Raw content of Bio::TreeIO
<![CDATA[# $Id: TreeIO.pm,v 1.11 2002/11/05 17:26:04 heikki Exp $
#
# BioPerl module for Bio::TreeIO
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::TreeIO - Parser for Tree files
=head1 SYNOPSIS
{
use Bio::TreeIO;
my $treeio = new Bio::TreeIO('-format' => 'newick',
'-file' => 'globin.dnd');
while( my $tree = $treeio->next_tree ) {
print "Tree is ", $tree->size, "\n";
}
}
=head1 DESCRIPTION
This is the driver module for Tree reading from data streams and
flatfiles. This is intended to be able to create Bio::Tree::TreeI
objects.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/MailList.shtml - About the mailing lists
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
email or the web:
bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
Describe contact details here
=head1 CONTRIBUTORS
Additional contributors names and emails here
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::TreeIO;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Root::IO;
use Bio::Event::EventGeneratorI;
use Bio::TreeIO::TreeEventBuilder;
use Bio::Factory::TreeFactoryI;
@ISA = qw(Bio::Root::Root Bio::Root::IO
Bio::Event::EventGeneratorI Bio::Factory::TreeFactoryI);
=head2 new
Title : new
Usage : my $obj = new Bio::TreeIO();
Function: Builds a new Bio::TreeIO object
Returns : Bio::TreeIO
Args :
=cut
sub new {
my($caller,@args) = @_;
my $class = ref($caller) || $caller;
# or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::TreeIO::(\S+)/ ) {
my ($self) = $class->SUPER::new(@args);
$self->_initialize(@args);
return $self;
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} ||
$class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
'newick';
$format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
return undef unless( $class->_load_format_module($format) );
return "Bio::TreeIO::$format"->new(@args);
}
}
=head2 next_tree
Title : next_tree
Usage : my $tree = $treeio->next_tree;
Function: Gets the next tree off the stream
Returns : Bio::Tree::TreeI or undef if no more trees
Args : none
=cut
sub next_tree{
my ($self) = @_;
$self->throw("Cannot call method next_tree on Bio::TreeIO object must use a subclass");
}
=head2 write_tree
Title : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI
=cut
sub write_tree{
my ($self,$tree) = @_;
$self->throw("Cannot call method write_tree on Bio::TreeIO object must use a subclass");
}
=head2 attach_EventHandler
Title : attach_EventHandler
Usage : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args : Bio::Event::EventHandlerI
=cut
sub attach_EventHandler{
my ($self,$handler) = @_;
return if( ! $handler );
if( ! $handler->isa('Bio::Event::EventHandlerI') ) {
$self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI');
}
$self->{'_handler'} = $handler;
return;
}
=head2 _eventHandler
Title : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : Bio::Event::EventHandlerI
Args : none
=cut
sub _eventHandler{
my ($self) = @_;
return $self->{'_handler'};
}
sub _initialize {
my($self, @args) = @_;
$self->{'_handler'} = undef;
# initialize the IO part
$self->_initialize_io(@args);
$self->attach_EventHandler(new Bio::TreeIO::TreeEventBuilder(-verbose => $self->verbose(), @args));
}
=head2 _load_format_module
Title : _load_format_module
Usage : *INTERNAL TreeIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
=cut
sub _load_format_module {
my ($self,$format) = @_;
my $module = "Bio::TreeIO::" . $format;
my $ok;
eval {
$ok = $self->_load_module($module);
};
if ( $@ ) {
print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the TreeIO system please see the TreeIO docs.
This includes ways of checking for formats at compile time, not run time
END
;
}
return $ok;
}
=head2 _guess_format
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
=cut
sub _guess_format {
my $class = shift;
return unless $_ = shift;
return 'newick' if /\.(dnd|newick|nh)$/i;
return 'nhx' if /\.(nhx)$/i;
return 'phyloxml' if /\.(xml)$/i;
}
sub DESTROY {
my $self = shift;
$self->close();
}
sub TIEHANDLE {
my $class = shift;
return bless {'treeio' => shift},$class;
}
sub READLINE {
my $self = shift;
return $self->{'treeio'}->next_tree() unless wantarray;
my (@list,$obj);
push @list,$obj while $obj = $self->{'treeio'}->next_tree();
return @list;
}
sub PRINT {
my $self = shift;
$self->{'treeio'}->write_tree(@_);
}
1;
]]>