Bio::Structure Entry
SummaryIncluded librariesPackage variablesSynopsisDescriptionGeneral documentationMethods
Summary
Bio::Structure::Entry - Bioperl structure Object, describes the whole entry
Package variables
No package variables defined.
Included modules
Bio::Annotation::Collection
Bio::Root::Root
Bio::Structure::Chain
Bio::Structure::Model
Bio::Structure::StructureI
Tie::RefHash
Inherit
Bio::Root::Root Bio::Structure::StructureI
Synopsis
  #add synopsis here
Description
This object stores a whole Bio::Structure entry. It can consist of one or
more models (Bio::Structure::Model), which in turn consist of one or more
chains (Bio::Structure::Chain). A chain is composed of residues
(Bio::Structure::Residue) and a residue consists of atoms (Bio::Structure::Atom)
If no specific model or chain is chosen, the first one is choosen.
Methods
newDescriptionCode
modelDescriptionCode
add_modelDescriptionCode
get_modelsDescriptionCode
idDescriptionCode
chainDescriptionCode
add_chainDescriptionCode
get_chainsDescriptionCode
residueDescriptionCode
add_residueDescriptionCode
get_residuesDescriptionCode
add_atomDescriptionCode
get_atomsDescriptionCode
conectDescriptionCode
get_all_conect_sourceDescriptionCode
masterDescriptionCode
seqresDescriptionCode
get_atom_by_serialDescriptionCode
parentDescriptionCode
DESTROY
No description
Code
annotationDescriptionCode
_remove_modelsDescriptionCode
_create_default_modelDescriptionCode
_create_default_chainDescriptionCode
_parentDescriptionCode
_childDescriptionCode
_remove_from_graphDescriptionCode
_print_stats_pc
No description
Code
Methods description
new()code    nextTop
 Title   : new()
 Usage   : $struc = Bio::Structure::Entry->new( 
                                           -id  => 'structure_id',
                                           );

