Bio/AnalysisResultI.pm

   1 #-----------------------------------------------------------------
   2 #
   3 # BioPerl module Bio::AnalysisResultI
   4 #
   5 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   6 #
   7 # Cared for by Steve Chervitz <sac@bioperl.org>
   8 #
   9 # Derived from Bio::Tools::AnalysisResult by Hilmar Lapp <hlapp@gmx.net>
  10 #
  11 # You may distribute this module under the same terms as perl itself
  12 #-----------------------------------------------------------------
  13
  14 # POD documentation - main docs before the code
  15
  16 =head1 NAME
  17
  18 Bio::AnalysisResultI - Interface for analysis result objects
  19
  20 =head1 SYNOPSIS
  21
  22 Bio::AnalysisResultI defines an interface that must be implemented by
  23 a subclass. So you cannot create Bio::AnalysisResultI objects,
  24 only objects that inherit from Bio::AnalysisResultI.
  25
  26 =head1 DESCRIPTION
  27
  28 The AnalysisResultI module provides an interface for modules
  29 encapsulating the result of an analysis that was carried out with a
  30 query sequence and an optional subject dataset.
  31
  32 The notion of an analysis represented by this base class is that of a unary or
  33 binary operator, taking either one query or a query and a subject and producing
  34 a result. The query is e.g. a sequence, and a subject is either a sequence,
  35 too, or a database of sequences.
  36
  37 This interface defines methods to access analysis result data and does
  38 not impose any constraints on how the analysis result data is acquired.
  39
  40 Note that this module does not provide support for B<running> an analysis.
  41 Rather, it is positioned in the subsequent parsing step (concerned with
  42 turning raw results into BioPerl objects).
  43
  44 =head1 FEEDBACK
  45
  46 =head2 Mailing Lists
  47
  48 User feedback is an integral part of the evolution of this and other
  49 Bioperl modules. Send your comments and suggestions preferably to one
  50 of the Bioperl mailing lists.  Your participation is much appreciated.
  51
  52   bioperl-l@bioperl.org                  - General discussion
  53   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  54
  55 =head2 Support
  56
  57 Please direct usage questions or support issues to the mailing list:
  58
  59 I<bioperl-l@bioperl.org>
  60
  61 rather than to the module maintainer directly. Many experienced and
  62 reponsive experts will be able look at the problem and quickly
  63 address it. Please include a thorough description of the problem
  64 with code and data examples if at all possible.
  65
  66 =head2 Reporting Bugs
  67
  68 Report bugs to the Bioperl bug tracking system to help us keep track
  69 the bugs and their resolution.  Bug reports can be submitted via the web:
  70
  71   https://redmine.open-bio.org/projects/bioperl/
  72
  73 =head1 AUTHOR - Steve Chervitz, Hilmar Lapp
  74
  75 Email sac@bioperl.org
  76 Email hlapp@gmx.net (author of Bio::Tools::AnalysisResult on which this module is based)
  77
  78 =head1 COPYRIGHT
  79
  80 Copyright (c) 2001 Steve Chervitz. All Rights Reserved.
  81
  82 =head1 DISCLAIMER
  83
  84 This software is provided "as is" without warranty of any kind.
  85
  86 =head1 APPENDIX
  87
  88 The rest of the documentation details each of the object
  89 methods. Internal methods are usually preceded with a _
  90
  91 =cut
  92
  93
  94 # Let the code begin...
  95
  96
  97 package Bio::AnalysisResultI;
  98 use strict;
  99
 100
 101 use base qw(Bio::Root::RootI);
 102
 103
 104 =head2 analysis_query
 105
 106  Usage     : $query_obj = $result->analysis_query();
 107  Purpose   : Get a Bio::PrimarySeqI-compatible object representing the entity
 108              on which the analysis was performed. Lacks sequence information.
 109  Argument  : n/a
 110  Returns   : A Bio::PrimarySeqI-compatible object without sequence information.
 111              The sequence will have display_id, description, moltype, and length data.
 112
 113 =cut
 114
 115 #---------------------
 116 sub analysis_query {
 117 #---------------------
 118     my ($self) = @_;
 119     $self->throw_not_implemented;
 120 }
 121
 122
 123 =head2 analysis_subject
 124
 125  Usage     : $obj = $result->analyis_subject();
 126  Purpose   : Get the subject of the analysis against which it was
 127              performed. For similarity searches it will probably be a database,
 128              and for sequence feature predictions (exons, promoters, etc) it
 129              may be a collection of models or homologous sequences that were
 130              used, or undefined.
 131  Returns   : An object of a type the depends on the implementation
 132              May also return undef for analyses that don\'t involve subjects.
 133  Argument  : n/a
 134  Comments  : Implementation of this method is optional.
 135              AnalysisResultI provides a default behavior of returning undef.
 136
 137 =cut
 138
 139 #---------------
 140 sub analysis_subject {
 141 #---------------
 142     my ($self) = @_;
 143     return;
 144 }
 145
 146 =head2 analysis_subject_version
 147
 148  Usage     : $vers = $result->analyis_subject_version();
 149  Purpose   : Get the version string of the subject of the analysis.
 150  Returns   : String or undef for analyses that don\'t involve subjects.
 151  Argument  : n/a
 152  Comments  : Implementation of this method is optional.
 153              AnalysisResultI provides a default behavior of returning undef.
 154
 155 =cut
 156
 157 #---------------
 158 sub analysis_subject_version {
 159 #---------------
 160     my ($self) = @_;
 161     return;
 162 }
 163
 164
 165 =head2 analysis_date
 166
 167  Usage     : $date = $result->analysis_date();
 168  Purpose   : Get the date on which the analysis was performed.
 169  Returns   : String
 170  Argument  : n/a
 171
 172 =cut
 173
 174 #---------------------
 175 sub analysis_date {
 176 #---------------------
 177     my ($self) = @_;
 178     $self->throw_not_implemented;
 179 }
 180
 181 =head2 analysis_method
 182
 183  Usage     : $meth = $result->analysis_method();
 184  Purpose   : Get the name of the sequence analysis method that was used
 185              to produce this result (BLASTP, FASTA, etc.). May also be the
 186              actual name of a program.
 187  Returns   : String
 188  Argument  : n/a
 189
 190 =cut
 191
 192 #-------------
 193 sub analysis_method {
 194 #-------------
 195     my ($self) = @_;
 196     $self->throw_not_implemented;
 197 }
 198
 199 =head2 analysis_method_version
 200
 201  Usage     : $vers = $result->analysis_method_version();
 202  Purpose   : Get the version string of the analysis program.
 203            : (e.g., 1.4.9MP, 2.0a19MP-WashU).
 204  Returns   : String
 205  Argument  : n/a
 206
 207 =cut
 208
 209 #---------------------
 210 sub analysis_method_version {
 211 #---------------------
 212     my ($self) = @_;
 213     $self->throw_not_implemented;
 214 }
 215
 216 =head2 next_feature
 217
 218  Title   : next_feature
 219  Usage   : $seqfeature = $obj->next_feature();
 220  Function: Returns the next feature available in the analysis result, or
 221            undef if there are no more features.
 222  Example :
 223  Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
 224            more features.
 225  Args    : none
 226
 227 =cut
 228
 229 #---------------------
 230 sub next_feature {
 231 #---------------------
 232     my ($self);
 233     $self->throw_not_implemented;
 234 }
 235
 236
 237 1;