Bio TreeIO
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Summary
Bio::TreeIO - Parser for Tree files
Package variables
No package variables defined.
Included modules
Bio::Event::EventGeneratorI
Bio::Factory::TreeFactoryI
Bio::Root::IO
Bio::Root::Root
Bio::TreeIO::TreeEventBuilder
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
DESTROY
No description
Code
PRINT
No description
Code
READLINE
No description
Code
TIEHANDLE
No description
Code
_eventHandlerDescriptionCode
_guess_formatDescriptionCode
_initialize
No description
Code
_load_format_moduleDescriptionCode
attach_EventHandlerDescriptionCode
newDescriptionCode
next_treeDescriptionCode
write_treeDescriptionCode
Methods description
_eventHandlercode    nextTop
 Title   : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : Bio::Event::EventHandlerI
Args : none
_guess_formatcodeprevnextTop
 Title   : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
_load_format_modulecodeprevnextTop
 Title   : _load_format_module
Usage : *INTERNAL TreeIO stuff*
Function: Loads up (like use) a module at run time on demand
Example :
Returns :
Args :
attach_EventHandlercodeprevnextTop
 Title   : attach_EventHandler
Usage : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args : Bio::Event::EventHandlerI
newcodeprevnextTop
 Title   : new
Usage : my $obj = new Bio::TreeIO();
Function: Builds a new Bio::TreeIO object
Returns : Bio::TreeIO
Args :
next_treecodeprevnextTop
 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
write_treecodeprevnextTop
 Title   : write_tree
Usage : $treeio->write_tree($tree);
Function: Writes a tree onto the stream
Returns : none
Args : Bio::Tree::TreeI
Methods code
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;

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

1;
}
READLINEdescriptionprevnextTop
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;
}
TIEHANDLEdescriptionprevnextTop
sub TIEHANDLE {
  my $class = shift;
  return bless {'treeio' => shift},$class;
}
_eventHandlerdescriptionprevnextTop
sub _eventHandler {
   my ($self) = @_;
   return $self->{'_handler'};
}
_guess_formatdescriptionprevnextTop
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;
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;
    $self->{'_handler'} = undef;
    
    # initialize the IO part
$self->_initialize_io(@args); $self->attach_EventHandler(new Bio::TreeIO::TreeEventBuilder(-verbose => $self->verbose(), @args));
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($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 $ok;
}
attach_EventHandlerdescriptionprevnextTop
sub attach_EventHandler {
    my ($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'} = $handler;
    return;
}
newdescriptionprevnextTop
sub new {
  my($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 undef unless( $class->_load_format_module($format) ); return "Bio::TreeIO::$format"->new(@args); }
}
next_treedescriptionprevnextTop
sub next_tree {
   my ($self) = @_;
   $self->throw("Cannot call method next_tree on Bio::TreeIO object must use a subclass");
}
write_treedescriptionprevnextTop
sub write_tree {
   my ($self,$tree) = @_;
   $self->throw("Cannot call method write_tree on Bio::TreeIO object must use a subclass");
}
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/MailList.shtml - About the mailing lists
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
email or the web:
  bioperl-bugs@bioperl.org
http://bugzilla.bioperl.org/
AUTHOR - Jason StajichTop
Email jason@bioperl.org
Describe contact details here
CONTRIBUTORSTop
Additional contributors names and emails here
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _