next feature available in the analysis result, or
209 undef if there are no more features.
211 Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
217 #---------------------
219 #---------------------
221 $self->throw_not_implemented;