Summary

Bio::TreeIO - Parser for Tree files

Package variables

Included modules

Inherit

Bio::Event::EventGeneratorI Bio::Factory::TreeFactoryI Bio::Root::IO Bio::Root::Root

Synopsis

  {
      use Bio::TreeIO;
      my $treeio = new Bio::TreeIO('-format' => 'newick',
  				   '-file'   => 'globin.dnd');
      while( my $tree = $treeio->next_tree ) {
  	  print "Tree is ", $tree->size, "\n";
      }
  }

Description

This is the driver module for Tree reading from data streams and
flatfiles. This is intended to be able to create Bio::Tree::TreeI
objects.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::TreeIO();
 Function: Builds a new Bio::TreeIO object 
 Returns : Bio::TreeIO
 Args    : a hash.  useful keys:
   -format : Specify the format of the file.  Supported formats:

     newick             Newick tree format
     nexus              Nexus tree format
     nhx                NHX tree format
     svggraph           SVG graphical representation of tree
     tabtree            ASCII text representation of tree
     lintree            lintree output format

 Title   : next_tree
 Usage   : my $tree = $treeio->next_tree;
 Function: Gets the next tree off the stream
 Returns : Bio::Tree::TreeI or undef if no more trees
 Args    : none

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : Bio::Tree::TreeI

 Title   : attach_EventHandler
 Usage   : $parser->attatch_EventHandler($handler)
 Function: Adds an event handler to listen for events
 Returns : none
 Args    : Bio::Event::EventHandlerI

 Title   : _eventHandler
 Usage   : private
 Function: Get the EventHandler
 Returns : Bio::Event::EventHandlerI
 Args    : none

 Title   : _load_format_module
 Usage   : *INTERNAL TreeIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :

 Title   : newline_each_node
 Usage   : $obj->newline_each_node($newval)
 Function: Get/set newline each node flag which is only applicable
           for writing tree formats for nhx and newick, will
           print a newline after each node or paren
 Returns : value of newline_each_node (boolean)
 Args    : on set, new value (a boolean or undef, optional)

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :

Methods code

sub new {

  my($caller,@args) = @_;
  my $class = ref($caller) || $caller;
    
    # or do we want to call SUPER on an object if $caller is an
    # object?
    if( $class =~ /Bio::TreeIO::(\S+)/ ) {
	my ($self) = $class->SUPER::new(@args);		
	$self->_initialize(@args);
	return $self;
    } else { 

	my %param = @args;
	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
	my $format = $param{'-format'} || 
	    $class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
	    'newick';
	$format = "\L$format";	# normalize capitalization to lower case
	
	# normalize capitalization
	return unless( $class->_load_format_module($format) );
	return "Bio::TreeIO::$format"->new(@args);
    }

}

sub next_tree {

   my ($self) = @_;
   $self->throw("Cannot call method next_tree on Bio::TreeIO object must use a subclass");

}

sub write_tree {

   my ($self,$tree) = @_;
   $self->throw("Cannot call method write_tree on Bio::TreeIO object must use a subclass");

}

sub attach_EventHandler {

    my ($self,$handler) = @_;
    return if( ! $handler );
    if( ! $handler->isa('Bio::Event::EventHandlerI') ) {
	$self->warn("Ignoring request to attatch handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI');
    }
    $self->{'_handler'} = $handler;
    return;

}

sub _eventHandler {

   my ($self) = @_;
   return $self->{'_handler'};

}

sub _initialize {

    my($self, @args) = @_;
    $self->{'_handler'} = undef;
    ($self->{'newline_each_node'}) = $self->_rearrange
	([qw(NEWLINE_EACH_NODE)],@args);
    
    # initialize the IO part
    $self->_initialize_io(@args);
    $self->attach_EventHandler(Bio::TreeIO::TreeEventBuilder->new
			       (-verbose => $self->verbose(), @args));

}

sub _load_format_module {

  my ($self,$format) = @_;
  my $module = "Bio::TreeIO::" . $format;
  my $ok;
  
  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END
$self: $format cannot be found
Exception $@
For more information about the TreeIO system please see the TreeIO docs.
This includes ways of checking for formats at compile time, not run time
END
  ;
  }
  return $ok;

}

sub newline_each_node {

    my $self = shift;
    return $self->{'newline_each_node'} = shift if @_;
    return $self->{'newline_each_node'};

}

sub _guess_format {

   my $class = shift;
   return unless $_ = shift;
   return 'newick'   if /\.(dnd|newick|nh)$/i;
   return 'nhx'   if /\.(nhx)$/i;
   return 'phyloxml' if /\.(xml)$/i;
   return 'svggraph' if /\.svg$/i;
   return 'lintree'  if( /\.(lin|lintree)$/i );

}

sub DESTROY {

    my $self = shift;

    $self->close();

}

sub TIEHANDLE {

  my $class = shift;
  return bless {'treeio' => shift},$class;

}

sub READLINE {

  my $self = shift;
  return $self->{'treeio'}->next_tree() unless wantarray;
  my (@list,$obj);
  push @list,$obj  while $obj = $self->{'treeio'}->next_tree();
  return @list;

}

sub PRINT {

  my $self = shift;
  $self->{'treeio'}->write_tree(@_);

}

General documentation

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

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:

  http://bugzilla.open-bio.org/

Email jason-at-bioperl-dot-org

Allen Day <allenday@ucla.edu>

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _