#
# bioperl module for Bio::Structure::Entry
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Kris Boulez <kris.boulez@algonomics.com>
#
# Copyright Kris Boulez
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Structure::Entry - Bioperl structure Object, describes the whole entry
=head1 SYNOPSIS
#add synopsis here
=head1 DESCRIPTION
This object stores a whole Bio::Structure entry. It can consist of one
or more models (L<Bio::Structure::Model>), which in turn consist of one
or more chains (L<Bio::Structure::Chain>). A chain is composed of residues
(L<Bio::Structure::Residue>) and a residue consists of atoms
(L<Bio::Structure::Atom>). If no specific model or chain is chosen, the
first one is chosen.
=head1 FEEDBACK
=head2 Mailing Lists
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://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
the bugs and their resolution. Bug reports can be submitted via the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Kris Boulez
Email kris.boulez@algonomics.com
=head1 APPENDIX
The rest of the documentation details each of the object methods. Internal
methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Structure::Entry;
use strict;
use Bio::Structure::Model;
use Bio::Structure::Chain;
use Bio::Annotation::Collection;
use Tie::RefHash;
use base qw(Bio::Root::Root Bio::Structure::StructureI);
=head2 new()
Title : new()
Usage : $struc = Bio::Structure::Entry->new(
-id => 'structure_id',
);
Function: Returns a new Bio::Structure::Entry object from basic
constructors. Probably most called from Bio::Structure::IO.
Returns : a new Bio::Structure::Model object
=cut
sub new {
my ($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 $self;
}
=head2 model()
Title : model
Function: Connects a (or a list of) Model objects to a Bio::Structure::Entry.
To add a Model (and keep the existing ones) use add_model()
It returns a list of Model objects.
Returns : List of Bio::Structure::Model objects
Args : One Model or a reference to an array of Model objects
=cut
sub model {
my ($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);
}
=head2 add_model()
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
=cut
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} : ();
}
=head2 get_models()
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
=cut
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);
}
=head2 id()
Title : id
Usage : $entry->id("identity");
Function: Gets/sets the ID
Returns : The ID
Args :
=cut
sub id {
my ($self, $value) = @_;
if (defined $value) {
$self->{'id'} = $value;
}
return $self->{'id'};
}
=head2 chain()
Title : chain
Usage : @chains = $structure->chain($chain);
Function: Connects a Chain or a list of Chain objects to a Bio::Structure::Entry.
Returns : List of Bio::Structure::Chain objects
Args : A Chain or a reference to an array of Chain objects
=cut
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);
}
=head2 add_chain()
Title : add_chain
Usage : @chains = $structure->add_chain($model,$chain);
Function: Adds one or more Chain objects to a Bio::Structure::Entry.
Returns : List of Chain objects associated with the Model
Args : A Model object and a Chain object or a reference to an array of
of Chain objects
=cut
sub add_chain {
my($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} : ();
}
=head2 get_chains()
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
=cut
sub get_chains {
my ($self, $model) = @_;
if (! defined $model) {
$model = ($self->get_models)[0];
}
# pass through to add_chain
$self->add_chain($model);
}
=head2 residue()
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
=cut
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);
}
=head2 add_residue()
Title : add_residue
Usage : @residues = $structure->add_residue($chain,$residue);
Function: Adds one or more Residue objects to a Bio::Structure::Entry.
Returns : List of Bio::Structure::Residue objects
Args : A Chain object and a Residue object or a reference to an array of
Residue objects
=cut
sub add_residue {
my($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} : ();
}
=head2 get_residues()
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
=cut
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);
}
=head2 add_atom()
Title : add_atom
Usage : @atoms = $structure->add_atom($residue,$atom);
Function: Adds a (or a list of) Atom objects to a Bio::Structure::Residue.