 Function: Returns a new Bio::Structure::Entry object from basic 
	constructors. Probably most called from Bio::Structure::IO.
 Returns : a new Bio::Structure::Model object
model()codeprevnextTop
 Title   : model
 Function: Connects a (or a list of) Model objects to a Bio::Structure::Entry.
 	To add a Model (and keep the existing ones) use add_model()
 	It returns a list of Model objects.
 Returns : list of Bio::Structure::Model objects
 Args    : One Model or a reference to an array of Model objects
add_model()codeprevnextTop
 Title   : add_model
 Usage   : $structure->add_model($model);
 Function: Adds a (or a list of) Model objects to a Bio::Structure::Entry.
 Returns : 
 Args    : One Model or a reference to an array of Model objects
get_models()codeprevnextTop
 Title   : get_models
 Usage   : $structure->get_models($structure);
 Function: general get method for models attached to an Entry
 Returns : a list of models attached to this entry
 Args    : an Entry
id()codeprevnextTop
 Title   : id
 Usage   : $entry->id("identity");
 Function: Gets/sets the ID 
 Returns : 
 Args    :
chain()codeprevnextTop
 Title   : chain
 Usage   : @chains  = $structure->chain($chain);
 Function: Connects a (or a list of) Chain objects to a Bio::Structure::Entry.
 Returns : list of Bio::Structure::Residue objects
 Args    : One Residue or a reference to an array of Residue objects
add_chain()codeprevnextTop
 Title   : add_chain
 Usage   : @chains  = $structure->add_chain($add_chain);
 Function: Adds a (or a list of) Chain objects to a Bio::Structure::Entry.
 Returns : 
 Args    :
get_chains()codeprevnextTop
 Title   : get_chains
 Usage   : $entry->get_chains($model);
 Function: general get method for chains attached to a Model
 Returns : a list of chains attached to this model
 Args    : a Model
residue()codeprevnextTop
 Title   : residue
 Usage   : @residues  = $structure->residue($residue);
 Function: Connects a (or a list of) Residue objects to a Bio::Structure::Entry.
 Returns : list of Bio::Structure::Residue objects
 Args    : One Residue or a reference to an array of Residue objects
add_residue()codeprevnextTop
 Title   : add_residue
 Usage   : @residues  = $structure->add_residue($residue);
 Function: Adds a (or a list of) Residue objects to a Bio::Structure::Entry.
 Returns : list of Bio::Structure::Residue objects
 Args    : One Residue or a reference to an array of Residue objects
get_residues()codeprevnextTop
 Title   : get_residues
 Usage   : $structure->get_residues($chain);
 Function: general get method for residues attached to a Chain
 Returns : a list of residues attached to this chain
 Args    : a chain
add_atom()codeprevnextTop
 Title   : add_atom
 Usage   : @atoms  = $structure->add_atom($residue,$atom);
 Function: Adds a (or a list of) Atom objects to a Bio::Structure::Residue.
 Returns : list of Bio::Structure::Atom objects
 Args    : a residue and an atom
get_atoms()codeprevnextTop
 Title   : get_atoms
 Usage   : $structure->get_atoms($residue);
 Function: general get method for atoms attached to a Residue
 Returns : a list of atoms attached to this residue
 Args    : a residue
conect()codeprevnextTop
 Title   : conect
 Usage   : $structure->conect($source);
 Function: get/set method for conect
 Returns : a list of serial numbers for atoms connected to source
 	(together with $entry->get_atom_by_serial($model, $serial) this should be OK for now)
 Args    : the serial number for the source atom
get_all_conect_source()codeprevnextTop
 Title   : get_all_conect_source
 Usage   : @sources = $structure->get_all_conect_source;
 Function: get all the sources for the conect records
 Returns : a list of serial numbers for atoms connected to source
 	(together with $entry->get_atom_by_serial($model, $serial) this should be OK for now)
 Args    : 
 Description : This is a bit of a kludge, but it's the best for now. Conect info might need
 	to go in a sepearte object
master()codeprevnextTop
 Title   : master
 Usage   : $structure->master($source);
 Function: get/set method for master
 Returns : the master line
 Args    : the master line for this entry
seqres()codeprevnextTop
 Title   : seqres
 Usage   : $seqobj = $structure->seqres("A");
 Function: gets a sequence object containing the sequence from the SEQRES record.
 	    if a chain-ID is given , the sequence for this chain is given, if none
	    is provided the first chain is choosen
 Returns : a Bio::PrimarySeq
 Args    : the chain-ID of the chain you want the sequence from
get_atom_by_serial()codeprevnextTop
 Title   : get_atom_by_serial
 Usage   : $structure->get_atom_by_serial($module, $serial);
 Function: get the Atom for a  for get_atom_by_serial
 Returns : the Atom object with this serial number in the model
 Args    : Model on which to work, serial number for atom
 	(if only a number is supplied, the first model is chosen)
parent()codeprevnextTop
 Title   : parent
 Usage   : $structure->parent($residue);
 Function: returns the parent of the argument
 Returns : the parent of the argument
 Args    : a Bio::Structure object
annotationcodeprevnextTop
 Title   : annotation
 Usage   : $obj->annotation($seq_obj)
 Function:
 Example :
 Returns : value of annotation
 Args    : newvalue (optional)
_remove_models()codeprevnextTop
 Title   : _remove_models
 Usage   : 
 Function: Removes the models attached to an Entry. Tells the models they
 	don't belong to this Entry any more
 Returns : 
 Args    :
_create_default_model()codeprevnextTop
 Title   : _create_default_model
 Usage   : 
 Function: Creates a default Model for this Entry. Typical situation
 	in an X-ray structure where there is only one model
 Returns : 
 Args    :
_create_default_chain()codeprevnextTop
 Title   : _create_default_chain
 Usage   : 
 Function: Creates a default Chain for this Model. Typical situation
 	in an X-ray structure where there is only one chain
 Returns : 
 Args    :
_parent()codeprevnextTop
 Title   : _parent
 Usage   : This is an internal function only. It is used to have one 
 	place that keeps track of which object has which other object 
	as parent. Thus allowing the underlying modules (Atom, Residue,...)
	to have no knowledge about all this (and thus removing the possibility
	of reference cycles).
	This method hides the details of manipulating references to an anonymous
	hash.
 Function: To get/set an objects parent 
 Returns : a reference to the parent if it exist, undef otherwise. In the 
 	current implementation each node should have a parent (except Entry).
 Args    :
_child()codeprevnextTop
 Title   : _child
 Usage   : This is an internal function only. It is used to have one 
 	place that keeps track of which object has which other object 
	as child. Thus allowing the underlying modules (Atom, Residue,...)
	to have no knowledge about all this (and thus removing the possibility
	to have no knowledge about all this (and thus removing the possibility
	of reference cycles).
	This method hides the details of manipulating references to an anonymous
	hash.
 Function: To get/set an object's child(ren) 
 Returns : a reference to an array of child(ren) if it exist, undef otherwise. 
 Args    :
_remove_from_graph()codeprevnextTop
 Title   : _remove_from_graph
 Usage   : This is an internal function only. It is used to remove from
 	the parent/child graph. We only remove the links from object to
	his parent. Not the ones from object to its children.
 Function: To remove an object from the parent/child graph
 Returns : 
 Args    : the object to be orphaned
Methods code
newdescriptionprevnextTop
sub new {
    my ($class, @args) = @_;
    my $self = $class->SUPER::new(@args);

