Raw content of Bio::TreeIO::TreeEventBuilder
<![CDATA[# $Id: TreeEventBuilder.pm,v 1.11.2.1 2003/09/13 21:51:05 jason Exp $
#
# BioPerl module for Bio::TreeIO::TreeEventBuilder
#
# 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::TreeEventBuilder - Build Bio::Tree::Tree's and
Bio::Tree::Node's from Events
=head1 SYNOPSIS
# internal use only
=head1 DESCRIPTION
This object will take events and build a Bio::Tree::TreeI compliant
object makde up of Bio::Tree::NodeI 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::TreeEventBuilder;
use vars qw(@ISA);
use strict;
use Bio::Root::Root;
use Bio::Event::EventHandlerI;
use Bio::Tree::Tree;
use Bio::Tree::Node;
@ISA = qw(Bio::Root::Root Bio::Event::EventHandlerI);
=head2 new
Title : new
Usage : my $obj = new Bio::TreeIO::TreeEventBuilder();
Function: Builds a new Bio::TreeIO::TreeEventBuilder object
Returns : Bio::TreeIO::TreeEventBuilder
Args :
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($treetype, $nodetype) = $self->_rearrange([qw(TREETYPE
NODETYPE)], @args);
$treetype ||= 'Bio::Tree::Tree';
$nodetype ||= 'Bio::Tree::Node';
eval {
$self->_load_module($treetype);
$self->_load_module($nodetype);
};
if( $@ ) {
$self->throw("Could not load module $treetype or $nodetype. \n$@\n")
}
$self->treetype($treetype);
$self->nodetype($nodetype);
$self->{'_treelevel'} = 0;
return $self;
}
=head2 treetype
Title : treetype
Usage : $obj->treetype($newval)
Function:
Returns : value of treetype
Args : newvalue (optional)
=cut
sub treetype{
my ($self,$value) = @_;
if( defined $value) {
$self->{'treetype'} = $value;
}
return $self->{'treetype'};
}
=head2 nodetype
Title : nodetype
Usage : $obj->nodetype($newval)
Function:
Returns : value of nodetype
Args : newvalue (optional)
=cut
sub nodetype{
my ($self,$value) = @_;
if( defined $value) {
$self->{'nodetype'} = $value;
}
return $self->{'nodetype'};
}
=head2 SAX methods
=cut
=head2 start_document
Title : start_document
Usage : $handler->start_document
Function: Begins a Tree event cycle
Returns : none
Args : none
=cut
sub start_document {
my ($self) = @_;
$self->{'_lastitem'} = {};
$self->{'_currentitems'} = [];
$self->{'_currentnodes'} = [];
return;
}
=head2 end_document
Title : end_document
Usage : my @trees = $parser->end_document
Function: Finishes a Phylogeny cycle
Returns : An array Bio::Tree::TreeI
Args : none
=cut
sub end_document {
my ($self) = @_;
my $vb = $self->verbose;
my $root = $self->nodetype->new(-verbose => $vb);
# aggregate the nodes into trees basically ad-hoc.
while ( @{$self->{'_currentnodes'}} ) {
my ($node) = ( shift @{$self->{'_currentnodes'}});
$root->add_Descendent($node);
}
$self->debug("Root node is " . $root->to_string()."\n");
if( $self->verbose > 0 ) {
foreach my $node ( $root->get_Descendents ) {
$self->debug("node is ". $node->to_string(). "\n");
}
}
my $tree = $self->treetype->new(-root => $root,
-verbose => $vb);
return $tree;
}
=head2 start_element
Title : start_element
Usage :
Function:
Example :
Returns :
Args : $data => hashref with key 'Name'
=cut
sub start_element{
my ($self,$data) =@_;
$self->{'_lastitem'}->{$data->{'Name'}}++;
$self->debug("starting element: $data->{Name}\n");
push @{$self->{'_lastitem'}->{'current'}},$data->{'Name'};
my %data;
if( $data->{'Name'} eq 'node' ) {
push @{$self->{'_currentitems'}}, \%data;
} elsif ( $data->{Name} eq 'tree' ) {
$self->{'_treelevel'}++;
}
}
=head2 end_element
Title : end_element
Usage :
Function:
Returns : none
Args : $data => hashref with key 'Name'
=cut
sub end_element{
my ($self,$data) = @_;
$self->debug("end of element: $data->{Name}\n");
if( $data->{'Name'} eq 'node' ) {
my $tnode;
my $node = pop @{$self->{'_currentitems'}};
$tnode = $self->nodetype->new(-verbose => $self->verbose,
%{$node});
unless ( $node->{'-leaf'} ) {
for ( splice( @{$self->{'_currentnodes'}},
- $self->{'_nodect'}->[$self->{'_treelevel'}+1])) {
$self->debug("adding desc: " . $_->to_string . "\n");
$tnode->add_Descendent($_);
}
$self->{_nodect}->[$self->{_treelevel}+1] = 0;
}
push @{$self->{'_currentnodes'}}, $tnode;
$self->{_nodect}->[$self->{'_treelevel'}]++;
$self->debug ("added node: nodes in stack is ". scalar @{$self->{'_currentnodes'}} . ", treelevel: $self->{_treelevel}, nodect: $self->{_nodect}->[$self->{_treelevel}]\n");
} elsif( $data->{'Name'} eq 'tree' ) {
$self->debug("end of tree: nodes in stack is ". scalar @{$self->{'_currentnodes'}}. "\n");
$self->{'_treelevel'}--;
}
$self->{'_lastitem'}->{ $data->{'Name'} }--;
pop @{$self->{'_lastitem'}->{'current'}};
}
=head2 in_element
Title : in_element
Usage :
Function:
Example :
Returns :
Args :
=cut
sub in_element{
my ($self,$e) = @_;
return 0 if ! defined $self->{'_lastitem'} ||
! defined $self->{'_lastitem'}->{'current'}->[-1];
return ($e eq $self->{'_lastitem'}->{'current'}->[-1]);
}
=head2 within_element
Title : within_element
Usage :
Function:
Example :
Returns :
Args :
=cut
sub within_element{
my ($self,$e) = @_;
return $self->{'_lastitem'}->{$e};
}
=head2 characters
Title : characters
Usage : $handler->characters($text);
Function: Processes characters
Returns : none
Args : text string
=cut
sub characters{
my ($self,$ch) = @_;
if( $self->within_element('node') ) {
my $hash = pop @{$self->{'_currentitems'}};
if( $self->in_element('bootstrap') ) {
$hash->{'-bootstrap'} = $ch;
} elsif( $self->in_element('branch_length') ) {
$hash->{'-branch_length'} = $ch;
} elsif( $self->in_element('id') ) {
$hash->{'-id'} = $ch;
} elsif( $self->in_element('description') ) {
$hash->{'-desc'} = $ch;
} elsif ( $self->in_element('tag_name') ) {
$hash->{'-NHXtagname'} = $ch;
} elsif ( $self->in_element('tag_value') ) {
$hash->{'-nhx'}->{$hash->{'-NHXtagname'}} = $ch;
delete $hash->{'-NHXtagname'};
} elsif( $self->in_element('leaf') ) {
$hash->{'-leaf'} = $ch;
}
push @{$self->{'_currentitems'}}, $hash;
}
$self->debug("chars: $ch\n");
}
1;
]]>