2 # BioPerl module for Bio::MapIO
4 # Please direct questions and support issues to <bioperl-l@bioperl.org>
6 # Cared for by Jason Stajich <jason@bioperl.org>
8 # Copyright Jason Stajich
10 # You may distribute this module under the same terms as perl itself
12 # POD documentation - main docs before the code
16 Bio::MapIO - A Map Factory object
21 my $mapio = Bio::MapIO->new(-format => "mapmaker",
22 -file => "mapfile.map");
24 while( my $map = $mapio->next_map ) {
26 foreach my $marker ( $map->each_element ) {
27 # loop through the markers associated with the map
33 This is the Factory object for reading Maps from a data stream or file.
39 User feedback is an integral part of the evolution of this and other
40 Bioperl modules. Send your comments and suggestions preferably to
41 the Bioperl mailing list. Your participation is much appreciated.
43 bioperl-l@bioperl.org - General discussion
44 http://bioperl.org/wiki/Mailing_lists - About the mailing lists
48 Please direct usage questions or support issues to the mailing list:
50 I<bioperl-l@bioperl.org>
52 rather than to the module maintainer directly. Many experienced and
53 reponsive experts will be able look at the problem and quickly
54 address it. Please include a thorough description of the problem
55 with code and data examples if at all possible.
59 Report bugs to the Bioperl bug tracking system to help us keep track
60 of the bugs and their resolution. Bug reports can be submitted the web:
62 https://redmine.open-bio.org/projects/bioperl/
64 =head1 AUTHOR - Jason Stajich
66 Email jason@bioperl.org
70 The rest of the documentation details each of the object methods.
71 Internal methods are usually preceded with a _
76 # Let the code begin...
83 use base
qw(Bio::Root::Root Bio::Root::IO Bio::Factory::MapFactoryI);
88 Usage : my $obj = Bio::MapIO->new();
89 Function: Builds a new Bio::MapIO object
97 my($caller,@args) = @_;
99 my $class = ref($caller) || $caller;
101 # or do we want to call SUPER on an object if $caller is an
103 if( $class =~ /Bio::MapIO::(\S+)/ ) {
104 my ($self) = $class->SUPER::new
(@args);
105 $self->_initialize(@args);
110 @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
111 my $format = $param{'-format'} ||
112 $class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
114 $format = "\L$format"; # normalize capitalization to lower case
116 # normalize capitalization
117 return unless( $class->_load_format_module($format) );
118 return "Bio::MapIO::$format"->new(@args);
123 =head2 Bio::Factory::MapFactoryI methods
130 Usage : my $map = $factory->next_map;
131 Function: Get a map from the factory
132 Returns : L<Bio::Map::MapI>
139 Usage : $factory->write_map($map);
140 Function: Write a map out through the factory
142 Args : L<Bio::Map::MapI>
147 =head2 attach_EventHandler
149 Title : attach_EventHandler
150 Usage : $parser->attatch_EventHandler($handler)
151 Function: Adds an event handler to listen for events
153 Args : L<Bio::Event::EventHandlerI>
157 sub attach_EventHandler
{
158 my ($self,$handler) = @_;
159 return if( ! $handler );
160 if( ! $handler->isa('Bio::Event::EventHandlerI') ) {
161 $self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI');
163 $self->{'_handler'} = $handler;
169 Title : _eventHandler
171 Function: Get the EventHandler
172 Returns : L<Bio::Event::EventHandlerI>
180 return $self->{'_handler'};
184 my($self, @args) = @_;
185 $self->{'_handler'} = undef;
187 # initialize the IO part
188 $self->_initialize_io(@args);
189 # $self->attach_EventHandler(Bio::MapIO::MapEventBuilder->new());
192 =head2 _load_format_module
194 Title : _load_format_module
195 Usage : *INTERNAL MapIO stuff*
196 Function: Loads up (like use) a module at run time on demand
203 sub _load_format_module
{
204 my ($self,$format) = @_;
205 my $module = "Bio::MapIO::" . $format;
208 $ok = $self->_load_module($module);
212 $self: $format cannot be found
214 For more information about the MapIO system please see the MapIO docs.
215 This includes ways of checking for formats at compile time, not run time
225 Title : _guess_format
226 Usage : $obj->_guess_format($filename)
229 Returns : guessed format of filename (lower case)
236 return unless $_ = shift;
237 return 'mapmaker' if /\.(map)$/i;
238 return 'mapxml' if /\.(xml)$/i;