Raw content of Bio::TreeIO::newick # $Id: newick.pm,v 1.13.2.4 2003/09/14 19:00:35 jason Exp $ # # BioPerl module for Bio::TreeIO::newick # # 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::newick - TreeIO implementation for parsing Newick/New Hampshire/PHYLIP format. =head1 SYNOPSIS # do not use this module directly use Bio::TreeIO; my $treeio = new Bio::TreeIO(-format => 'newick', -file => 't/data/LOAD_Ccd1.dnd'); my $tree = $treeio->next_tree; =head1 DESCRIPTION This module handles parsing and writing of Newick/PHYLIP/New Hampshire format. =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::newick; use vars qw(@ISA); use strict; # Object preamble - inherits from Bio::Root::Root use Bio::TreeIO; use Bio::Event::EventGeneratorI; #use XML::Handler::Subs; @ISA = qw(Bio::TreeIO ); =head2 next_tree Title : next_tree Usage : my $tree = $treeio->next_tree Function: Gets the next tree in the stream Returns : Bio::Tree::TreeI Args : none =cut sub next_tree{ my ($self) = @_; local $/ = ";\n"; return unless $_ = $self->_readline; # s/\s+//g; my $despace = sub {my $dirty = shift; $dirty =~ s/\s+//gs; return $dirty}; my $dequote = sub {my $dirty = shift; $dirty =~ s/^"?\s*(.+?)\s*"?$/$1/; return $dirty}; s/([^"]*)(".+?")([^"]*)/$despace->($1) . $dequote->($2) . $despace->($3)/egsx; $self->debug("entry is $_\n"); # my $empty = chr(20); # replace empty labels with a tag # s/\(,/\($empty,/ig; # s/,,/,$empty,/ig; # s/,,/,/ig; # s/,\)/,$empty\)/ig; # s/\"/\'/ig; my $chars = ''; $self->_eventHandler->start_document; my ($prev_event,$lastevent,$id) = ('','',''); foreach my $ch ( split(//,$_) ) { if( $ch eq ';' ) { return $self->_eventHandler->end_document; } elsif( $ch eq '(' ) { $chars = ''; $self->_eventHandler->start_element( {'Name' => 'tree'} ); } elsif($ch eq ')' ) { if( length $chars ) { if( $lastevent eq ':' ) { $self->_eventHandler->start_element( { 'Name' => 'branch_length'}); $self->_eventHandler->characters($chars); $self->_eventHandler->end_element( {'Name' => 'branch_length'}); $lastevent = $prev_event; } else { $self->debug("id with no branchlength is $chars\n"); $self->_eventHandler->start_element( { 'Name' => 'node' } ); $self->_eventHandler->start_element( { 'Name' => 'id' } ); $self->_eventHandler->characters($chars); $self->_eventHandler->end_element( { 'Name' => 'id' } ); $id = $chars; } my $leafstatus = 0; if( $lastevent ne ')' ) { $leafstatus = 1; } $self->_eventHandler->start_element({'Name' => 'leaf'}); $self->_eventHandler->characters($leafstatus); $self->_eventHandler->end_element({'Name' => 'leaf'}); $id = ''; } else { $self->_eventHandler->start_element( {'Name' => 'node'} ); } $self->_eventHandler->end_element( {'Name' => 'node'} ); $self->_eventHandler->end_element( {'Name' => 'tree'} ); $chars = ''; } elsif ( $ch eq ',' ) { if( $chars ) { if( $lastevent eq ':' ) { $self->_eventHandler->start_element( { 'Name' => 'branch_length'}); $self->_eventHandler->characters($chars); $self->_eventHandler->end_element( {'Name' => 'branch_length'}); $lastevent = $prev_event; $chars = ''; } else { $self->debug("id with no branchlength is $chars\n"); $self->_eventHandler->start_element( { 'Name' => 'node' } ); $self->_eventHandler->start_element( { 'Name' => 'id' } ); $self->_eventHandler->characters($chars); $self->_eventHandler->end_element( { 'Name' => 'id' } ); $id = $chars; } } else { $self->_eventHandler->start_element( { 'Name' => 'node' } ); } my $leafstatus = ( $lastevent ne ')' ) ? 1 : 0; $self->_eventHandler->start_element({'Name' => 'leaf'}); $self->_eventHandler->characters($leafstatus); $self->_eventHandler->end_element({'Name' => 'leaf'}); $self->_eventHandler->end_element( {'Name' => 'node'} ); $chars = ''; $id = ''; } elsif( $ch eq ':' ) { $self->debug("id with a branchlength coming is $chars\n"); $self->_eventHandler->start_element( { 'Name' => 'node' } ); $self->_eventHandler->start_element( { 'Name' => 'id' } ); $self->_eventHandler->characters($chars); $self->_eventHandler->end_element( { 'Name' => 'id' } ); $id = $chars; $chars = ''; } else { $chars .= $ch; next; } $prev_event = $lastevent; $lastevent = $ch; } return undef; } =head2 write_tree Title : write_tree Usage : $treeio->write_tree($tree); Function: Write a tree out to data stream in newick/phylip format Returns : none Args : Bio::Tree::TreeI object =cut sub write_tree{ my ($self,@trees) = @_; foreach my $tree( @trees ) { my @data = _write_tree_Helper($tree->get_root_node); if($data[-1] !~ /\)$/ ) { $data[0] = "(".$data[0]; $data[-1] .= ")"; } $self->_print(join(',', @data), ";\n"); } $self->flush if $self->_flush_on_write && defined $self->_fh; return; } sub _write_tree_Helper { my ($node) = @_; return () if (!defined $node); my @data; foreach my $n ( $node->each_Descendent() ) { push @data, _write_tree_Helper($n); } if( @data > 1 ) { $data[0] = "(" . $data[0]; $data[-1] .= ")"; # let's explicitly write out the bootstrap if we've got it my $b; if( defined ($b = $node->bootstrap) ) { $data[-1] .= $b; } elsif( defined ($b = $node->id) ) { $data[-1] .= $b; } $data[-1] .= ":". $node->branch_length if( $node->branch_length); } else { if( defined $node->id || defined $node->branch_length ) { push @data, sprintf("%s%s", defined $node->id ? $node->id : '', defined $node->branch_length ? ":" . $node->branch_length : ''); } } return @data; } 1;