Returns : List of Bio::Structure::Atom objects
Args : A Residue and an Atom
=cut
sub add_atom {
my($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} : ();
}
=head2 get_atoms()
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
=cut
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);
}
=head2 parent()
Title : parent
Usage : $structure->parent($residue);
Function: Returns the parent of the argument
Returns : The parent of the argument
Args : A Bio::Structure object
=cut
=head2 connect
Title : connect
Usage :
Function: Alias to conect()
Returns :
Args :
=cut
sub connect {
my $self = shift;
return $self->conect(@_);
}
=head2 conect()
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, $serial),
this should be OK for now)
Args : The source, the serial number for the source Atom, and the type
=cut
sub conect {
my ($self, $source, $serial, $type) = @_;
if ( !defined $source ) {
$self->throw("You need to supply at least a source to connect");
}
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;
}
# Bug 1894
return () if ( !exists $self->{'conect'}{$source} ||
!defined $self->{'conect'}{$source} );
return @{ ${$self->{'conect'}}{$source} };
}
=head2 get_all_connect_source
Title : get_all_connect_source
Usage :
Function: Alias to get_all_conect_source()
Returns :
Args :
=cut
sub get_all_connect_source {
my $self = shift;
return get_all_conect_source(@_);
}
=head2 get_all_conect_source()
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, $serial),
this should be OK for now)
Args :
Notes : This is a bit of a kludge, but it is the best for now. Conect info might need
to go in a separate object
=cut
sub get_all_conect_source {
my ($self) = shift;
my (@sources);
for my $source (sort {$a<=>$b} keys %{$self->{'conect'}}) {
push @sources, $source;
}
return @sources;
}
=head2 master()
Title : master
Usage : $structure->master($source);
Function: Get/set method for master
Returns : The master line
Args : The master line for this entry
=cut
sub master {
my ($self, $value) = @_;
if (defined $value) {
$self->{'master'} = $value;
}
return $self->{'master'};
}
=head2 seqres()
Title : seqres
Usage : $seqobj = $structure->seqres("A");
Function: Gets a sequence object containing the sequence from the SEQRES record.
if a chain-ID is given, the sequence for this chain is given, if none
is provided the first chain is chosen
Returns : A Bio::PrimarySeq
Args : The chain-ID of the chain you want the sequence from
=cut
sub seqres {
my ($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;
}
# 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;
}
=head2 get_atom_by_serial()
Title : get_atom_by_serial
Usage : $structure->get_atom_by_serial($model,$serial);
Function: Get the Atom by serial
Returns : The Atom object with this serial number in the model
Args : Model on which to work, serial number for atom
(if only a number is supplied, the first model is chosen)
=cut
sub get_atom_by_serial {
my ($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 $atom;
}
}
}
}
sub parent {
my ($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);
}
sub DESTROY {
my $self = shift;
%{ $self->{'p_c'} } = ();
%{ $self->{'c_p'} } = ();
}
=head2 annotation
Title : annotation
Usage : $obj->annotation($seq_obj)
Function:
Example :
Returns : value of annotation
Args : newvalue (optional)
=cut
sub annotation {
my ($obj,$value) = @_;
if( defined $value) {
$obj->{'annotation'} = $value;
}
return $obj->{'annotation'};
}
#
# from here on only private methods
#
=head2 _remove_models()
Title : _remove_models
Usage :
Function: Removes the models attached to an Entry. Tells the models they
do not belong to this Entry any more
Returns :
Args :
=cut
#
sub _remove_models {
my ($self) = shift;
;
}
=head2 _create_default_model()
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 :
=cut
sub _create_default_model {
my ($self) = shift;
my $model = Bio::Structure::Model->new(-id => "default");
return $model;
}
=head2 _create_default_chain()
Title : _create_default_chain
Usage :
Function: Creates a default Chain for this Model. Typical situation
in an X-ray structure where there is only one chain
Returns :
Args :
=cut
sub _create_default_chain {
my ($self) = shift;
my $chain = Bio::Structure::Chain->new(-id => "default");
return $chain;
}
=head2 _parent()
Title : _parent
Usage : This is an internal function only. It is used to have one
place that keeps track of which object has which other object
as parent. Thus allowing the underlying modules (Atom, Residue,...)
to have no knowledge about all this (and thus removing the possibility
of reference cycles).
This method hides the details of manipulating references to an anonymous
hash.
Function: To get/set an objects parent
Returns : A reference to the parent if it exist, undef otherwise. In the
current implementation each node should have a parent (except Entry).
Args :
=cut
# manipulating the c_p hash
sub _parent {
no strict "refs";
my ($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'}}{$key};
}
=head2 _child()
Title : _child
Usage : This is an internal function only. It is used to have one
place that keeps track of which object has which other object
as child. Thus allowing the underlying modules (Atom, Residue,...)
to have no knowledge about all this (and thus removing the possibility
to have no knowledge about all this (and thus removing the possibility
of reference cycles).
This method hides the details of manipulating references to an anonymous
hash.
Function: To get/set an the children of an object
Returns : A reference to an array of child(ren) if they exist, undef otherwise.
Args :
=cut
# manipulating the p_c hash
sub _child {
my ($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'}}{$key};
}
=head2 _remove_from_graph()
Title : _remove_from_graph
Usage : This is an internal function only. It is used to remove from
the parent/child graph. We only remove the links from object to
his parent. Not the ones from object to its children.
Function: To remove an object from the parent/child graph
Returns :
Args : The object to be orphaned
=cut
sub _remove_from_graph {
my ($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});
}
}
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");
}
1;