File Coverage

Bio/TreeIO/NewickParser.pm

Criterion	Covered	Total	%
statement	115	121	95.0
branch	49	60	81.6
condition	5	6	83.3
subroutine	7	7	100.0
pod	0	2	0.0
total	176	196	89.8

# POD documentation - main docs before the code

=head1 NAME

Module which implements a newick string parser as a finite state
machine which enables it to parse the full Newick specification.

Taken largely from the Ensembl Compara file with the same name
(Bio::EnsEMBL::Compara::Graph::NewickParser), this module adapts the
parser to work with BioPerl's event handler-based parsing scheme.

This module is used by nhx.pm and newick.pm, and is NOT called
directly. Instead, both of those parsing modules extend this module in
order to gain access to the main parsing method.

=head1 SYNOPSIS

  # From newick.pm
  use base qw(Bio::TreeIO Bio::TreeIO::NewickParser);

  # in the next_tree method...
  $self->parse_newick($_);

=head1 DESCRIPTION

This module correctly parses the Newick and NHX formats, sending calls
to the BioPerl TreeEventHandler when appropriate in order to build and
populate the node 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.

  [e-mail]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

=head2 Support

Please direct usage questions or support issues to the mailing list:

I

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.

=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 the
web:

  https://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jessica Severin (EnsEMBL implementation), Greg Jordan (BioPerl adaptation)

=cut

package Bio::TreeIO::NewickParser;

use strict;
use base qw(Bio::Root::Root);

sub parse_newick {
  my $self = shift;
  my $newick = shift;

  $newick = $newick . ";" unless ($newick =~ m/;/);

  my $count=1;
  my $debug = $self->verbose;
  my $token = next_token(\$newick, "(;");
  my $state=1;
  my $bracket_level = 0;

  $self->_start('tree');

  my $leaf_flag = 0;

  while(defined($token)) {
    # backwards-compat. with 5.8.1, no Switch (but we hate if-elsif-ad-infinitum
    if ($state == 1) { #new node

        $self->_start('node');

        $self->debug("   -> [$token]\n");
        if($token eq '(') { #create new set
          $self->debug("    create set\n")  if($debug);
          $token = next_token(\$newick, "[(:,)");
          $state = 1;
          $bracket_level++;
        } else {
          $state = 2;
          $leaf_flag = 1;
        }
      } elsif ($state == 2) { #naming a node
        if(!($token =~ /[\[\:\,\)\;]/)) {

          if (!$leaf_flag && $self->param('internal_node_id') eq 'bootstrap') {
            $self->_start('bootstrap');
            $self->_chars($token);
            $self->_end('bootstrap');
            $token = '';
          }

          $self->_start('id');
          $self->_chars($token);
          $self->_end('id');

          $self->debug("    naming leaf\n") if ($debug);
          $token = next_token(\$newick, "[:,);");
        }
        $state = 3;
      } elsif ($state == 3) { # optional : and distance
        if($token eq ':') {
          $token = next_token(\$newick, "[,);");

          $self->_start('branch_length');
          $self->_chars($token);
          $self->_end('branch_length');

          $token = next_token(\$newick, ",);"); #move to , or )
        } elsif ($token eq '[') { # NHX tag without previous blength
          $token .= next_token(\$newick, ",);");
        }
        $state = 4;
      } elsif ($state == 4) { # optional NHX tags
        if($token =~ /\[\&\&NHX/) {
            # careful: this regexp gets rid of all NHX wrapping in one step

            $self->_start('nhx_tag');
            $token =~ /\[\&\&NHX\:(\S+)\]/;
            if ($1) {
                # NHX may be empty, presumably at end of file, just before ";"
                my @attributes = split ':', $1;
                foreach my $attribute (@attributes) {
                    $attribute =~ s/\s+//;
                    my($key,$value) = split '=', $attribute;

                    $self->_start('tag_name');
                    $self->_chars($key);
                    $self->_end('tag_name');

		    $self->_start('tag_value');
		    $self->_chars($value);
		    $self->_end('tag_value');
                  }
            }
            $self->_end('nhx_tag');

            $token = next_token(\$newick, ",);"); #move to , or )
        } elsif ($token =~ /\[/) {
            # This is a hack to make AMPHORA2 work
            if ($token =~ /\[(\S+)\]/) {
                $self->_start('bootstrap');
                $self->_chars($1);
                $self->_end('bootstrap');
             }
            $token = next_token(\$newick, ",);");        }
        $state = 5;
      } elsif ($state == 5) { # end node
        if($token eq ')') {

          $self->_end('node');

          $token = next_token(\$newick, "[:,);");
          if (defined $token && $token eq '[') {
            # It is possible to have anonymous internal nodes w/ no name
            # and no blength but with NHX tags
            #
            # We use leaf_flag=0 to let the parser know that it's labeling an internal
            # node. This affects how potential bootstrap values are handled in state 2.
            $leaf_flag = 0;
            $state = 2;
          } else {
            $leaf_flag = 0;
            $state = 2;
          }
          $bracket_level--;
        } elsif($token eq ',') {

          $self->_end('node');

          $token = next_token(\$newick, "[(:,)"); #can be un_blengthed nhx nodes
          $state=1;
        } elsif($token eq ';') {
          #done with tree
          $self->throw("parse error: unbalanced ()\n") if($bracket_level ne 0);

          $self->_end('node');
          $self->_end('tree');

          $token = next_token(\$newick, "(");
          $state=13;
        } else {
          $self->debug("[$token]]\n");
          $self->throw("parse error: expected ; or ) or ,\n");
        }
      } elsif ($state == 13) {
        $self->throw("parse error: nothing expected after ;");
      }
    }

  if ($self->_eventHandler->within_element('tree')) {
    $self->_end('node');
    $self->_end('tree');
  }
}

sub _chars {
  my $self = shift;
  my $chars = shift;

  $self->_eventHandler->characters($chars);
}

sub _start {
  my $self = shift;
  my $name = shift;

  $self->_eventHandler->start_element({Name=>$name});
}

sub _end {
  my $self = shift;
  my $name = shift;

  $self->_eventHandler->end_element({Name=>$name});
}

sub next_token {
  my $string = shift;
  my $delim = shift;

  $$string =~ s/^(\s)+//;

  return undef unless(length($$string));

  #print("input =>$$string\n");
  #print("delim =>$delim\n");
  my $index=undef;

  my @delims = split(/ */, $delim);
  foreach my $dl (@delims) {
    my $pos = index($$string, $dl);
    if($pos>=0) {
      $index = $pos unless(defined($index));
      $index = $pos if($pos<$index);
    }
  }
  unless(defined($index)) {
    # have to call as class here (this is not an instance method)
    Bio::Root::Root->throw("couldn't find delimiter $delim\n $$string");
  }

  my $token ='';

  if($index==0) {
    $token = substr($$string,0,1);
    $$string = substr($$string, 1);
  } else {
    $token = substr($$string, 0, $index);
    $$string = substr($$string, $index);
  }

  #print("  token     =>$token\n");
  #print("  outstring =>$$string\n\n");

  return $token;
}



1;