Bio
TreeIO
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Summary
Bio::TreeIO - Parser for Tree files
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
{
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'newick',
-file => 'globin.dnd');
while( my $tree = $treeio->next_tree ) {
print "Tree is ", $tree->number_nodes, "\n";
}
}
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.
Methods
Methods description
Title : new
Usage : my $obj = Bio::TreeIO->new();
Function: Builds a new Bio::TreeIO object
Returns : Bio::TreeIO
Args : a hash. useful keys:
-format : Specify the format of the file. Supported formats:
newick Newick tree format
nexus Nexus tree format
nhx NHX tree format
svggraph SVG graphical representation of tree
tabtree ASCII text representation of tree
lintree lintree output format |
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 |
Title : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI |
Title : attach_EventHandler
Usage : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args : Bio::Event::EventHandlerI |
Title : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : Bio::Event::EventHandlerI
Args : none |
Title : _load_format_module
Usage : *INTERNAL TreeIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args : |
Title : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args : |
Methods code
sub new
{ my($caller,@args) = @_;
my $class = ref($caller) || $caller;
my $obj;
if( $class =~ /Bio::TreeIO::(\S+)/ ) {
$obj = $class->SUPER::new(@args);
$obj->_initialize(@args);
} else {
my %param = @args;
@param{ map { lc $_ } keys %param } = values %param;
my $format = $param{'-format'} ||
$class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
'newick';
$format = "\L$format";
return undef unless( $class->_load_format_module($format) );
$obj = "Bio::TreeIO::$format"->new(@args);
}
return $obj;} | sub next_tree
{ my ($self) = @_;
$self->throw("Cannot call method next_tree on Bio::TreeIO object must use a subclass");} | sub write_tree
{ my ($self,$tree) = @_;
$self->throw("Cannot call method write_tree on Bio::TreeIO object must use a subclass");} | sub attach_EventHandler
{ my ($self,$handler) = @_;
return if( ! $handler );
if( ! $handler->isa('Bio::Event::EventHandlerI') ) {
$self->warn("Ignoring request to attach handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI');
}
$self->{'_handler'} = $handler;
return;} | sub _eventHandler
{ my ($self) = @_;
return $self->{'_handler'};} | sub _initialize
{ my($self, @args) = @_;
$self->{'_handler'} = undef;
$self->get_params;
my ($nen,$ini) = $self->_rearrange
([qw(NEWLINE_EACH_NODE INTERNAL_NODE_ID)],@args);
$self->set_param('newline_each_node',$nen);
$self->set_param('internal_node_id',$ini);
$self->attach_EventHandler(Bio::TreeIO::TreeEventBuilder->new
(-verbose => $self->verbose(), @args));
$self->_initialize_io(@args);
} | sub _load_format_module
{ my ($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;} | sub param
{ my $self = shift;
my $param = shift;
my $value = shift;
if (defined $value) {
$self->get_params->{$param} = $value;
}
return $self->get_params->{$param};} | sub set_param
{ my $self = shift;
my $param = shift;
my $value = shift;
return unless (defined $value);
$self->get_params->{$param} = $value;
return $self->param($param); } | sub params
{ my $self = shift;
return $self->get_params; } | sub get_params
{ my $self = shift;
if (!defined $self->{_params}) {
$self->{_params} = $self->get_default_params;
}
return $self->{_params};} | sub set_params
{ my $self = shift;
my $params = shift;
my $cur_params = $self->get_params;
$self->{_params} = { %$cur_params, %$params };
return $self->get_params; } | sub get_default_params
{ my $self = shift;
return {};} | sub debug_params
{ my $self = shift;
my $params = $self->get_params;
print STDERR "{\n";
foreach my $param (keys %$params) {
my $value = $params->{$param};
print STDERR " [$param] -> [$value]\n";
}
print STDERR "}\n";} | 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;
return 'svggraph' if /\.svg$/i;
return 'lintree' if( /\.(lin|lintree)$/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;} | General documentation
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/wiki/Mailing_lists - About the mailing lists
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
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 the
web:
https://redmine.open-bio.org/projects/bioperl/
| AUTHOR - Jason Stajich | Top |
Email jason-at-bioperl-dot-org
Allen Day <allenday@ucla.edu>
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : format
Usage : $format = $obj->format()
Function: Get the tree format
Returns : tree format
Args : none