    my($id, $model, $chain, $residue ) =
        $self->_rearrange([qw(
			      ID
			      MODEL
			      CHAIN
			      RESIDUE
                              )],
                          @args);

    # where to store parent->child relations (1 -> 1..n)
# value to this hash will be an array ref
# by using Tie::RefHash we can store references in this hash
$self->{'p_c'} = (); tie %{ $self->{'p_c'} } , "Tie::RefHash"; # where to store child->parent relations (1 -> 1)
$self->{'c_p'} = (); tie %{ $self->{'c_p'} } , "Tie::RefHash"; $id && $self->id($id); $self->{'model'} = []; $model && $self->model($model); if($chain) { if ( ! defined($self->model) ) { # no model yet, create default one
$self->_create_default_model; } for my $m ($self->model) { # add this chain on all models
$m->chain($chain); } } $residue && $self->residue($residue); # taken from Bio::Seq (or should we just inherit Bio::Seq and override some methods)
my $ann = Bio::Annotation::Collection->new; $self->annotation($ann); return $self;
}
modeldescriptionprevnextTop
sub model {
	my ($self, $model) = @_;
	
	if( defined $model) {
		if( (ref($model) eq "ARRAY") ||
		      ($model->isa('Bio::Structure::Model')) ) {
			# remove existing ones, tell they've become orphan
my @obj = $self->model; if (@obj) { for my $m (@obj) { $self->_remove_from_graph($m); $self->{'model'} = []; } } # add the new ones
$self->add_model($self,$model); } else { $self->throw("Supplied a $model to model, we want a Bio::Structure::Model or a list of these\n"); } } # give back list of models via general get method
$self->get_models($self);
}
add_modeldescriptionprevnextTop
sub add_model {
	my($self,$entry,$model) = @_;

	# if only one argument and it's a model, change evrything one place
# this is for people calling $entry->add_model($model);
if ( !defined $model && ref($entry) =~ /^Bio::Structure::Model/) { $model = $entry; $entry = $self; } # $self and $entry are the same here, but it's used for uniformicity
if ( !defined($entry) || ref($entry) !~ /^Bio::Structure::Entry/) { $self->throw("first argument to add_model needs to be a Bio::Structure::Entry object\n"); } if (defined $model) { if (ref($model) eq "ARRAY") { # if the user passed in a reference to an array
for my $m ( @{$model} ) { if( ! $m->isa('Bio::Structure::Model') ) { $self->throw("$m is not a Model\n"); } if ( $self->_parent($m) ) { $self->throw("$m already assigned to a parent\n"); } push @{$self->{'model'}}, $m; # create a stringified version of our ref
# not used untill we get symbolic ref working
#my $str_ref = "$self";
#$m->_grandparent($str_ref);
} } elsif ( $model->isa('Bio::Structure::Model') ) { if ( $self->_parent($model) ) { # already assigned to a parent
$self->throw("$model already assigned\n"); } push @{$self->{'model'}}, $model; # create a stringified version of our ref
#my $str_ref = "$self";
#$model->_grandparent($str_ref);
} else { $self->throw("Supplied a $model to add_model, we want a Model or list of Models\n"); } } my $array_ref = $self->{'model'}; return $array_ref ? @{$array_ref} : ();
}
get_modelsdescriptionprevnextTop
sub get_models {
	my ($self, $entry) = @_;

	# self and entry can be the same
if ( !defined $entry) { $entry = $self; } # pass through to add_model
$self->add_model($entry);
}
iddescriptionprevnextTop
sub id {
	my ($self, $value) = @_;
	if (defined $value) {
		$self->{'id'} = $value;
	}
	return $self->{'id'};
}
chaindescriptionprevnextTop
sub chain {
	my ($self, $chain) = @_;

	if ( ! $self->model ) {
		$self->_create_default_model;
	}
	my @models = $self->model;
	my $first_model = $models[0];

	if ( defined $chain) {
	
		if( (ref($chain) eq "ARRAY") ||
		      ($chain->isa('Bio::Structure::Chain')) ) {
			# remove existing ones, tell they've become orphan
my @obj = $self->get_chains($first_model); if (@obj) { for my $c (@obj) { $self->_remove_from_graph($c); } } # add the new ones
$self->add_chain($first_model,$chain); } else { $self->throw("Supplied a $chain to chain, we want a Bio::Structure::Chain or a list of these\n"); } } $self->get_chains($first_model);
}
add_chaindescriptionprevnextTop
sub add_chain {
	my($self, $model, $chain) = @_;

	if (ref($model) !~ /^Bio::Structure::Model/) {
		$self->throw("add_chain: first argument needs to be a Model object ($model)\n");
	}
	if (defined $chain) {
		if (ref($chain) eq "ARRAY") {
    			# if the user passed in a reference to an array
for my $c ( @{$chain} ) { if( ! $c->isa('Bio::Structure::Chain') ) { $self->throw("$c is not a Chain\n"); } if ( $self->_parent($c) ) { $self->throw("$c already assigned to a parent\n"); } $self->_parent($c, $model); $self->_child($model, $c); # stringify $self ref
#my $str_ref = "$self";
#$c->_grandparent($str_ref);
} } elsif ( $chain->isa('Bio::Structure::Chain') ) { if ( $self->_parent($chain) ) { # already assigned to parent
$self->throw("$chain already assigned to a parent\n"); } $self->_parent($chain,$model); $self->_child($model, $chain); # stringify $self ref
#my $str_ref = "$self";
#$chain->_grandparent($str_ref);
} else { $self->throw("Supplied a $chain to add_chain, we want a Chain or list of Chains\n"); } } my $array_ref = $self->_child($model); return $array_ref ? @{$array_ref} : ();
}
get_chainsdescriptionprevnextTop
sub get_chains {
	my ($self, $model) = @_;

	if (! defined $model) {
		$model = ($self->get_models)[0];
	}
	# pass through to add_chain
$self->add_chain($model);
}
residuedescriptionprevnextTop
sub residue {
	my ($self, $residue) = @_;

	if ( ! $self->model ) {
		my $m = $self->_create_default_model;
		$self->add_model($self,$m);
	}
	my @models = $self->model;
	my $first_model = $models[0];
	
	if ( ! $self->get_chains($first_model) ) {
		my $c = $self->_create_default_chain;
		$self->add_chain($first_model, $c);
	}
	my @chains = $self->get_chains($first_model);
	my $first_chain = $chains[0];

