lib/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://github.com/bioperl/bioperl-live/issues
  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
  99 use strict;
 100
 101
 102 use base qw(Bio::Root::RootI);
 103
 104
 105 =head2 analysis_query
 106
 107  Usage     : $query_obj = $result->analysis_query();
 108  Purpose   : Get a Bio::PrimarySeqI-compatible object representing the entity
 109              on which the analysis was performed. Lacks sequence information.
 110  Argument  : n/a
 111  Returns   : A Bio::PrimarySeqI-compatible object without sequence information.
 112              The sequence will have display_id, description, moltype, and length data.
 113
 114 =cut
 115
 116 #---------------------
 117 sub analysis_query {
 118 #---------------------
 119     my ($self) = @_;
 120     $self->throw_not_implemented;
 121 }
 122
 123
 124 =head2 analysis_subject
 125
 126  Usage     : $obj = $result->analyis_subject();
 127  Purpose   : Get the subject of the analysis against which it was
 128              performed. For similarity searches it will probably be a database,
 129              and for sequence feature predictions (exons, promoters, etc) it
 130              may be a collection of models or homologous sequences that were
 131              used, or undefined.
 132  Returns   : An object of a type the depends on the implementation
 133              May also return undef for analyses that don\'t involve subjects.
 134  Argument  : n/a
 135  Comments  : Implementation of this method is optional.
 136              AnalysisResultI provides a default behavior of returning undef.
 137
 138 =cut
 139
 140 #---------------
 141 sub analysis_subject {
 142 #---------------
 143     my ($self) = @_;
 144     return;
 145 }
 146
 147 =head2 analysis_subject_version
 148
 149  Usage     : $vers = $result->analyis_subject_version();
 150  Purpose   : Get the version string of the subject of the analysis.
 151  Returns   : String or undef for analyses that don\'t involve subjects.
 152  Argument  : n/a
 153  Comments  : Implementation of this method is optional.
 154              AnalysisResultI provides a default behavior of returning undef.
 155
 156 =cut
 157
 158 #---------------
 159 sub analysis_subject_version {
 160 #---------------
 161     my ($self) = @_;
 162     return;
 163 }
 164
 165
 166 =head2 analysis_date
 167
 168  Usage     : $date = $result->analysis_date();
 169  Purpose   : Get the date on which the analysis was performed.
 170  Returns   : String
 171  Argument  : n/a
 172
 173 =cut
 174
 175 #---------------------
 176 sub analysis_date {
 177 #---------------------
 178     my ($self) = @_;
 179     $self->throw_not_implemented;
 180 }
 181
 182 =head2 analysis_method
 183
 184  Usage     : $meth = $result->analysis_method();
 185  Purpose   : Get the name of the sequence analysis method that was used
 186              to produce this result (BLASTP, FASTA, etc.). May also be the
 187              actual name of a program.
 188  Returns   : String
 189  Argument  : n/a
 190
 191 =cut
 192
 193 #-------------
 194 sub analysis_method {
 195 #-------------
 196     my ($self) = @_;
 197     $self->throw_not_implemented;
 198 }
 199
 200 =head2 analysis_method_version
 201
 202  Usage     : $vers = $result->analysis_method_version();
 203  Purpose   : Get the version string of the analysis program.
 204            : (e.g., 1.4.9MP, 2.0a19MP-WashU).
 205  Returns   : String
 206  Argument  : n/a
 207
 208 =cut
 209
 210 #---------------------
 211 sub analysis_method_version {
 212 #---------------------
 213     my ($self) = @_;
 214     $self->throw_not_implemented;
 215 }
 216
 217 =head2 next_feature
 218
 219  Title   : next_feature
 220  Usage   : $seqfeature = $obj->next_feature();
 221  Function: Returns the next feature available in the analysis result, or
 222            undef if there are no more features.
 223  Example :
 224  Returns : A Bio::SeqFeatureI implementing object, or undef if there are no
 225            more features.
 226  Args    : none
 227
 228 =cut
 229
 230 #---------------------
 231 sub next_feature {
 232 #---------------------
 233     my ($self);
 234     $self->throw_not_implemented;
 235 }
 236
 237
 238 1;