Bio TreeIO
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Summary
Bio::TreeIO - Parser for Tree files
Package variables
No package variables defined.
Included modules
Bio::TreeIO::TreeEventBuilder
Inherit
Bio::Event::EventGeneratorI Bio::Factory::TreeFactoryI Bio::Root::IO Bio::Root::Root
Synopsis
  {
use Bio::TreeIO;
my $treeio = Bio::TreeIO->new(-format => 'newick',
-file => 'globin.dnd');
while( my $tree = $treeio->next_tree ) {
print "Tree is ", $tree->number_nodes, "\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
newDescriptionCode
next_treeDescriptionCode
write_treeDescriptionCode
attach_EventHandlerDescriptionCode
_eventHandlerDescriptionCode
_initialize
No description
Code
_load_format_moduleDescriptionCode
param
No description
Code
set_param
No description
Code
params
No description
Code
get_params
No description
Code
set_params
No description
Code
get_default_params
No description
Code
debug_params
No description
Code
_guess_formatDescriptionCode
DESTROY
No description
Code
TIEHANDLE
No description
Code
READLINE
No description
Code
PRINT
No description
Code
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::TreeIO->new();
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
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
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
_eventHandlercodeprevnextTop
 Title   : _eventHandler
Usage : private
Function: Get the EventHandler
Returns : Bio::Event::EventHandlerI
Args : none
_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 :
_guess_formatcodeprevnextTop
 Title   : _guess_format
Usage : $obj->_guess_format($filename)
Function:
Example :
Returns : guessed format of filename (lower case)
Args :
Methods code
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?n
my $obj; if( $class =~ /Bio::TreeIO::(\S+)/ ) { $obj = $class->SUPER::new(@args); $obj->_initialize(@args); } 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) ); $obj = "Bio::TreeIO::$format"->new(@args); } return $obj;
}
next_treedescriptionprevnextTop
sub next_tree {
   my ($self) = @_;
   $self->throw("Cannot call method next_tree on Bio::TreeIO object must use a subclass");
}
write_treedescriptionprevnextTop
sub write_tree {
   my ($self,$tree) = @_;
   $self->throw("Cannot call method write_tree on Bio::TreeIO object must use a subclass");
}
attach_EventHandlerdescriptionprevnextTop
sub attach_EventHandler {
    my ($self,$handler) = @_;
    return if( ! $handler );
    if( ! $handler->isa('Bio::Event::EventHandlerI') ) {
    $self->warn("Ignoring request to attach handler ".ref($handler). ' because it is not a Bio::Event::EventHandlerI');
    }
    $self->{'_handler'} = $handler;
    return;
}
_eventHandlerdescriptionprevnextTop
sub _eventHandler {
   my ($self) = @_;
   return $self->{'_handler'};
}
_initializedescriptionprevnextTop
sub _initialize {
    my($self, @args) = @_;
    $self->{'_handler'} = undef;

    $self->get_params; # Initialize the default parameters.
my ($nen,$ini) = $self->_rearrange ([qw(NEWLINE_EACH_NODE INTERNAL_NODE_ID)],@args); $self->set_param('newline_each_node',$nen); $self->set_param('internal_node_id',$ini); $self->attach_EventHandler(Bio::TreeIO::TreeEventBuilder->new (-verbose => $self->verbose(), @args)); $self->_initialize_io(@args); #$self->debug_params;
}
_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;
}
paramdescriptionprevnextTop
sub param {
  my $self = shift;
  my $param = shift;
  my $value = shift;

  if (defined $value) {
    $self->get_params->{$param} = $value;
  }
  return $self->get_params->{$param};
}
set_paramdescriptionprevnextTop
sub set_param {
  my $self = shift;
  my $param = shift;
  my $value = shift;

  #print STDERR "[$param] -> [undef]\n" if (!defined $value);
return unless (defined $value); #print STDERR "[$param] -> [$value]\n";
$self->get_params->{$param} = $value; return $self->param($param);
}
paramsdescriptionprevnextTop
sub params {
  my $self = shift;
  return $self->get_params;
}
get_paramsdescriptionprevnextTop
sub get_params {
  my $self = shift;

  if (!defined $self->{_params}) {
    $self->{_params} = $self->get_default_params;
  }

  return $self->{_params};
}
set_paramsdescriptionprevnextTop
sub set_params {
  my $self = shift;
  my $params = shift;

  # Apply all the passed parameters to our internal parm hashref.
my $cur_params = $self->get_params; $self->{_params} = { %$cur_params, %$params }; return $self->get_params;
}
get_default_paramsdescriptionprevnextTop
sub get_default_params {
  my $self = shift;
  
  return {};
}
debug_paramsdescriptionprevnextTop
sub debug_params {
  my $self = shift;

  my $params = $self->get_params;

  print STDERR "{\n";
  foreach my $param (keys %$params) {
    my $value = $params->{$param};
    print STDERR "  [$param] -> [$value]\n";
  }
  print STDERR "}\n";
}
_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;
   return 'svggraph' if /\.svg$/i;
   return 'lintree'  if( /\.(lin|lintree)$/i );
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;

    $self->close();
}
TIEHANDLEdescriptionprevnextTop
sub TIEHANDLE {
  my $class = shift;
  return bless {'treeio' => shift},$class;
}
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;
}
PRINTdescriptionprevnextTop
sub PRINT {
  my $self = shift;
  $self->{'treeio'}->write_tree(@_);
}

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-dot-org
CONTRIBUTORSTop
Allen Day <allenday@ucla.edu>
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
formatTop
 Title   : format
Usage : $format = $obj->format()
Function: Get the tree format
Returns : tree format
Args : none