	if( defined $residue) {
		if( (ref($residue) eq "ARRAY") ||
		      ($residue->isa('Bio::Structure::Residue')) ) {
			# remove existing ones, tell they've become orphan
my @obj = $self->get_residues($first_chain); if (@obj) { for my $r (@obj) { $self->_remove_from_graph($r); } } # add the new ones
$self->add_residue($first_chain,$residue); } else { $self->throw("Supplied a $residue to residue, we want a Bio::Structure::Residue or a list of these\n"); } } $self->get_residues($first_chain);
}
add_residuedescriptionprevnextTop
sub add_residue {
	my($self,$chain,$residue) = @_;

	if (ref($chain) !~ /^Bio::Structure::Chain/) {
		$self->throw("add_residue: first argument needs to be a Chain object\n");
	}
	if (defined $residue) {
		if (ref($residue) eq "ARRAY") {
    			# if the user passed in a reference to an array
for my $r ( @{$residue} ) { if( ! $r->isa('Bio::Structure::Residue') ) { $self->throw("$r is not a Residue\n"); } if ( $self->_parent($r) ) { $self->throw("$r already belongs to a parent\n"); } $self->_parent($r, $chain); $self->_child($chain, $r); # stringify
my $str_ref = "$self"; $r->_grandparent($str_ref); } } elsif ( $residue->isa('Bio::Structure::Residue') ) { if ( $self->_parent($residue) ) { $self->throw("$residue already belongs to a parent\n"); } $self->_parent($residue, $chain); $self->_child($chain, $residue); # stringify
my $str_ref = "$self"; $residue->_grandparent($str_ref); } else { $self->throw("Supplied a $residue to add_residue, we want a Residue or list of Residues\n"); } } my $array_ref = $self->_child($chain); return $array_ref ? @{$array_ref} : ();
}
get_residuesdescriptionprevnextTop
sub get_residues {
	my ($self, $chain) = @_;

	if ( !defined $chain) {
		$self->throw("get_residues needs a Chain as argument");
	}
	# pass through to add_residue
$self->add_residue($chain);
}
add_atomdescriptionprevnextTop
sub add_atom {
	my($self,$residue,$atom) = @_;

	if (ref($residue) !~ /^Bio::Structure::Residue/) {
		$self->throw("add_atom: first argument needs to be a Residue object\n");
	}
	if (defined $atom) {
		if (ref($atom) eq "ARRAY") {
    			# if the user passed in a reference to an array
for my $a ( @{$atom} ) { if( ! $a->isa('Bio::Structure::Atom') ) { $self->throw("$a is not an Atom\n"); } if ( $self->_parent($a) ) { $self->throw("$a already belongs to a parent\n"); } $self->_parent($a, $residue); $self->_child($residue, $a); # stringify
#my $str_ref = "$self";
#$r->_grandparent($str_ref);
} } #elsif ( $atom->isa('Bio::Structure::Atom') ) {
elsif ( ref($atom) =~ /^Bio::Structure::Atom/ ) { if ( $self->_parent($atom) ) { $self->throw("$atom already belongs to a parent\n"); } $self->_parent($atom, $residue); $self->_child($residue, $atom); # stringify
#my $str_ref = "$self";
#$atom->_grandparent($str_ref);
} } my $array_ref = $self->_child($residue); return $array_ref ? @{$array_ref} : ();
}
get_atomsdescriptionprevnextTop
sub get_atoms {
	my ($self, $residue) = @_;

	if ( !defined $residue) {
		$self->throw("get_atoms needs a Residue as argument");
	}
	# pass through to add_atom
$self->add_atom($residue);
}
conectdescriptionprevnextTop
sub conect {
	my ($self, $source, $serial, $type) = @_;
	
	if ( !defined $source ) {
		$self->throw("You need to supply at least a source to conect");
	}
	if ( defined $serial && defined $type ) {
		if ( !exists(${$self->{'conect'}}{$source}) || ref(${$self->{'conect'}}{$source} !~ /^ARRAY/ ) ) {
			${$self->{'conect'}}{$source} = [];
		}
		# we also need to store type, a conect object might be better 
my $c = $serial . "_" . $type; push @{ ${$self->{'conect'}}{$source} }, $c; } return @{ ${$self->{'conect'}}{$source} };
}
get_all_conect_sourcedescriptionprevnextTop
sub get_all_conect_source {
	my ($self) = shift;
	my (@sources);

