Raw content of Bio::TreeIO::TreeEventBuilder # $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;