lib/Bio/SearchIO/EventHandlerI.pm

   1 #
   2 # BioPerl module for Bio::SearchIO::EventHandlerI
   3 #
   4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
   5 #
   6 # Cared for by Jason Stajich <jason@bioperl.org>
   7 #
   8 # Copyright Jason Stajich
   9 #
  10 # You may distribute this module under the same terms as perl itself
  11
  12 # POD documentation - main docs before the code
  13
  14 =head1 NAME
  15
  16 Bio::SearchIO::EventHandlerI - An abstract Event Handler for Search Result parsing
  17
  18 =head1 SYNOPSIS
  19
  20 # do not use this object directly it is an interface
  21 # See Bio::SearchIO::SearchResultEventBuilder for an implementation
  22
  23     use Bio::SearchIO::SearchResultEventBuilder;
  24     my $handler = Bio::SearchIO::SearchResultEventBuilder->new();
  25
  26 =head1 DESCRIPTION
  27
  28 This interface describes the basic methods needed to handle Events
  29 thrown from parsing a Search Result such as FASTA, BLAST, or HMMer.
  30
  31 =head1 FEEDBACK
  32
  33 =head2 Mailing Lists
  34
  35 User feedback is an integral part of the evolution of this and other
  36 Bioperl modules. Send your comments and suggestions preferably to
  37 the Bioperl mailing list.  Your participation is much appreciated.
  38
  39   bioperl-l@bioperl.org                  - General discussion
  40   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
  41
  42 =head2 Support
  43
  44 Please direct usage questions or support issues to the mailing list:
  45
  46 I<bioperl-l@bioperl.org>
  47
  48 rather than to the module maintainer directly. Many experienced and
  49 reponsive experts will be able look at the problem and quickly
  50 address it. Please include a thorough description of the problem
  51 with code and data examples if at all possible.
  52
  53 =head2 Reporting Bugs
  54
  55 Report bugs to the Bioperl bug tracking system to help us keep track
  56 of the bugs and their resolution. Bug reports can be submitted via the
  57 web:
  58
  59   https://github.com/bioperl/bioperl-live/issues
  60
  61 =head1 AUTHOR - Jason Stajich
  62
  63 Email jason-at-bioperl.org
  64
  65 =head1 APPENDIX
  66
  67 The rest of the documentation details each of the object methods.
  68 Internal methods are usually preceded with a _
  69
  70 =cut
  71
  72
  73 # Let the code begin...
  74
  75
  76 package Bio::SearchIO::EventHandlerI;
  77
  78 use strict;
  79 use Carp;
  80
  81
  82 use base qw(Bio::Event::EventHandlerI);
  83
  84 =head2 start_result
  85
  86  Title   : start_result
  87  Usage   : $handler->start_result($data)
  88  Function: Begins a result event cycle
  89  Returns : none
  90  Args    : Type of Result
  91
  92 =cut
  93
  94 sub start_result {
  95     my ($self) = @_;
  96     $self->throw_not_implemented();
  97 }
  98
  99 =head2 end_result
 100
 101  Title   : end_result
 102  Usage   : $handler->end_result($data)
 103  Function: Ends a result event cycle
 104  Returns : Bio::Search::Result::ResultI object
 105  Args    : none
 106
 107
 108 =cut
 109
 110 sub end_result{
 111    my ($self,@args) = @_;
 112    $self->throw_not_implemented();
 113 }
 114
 115 =head2 start_hsp
 116
 117  Title   : start_hsp
 118  Usage   : $handler->start_hsp($data)
 119  Function: Start a HSP event cycle
 120  Returns : none
 121  Args    : type of element
 122            associated hashref
 123
 124 =cut
 125
 126 sub start_hsp{
 127    my ($self,@args) = @_;
 128    $self->throw_not_implemented();
 129 }
 130
 131 =head2 end_hsp
 132
 133  Title   : end_hsp
 134  Usage   : $handler->end_hsp()
 135  Function: Ends a HSP event cycle
 136  Returns : Bio::Search::HSP::HSPI object
 137  Args    : type of event and associated hashref
 138
 139 =cut
 140
 141 sub end_hsp{
 142    my ($self,@args) = @_;
 143    $self->throw_not_implemented();
 144 }
 145
 146 =head2 start_hit
 147
 148  Title   : start_hit
 149  Usage   : $handler->start_hit()
 150  Function: Starts a Hit event cycle
 151  Returns : none
 152  Args    : type of event and associated hashref
 153
 154
 155 =cut
 156
 157 sub start_hit {
 158    my ($self,@args) = @_;
 159    $self->throw_not_implemented
 160 }
 161
 162 =head2 end_hit
 163
 164  Title   : end_hit
 165  Usage   : $handler->end_hit()
 166  Function: Ends a Hit event cycle
 167  Returns : Bio::Search::Hit::HitI object
 168  Args    : type of event and associated hashref
 169
 170
 171 =cut
 172
 173 sub end_hit {
 174    my ($self,@args) = @_;
 175    $self->throw_not_implemented();
 176 }
 177
 178 =head2 start_iteration
 179
 180  Title   : start_iteration
 181  Usage   : $handler->start_iteration()
 182  Function: Starts an Iteration event cycle
 183  Returns : none
 184  Args    : type of event and associated hashref
 185
 186
 187 =cut
 188
 189 sub start_iteration {
 190    my ($self,@args) = @_;
 191    $self->throw_not_implemented
 192 }
 193
 194 =head2 end_iteration
 195
 196  Title   : end_iteration
 197  Usage   : $handler->end_iteration()
 198  Function: Ends an Iterationevent cycle
 199  Returns : Bio::Search::Iteration::IterationI object
 200  Args    : type of event and associated hashref
 201
 202
 203 =cut
 204
 205 sub end_iteration {
 206    my ($self,@args) = @_;
 207    $self->throw_not_implemented();
 208 }
 209
 210 =head2 register_factory
 211
 212  Title   : register_factory
 213  Usage   : $handler->register_factory('TYPE',$factory);
 214  Function: Register a specific factory for a object type class
 215  Returns : none
 216  Args    : string representing the class and
 217            Bio::Factory::ObjectFactoryI
 218
 219 See L<Bio::Factory::ObjectFactoryI> for more information
 220
 221 =cut
 222
 223 sub register_factory{
 224    my ($self,@args) = @_;
 225    $self->throw_not_implemented();
 226 }
 227
 228
 229 =head2 factory
 230
 231  Title   : factory
 232  Usage   : my $f = $handler->factory('TYPE');
 233  Function: Retrieves the associated factory for requested 'TYPE'
 234  Returns : a Bio::Factory::ObjectFactoryI
 235  Throws  : Bio::Root::BadParameter if none registered for the supplied type
 236  Args    : name of factory class to retrieve
 237
 238 See L<Bio::Factory::ObjectFactoryI> for more information
 239
 240 =cut
 241
 242 sub factory{
 243    my ($self,@args) = @_;
 244    $self->throw_not_implemented();
 245 }
 246
 247
 248 =head2 Bio::Event::EventHandlerI methods
 249
 250 =cut
 251
 252 =head2 will_handle
 253
 254  Title   : will_handle
 255  Usage   : if( $handler->will_handle($event_type) ) { ... }
 256  Function: Tests if this event builder knows how to process a specific event
 257  Returns : boolean
 258  Args    : event type name
 259
 260
 261 =cut
 262
 263 =head2 SAX methods
 264
 265 See L<Bio::Event::EventHandlerI> for the additional SAX methods.
 266
 267 =cut
 268
 269
 270 1;