	for my $source (sort {$a<=>$b} keys %{$self->{'conect'}}) {
		push @sources, $source;
	}
	return @sources;
}
masterdescriptionprevnextTop
sub master {
	my ($self, $value) = @_;
	if (defined $value) {
		$self->{'master'} = $value;
	}
	return $self->{'master'};
}
seqresdescriptionprevnextTop
sub seqres {
	my ($self, $chainid) = @_;
	my $s_u = "x3 A1 x7 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3 x1 A3";
	my (%seq_ch);
	if ( !defined $chainid) {
		my $m = ($self->get_models($self))[0];
		my $c = ($self->get_chains($m))[0];
		$chainid = $c->id;
	}
	my $seqres = ($self->annotation->get_Annotations("seqres"))[0];
	my $seqres_string = $seqres->as_text;
$self->debug("seqres : $seqres_string\n");
	$seqres_string =~ s/^Value: //;
	# split into lines of 62 long
my @l = unpack("A62" x (length($seqres_string)/62), $seqres_string);
for my $line (@l) { # get out chain_id and sequence
# we use a1, as A1 strips all spaces :(
my ($chid, $seq) = unpack("x3 a1 x7 A51", $line); if ($chid eq " ") { $chid = "default"; } $seq =~ s/(\w+)/\u\L$1/g; # ALA -> Ala (for SeqUtils)
$seq =~ s/\s//g; # strip all spaces
$seq_ch{$chid} .= $seq; $self->debug("seqres : $chid $seq_ch{$chid}\n"); } # do we have a seqres for this chainid
if(! exists $seq_ch{$chainid} ) { $self->warn("There is no SEQRES known for chainid\" $chainid\""); return undef; } # this will break for non-protein structures (about 10% for now) XXX KB
my $pseq = Bio::PrimarySeq->new(-alphabet => 'protein'); $pseq = Bio::SeqUtils->seq3in($pseq,$seq_ch{$chainid}); my $id = $self->id . "_" . $chainid; $pseq->id($id); return $pseq;
}
get_atom_by_serialdescriptionprevnextTop
sub get_atom_by_serial {
	my ($self, $model, $serial) = @_;

	if ($model =~ /^\d+$/ && !defined $serial) { # only serial given
$serial = $model; my @m = $self->get_models($self); $model = $m[0]; } if ( !defined $model || ref($model) !~ /^Bio::Structure::Model/ ) { $self->throw("Could not find (first) model\n"); } if ( !defined $serial || ($serial !~ /^\d+$/) ) { $self->throw("The serial number you provided looks fishy ($serial)\n"); } for my $chain ($self->get_chains($model) ) { for my $residue ($self->get_residues($chain) ) { for my $atom ($self->get_atoms($residue) ) { # this could get expensive, do we cache ???
next unless ($atom->serial == $serial); return $atom; } } }
}
parentdescriptionprevnextTop
sub parent {
	my ($self, $obj) = @_;
	
	if ( !defined $obj) {
		$self->throw("parent: you need to supply an argument to get the parent from\n");
	}

	# for now we pass on to _parent, untill we get the symbolic ref thing working.
$self->_parent($obj);
}
DESTROYdescriptionprevnextTop
sub DESTROY {
	my $self = shift;

	#print STDERR "DESTROY on $self being called\n";
## for my $pc (keys %{ $self->{'p_c'} } ) {
## next unless ( defined ${ $self->{'p_c'} }{$pc} );
## delete ${$self->{'p_c'}}{$pc};
## }
## for my $cp (keys %{ $self->{'c_p'} } ) {
## next unless ( defined ${ $self->{'c_p'} }{$cp} );
## delete ${$self->{'c_p'}}{$cp};
## }
%{ $self->{'p_c'} } = (); %{ $self->{'c_p'} } = ();
}
annotationdescriptionprevnextTop
sub annotation {
   my ($obj,$value) = @_;
   if( defined $value) {
      $obj->{'annotation'} = $value;
    }
    return $obj->{'annotation'};
}
_remove_modelsdescriptionprevnextTop
sub _remove_models {
	my ($self) = shift;

