Bio::TreeIO TreeEventBuilder
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Summary
Bio::TreeIO::TreeEventBuilder - Build Bio::Tree::Tree's and
Bio::Tree::Node's from Events
Package variables
No package variables defined.
Included modules
Bio::Tree::Node
Bio::Tree::Tree
Inherit
Bio::Event::EventHandlerI Bio::Root::Root
Synopsis
# internal use only
Description
This object will take events and build a Bio::Tree::TreeI compliant
object makde up of Bio::Tree::NodeI objects.
Methods
newDescriptionCode
treetypeDescriptionCode
nodetypeDescriptionCode
start_documentDescriptionCode
end_documentDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
in_elementDescriptionCode
within_elementDescriptionCode
charactersDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::TreeIO::TreeEventBuilder->new();
Function: Builds a new Bio::TreeIO::TreeEventBuilder object
Returns : Bio::TreeIO::TreeEventBuilder
Args :
treetypecodeprevnextTop
 Title   : treetype
Usage : $obj->treetype($newval)
Function:
Returns : value of treetype
Args : newvalue (optional)
nodetypecodeprevnextTop
 Title   : nodetype
Usage : $obj->nodetype($newval)
Function:
Returns : value of nodetype
Args : newvalue (optional)
start_documentcodeprevnextTop
 Title   : start_document
Usage : $handler->start_document
Function: Begins a Tree event cycle
Returns : none
Args : none
end_documentcodeprevnextTop
 Title   : end_document
Usage : my @trees = $parser->end_document
Function: Finishes a Phylogeny cycle
Returns : An array Bio::Tree::TreeI
Args : none
start_elementcodeprevnextTop
 Title   : start_element
Usage :
Function:
Example :
Returns :
Args : $data => hashref with key 'Name'
end_elementcodeprevnextTop
 Title   : end_element
Usage :
Function:
Returns : none
Args : $data => hashref with key 'Name'
in_elementcodeprevnextTop
 Title   : in_element
Usage :
Function:
Example :
Returns :
Args :
within_elementcodeprevnextTop
 Title   : within_element
Usage :
Function:
Example :
Returns :
Args :
characterscodeprevnextTop
 Title   : characters
Usage : $handler->characters($text);
Function: Processes characters
Returns : none
Args : text string
Methods code
newdescriptionprevnextTop
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 $self;
}
treetypedescriptionprevnextTop
sub treetype {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'treetype'} = $value;
    }
    return $self->{'treetype'};
}
nodetypedescriptionprevnextTop
sub nodetype {
   my ($self,$value) = @_;
   if( defined $value) {
      $self->{'nodetype'} = $value;
    }
    return $self->{'nodetype'};
}
start_documentdescriptionprevnextTop
sub start_document {
   my ($self) = @_;   
   $self->{'_lastitem'} = {};
   $self->{'_currentitems'} = [];
   $self->{'_currentnodes'} = [];
   return;
}
end_documentdescriptionprevnextTop
sub end_document {
    my ($self,$label) = @_; 

    my ($root) = @{$self->{'_currentnodes'}};

    $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(-verbose => $self->verbose,
				    -root => $root);
    return $tree;
}
start_elementdescriptionprevnextTop
sub start_element {
   my ($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; 
       $self->{'_treelevel'}++;
   } elsif ( $data->{Name} eq 'tree' ) {
   }
}
end_elementdescriptionprevnextTop
sub end_element {
   my ($self,$data) = @_;   

   $self->debug("end of element: $data->{Name}\n");
   # this is the stack where we push/pop items from it
my $curcount = scalar @{$self->{'_currentnodes'}}; my $level = $self->{'_treelevel'}; my $levelct = $self->{'_nodect'}->[$self->{'_treelevel'}+1] || 0; if( $data->{'Name'} eq 'node' ) { my $tnode; my $node = pop @{$self->{'_currentitems'}}; $tnode = $self->nodetype->new( -verbose => $self->verbose, %{$node}); $self->debug( "new node will be ".$tnode->to_string."\n"); if ( !$node->{'-leaf'} && $levelct > 0) { $self->debug(join(',', map { $_->to_string } @{$self->{'_currentnodes'}}). "\n"); $self->throw("something wrong with event construction treelevel ". "$level is recorded as having $levelct nodes ". "but current nodes at this level is $curcount\n") if( $levelct > $curcount); for ( splice( @{$self->{'_currentnodes'}}, - $levelct)) { $self->debug("adding desc: " . $_->to_string . "\n"); $tnode->add_Descendent($_); } $self->{'_nodect'}->[$self->{'_treelevel'}+1] = 0; } push @{$self->{'_currentnodes'}}, $tnode; $self->{'_nodect'}->[$self->{'_treelevel'}]++; $curcount = scalar @{$self->{'_currentnodes'}}; $self->debug ("added node: count is now $curcount, treelevel: $level, nodect: $levelct\n"); $self->{'_treelevel'}--; } elsif( $data->{'Name'} eq 'tree' ) { $self->debug("end of tree: nodes in stack is $curcount\n"); } $self->{'_lastitem'}->{ $data->{'Name'} }--; pop @{$self->{'_lastitem'}->{'current'}};
}
in_elementdescriptionprevnextTop
sub in_element {
   my ($self,$e) = @_;

   return 0 if ! defined $self->{'_lastitem'} || 
       ! defined $self->{'_lastitem'}->{'current'}->[-1];
   return ($e eq $self->{'_lastitem'}->{'current'}->[-1]);
}
within_elementdescriptionprevnextTop
sub within_element {
   my ($self,$e) = @_;
   return $self->{'_lastitem'}->{$e};
}
charactersdescriptionprevnextTop
sub characters {
   my ($self,$ch) = @_;
   if( $self->within_element('node') ) {
       my $hash = pop @{$self->{'_currentitems'}};
       if( $self->in_element('bootstrap') ) {
	   # leading/trailing Whitespace-B-Gone
$ch =~ s/^\s+//; $ch =~ s/\s+$//; $hash->{'-bootstrap'} = $ch; } elsif( $self->in_element('branch_length') ) { # leading/trailing Whitespace-B-Gone
$ch =~ s/^\s+//; $ch =~ s/\s+$//; $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;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
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.
Reporting BugsTop
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 StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
SAX methodsTop