	;
}
_create_default_modeldescriptionprevnextTop
sub _create_default_model {
	my ($self) = shift;

	my $model = Bio::Structure::Model->new(-id => "default");
	return $model;
}
_create_default_chaindescriptionprevnextTop
sub _create_default_chain {
	my ($self) = shift;

	my $chain = Bio::Structure::Chain->new(-id => "default");
	return $chain;
}
_parentdescriptionprevnextTop
sub _parent {
    no strict "refs";
    my ($self, $key, $value) = @_;

    if ( (!defined $key) || (ref($key) !~ /^Bio::/) ) {
	$self->throw("First argument to _parent needs to be a reference to a Bio:: object ($key)\n");
    }
    if ( (defined $value) && (ref($value) !~ /^Bio::/) ) {
	$self->throw("Second argument to _parent needs to be a reference to a Bio:: object\n");
    }
    # no checking here for consistency of key and value, needs to happen in caller
if (defined $value) { # is this value already in, shout
if (defined ( $self->{'c_p'}->{$key}) && exists ( $self->{'c_p'}->{$key}) ) { $self->throw("_parent: $key already has a parent ${$self->{'c_p'}}{$key}\n"); } ${$self->{'c_p'}}{$key} = $value; } return ${$self->{'c_p'}}{$key};
}
_childdescriptionprevnextTop
sub _child {
	my ($self, $key, $value) = @_;
	
	if ( (!defined $key) || (ref($key) !~ /^Bio::/) ) {
		$self->throw("First argument to _child needs to be a reference to a Bio:: object\n");
	}
	if ( (defined $value) && (ref($value) !~ /^Bio::/) ) {
		$self->throw("Second argument to _child needs to be a reference to a Bio:: object\n");
	}
	# no checking here for consistency of key and value, needs to happen in caller
if (defined $value) { if ( !exists(${$self->{'p_c'}}{$key}) || ref(${$self->{'p_c'}}{$key}) !~ /^ARRAY/ ) { ${$self->{'p_c'}}{$key} = []; } push @{ ${$self->{'p_c'}}{$key} }, $value; } return ${$self->{'p_c'}}{$key};
}
_remove_from_graphdescriptionprevnextTop
sub _remove_from_graph {
	my ($self, $object) = @_;
	
	if ( !defined($object) && ref($object) !~ /^Bio::/) {
		$self->throw("_remove_from_graph needs a Bio object as argument");
	}
	if ( $self->_parent($object) ) {
		my $dad = $self->_parent($object);
		# if we have a parent, remove me as being a child
for my $k (0 .. $#{$self->_child($dad)}) { if ($object eq ${$self->{'p_c'}{$dad}}[$k]) { splice(@{$self->{'p_c'}{$dad}}, $k,1); } } delete( $self->{'c_p'}{$object}); }
}
_print_stats_pcdescriptionprevnextTop
sub _print_stats_pc {
	# print stats about the parent/child hashes
my ($self) =@_; my $pc = scalar keys %{$self->{'p_c'}}; my $cp = scalar keys %{$self->{'c_p'}}; my $now_time = Time::HiRes::time(); $self->debug("pc stats: P_C $pc C_P $cp $now_time\n");
}
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 one
of the Bioperl mailing lists. Your participation is much appreciated.
  bioperl-l@bioperl.org             - General discussion
  http://bio.perl.org/MailList.html - About the mailing lists
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via email
or the web:
  bioperl-bugs@bio.perl.org
  http://bio.perl.org/bioperl-bugs/
AUTHOR - Kris BoulezTop
Email kris.boulez@algonomics.com
APPENDIXTop
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _