/usr/share/perl5/GO/Model/TreeIterator.pm is in libgo-perl 0.15-5.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#
# This GO module is maintained by Chris Mungall <cjm@fruitfly.org>
#
# see also - http://www.geneontology.org
# - http://www.godatabase.org/dev
#
# You may distribute this module under the same terms as perl itself
#
package GO::Model::TreeIterator;
=head1 NAME
GO::Model::GraphIterator - wraps GO::Model::GraphIterator
=head1 SYNOPSIS
=head1 DESCRIPTION
This is a hack. It wraps GO::Model::GraphIterator and provides
a tree like iteration, rather than a graph-like iteration.
This is done by giving TreeIterator a template array.
The array looks like this :
[
[3674, 'isa', 3673],
[9277, 'isa', 5618]
]
3674 is selected iff it is the child of 3673.
9277 is selected iff it is the child of 5618.
=cut
use Carp;
use strict;
use Exporter;
use GO::Utils qw(rearrange);
use GO::Model::Graph;
use GO::Model::GraphNodeInstance;
use FileHandle;
use Exporter;
use Data::Dumper;
use vars qw(@EXPORT_OK %EXPORT_TAGS);
use base qw(GO::Model::Root Exporter);
sub _valid_params {
return qw(graph order sort_by noderefs direction no_duplicates reltype_filter visited arcs_visited);
}
=head2 order
Usage - $graphiter->order("breadth");
Returns - string
Args - string
gets/sets traversal order; breadth or depth; default is depth
=cut
=head2 direction
Usage - $graphiter->direction("up");
Returns - string
Args - string
gets/sets direction; default is "down"
=cut
#sub _initialize {
# my $self = shift;
# my $acc;
# if (!ref($_[0])) {
# $acc = shift;
# }
# $self->SUPER::_initialize(@_);
# $self->reset_cursor($acc);
#}
sub new {
my $class = shift;
my $self = {};
bless $self, $class;
$self->{'graph'} = shift || $self->throw("no graph passed in to constructor");
$self->{'selected_array'} = shift;
$self->{'show_kids'} = shift;
$self->{'closed_below'} = shift;
my $compact = shift || 0;
$self->{'nit'} = $self->{'graph'}->create_iterator({compact=>$compact});
$self->{'bootstrap_mode'} = 0;
# $self->SUPER::_initialize(@_);
# $self->{'current_path'};
$self->{'nit'}->reset_cursor();
return $self;
}
=head2 reset_cursor
Usage -
Returns - GO::Model::Term
Args -
=cut
sub reset_cursor {
my $self = shift;
$self->{'nit'}->reset_cursor();
}
=head2 next_node
Usage -
Returns - GO::Model::Term
Args -
=cut
sub next_node {
my $self = shift;
my $ni = $self->next_node_instance;
return $ni ? $ni->term : undef;
}
=head2 set_bootstrap_mode
Usage -
Returns -
Args -
=cut
sub set_bootstrap_mode {
my $self = shift;
$self->{'bootstrap_mode'} = 1;
}
=head2 get_bootstrap_mode
Usage -
Returns -
Args -
=cut
sub get_bootstrap_mode {
my $self = shift;
return $self->{'bootstrap_mode'};
}
=head2 get_current_path
Usage -
Returns - array ref
Args - none
=cut
sub get_current_path {
my $self = shift;
return $self->{'current_path'};
}
=head2 next_node_instance
Usage -
Returns - GO::Model::GraphNodeInstance
Args -
=cut
sub next_node_instance {
my $self = shift;
my $current_coords = $self->{'current_coords'} || [];
my $nit = $self->{'nit'};
my $previous_depth = $self->{'previous_depth'} || 1;
my $parent_array = $self->{'current_path'};
my $ni = $nit->next_node_instance;
if ($ni) {
my $depth = $ni->depth;
if ($previous_depth == $depth) {
$parent_array->[$depth] = $ni->term->public_acc;
} elsif ($previous_depth > $depth) {
while ($previous_depth > $depth) {
$previous_depth -= 1;
pop @$parent_array;
}
$parent_array->[$depth] = $ni->term->public_acc;
} elsif ($previous_depth < $depth) {
push @$parent_array, $ni->term->public_acc;
}
$self->{'previous_depth'} = $ni->depth;
$self->{'current_path'} = $parent_array;
if ($self->get_bootstrap_mode) {
return $ni;
}
if ($self->should_draw_below($parent_array)) {
return $ni;
} else {
$self->next_node_instance;
}
} else {
return 0;
}
}
sub should_draw_below {
my $self = shift;
my $current_coords = shift;
my $coord_list = $self->{'selected_array'};
foreach my $coords (@$coord_list) {
if (scalar(@$current_coords) <= scalar(@$coords)) {
my $result = 1;
my $i = 0;
my $length;
while ($i < scalar(@$current_coords)) {
if ($coords->[$i] ne $current_coords->[$i]) {
$result = 0;
}
} continue {
$i++;
}
if ($result == 1) {
return 1;
}
} elsif (scalar(@$current_coords) > scalar(@$coords)) {
my $i = 0;
my $test = 1;
while ($i < scalar(@$coords)) {
if ($current_coords->[$i] ne $coords->[$i]) {
$test = 0;
}
} continue {
$i++;
}
if ($test) {
my $parent_coords;
foreach my $anc(@$current_coords) {
push @$parent_coords, $anc;
}
pop @$parent_coords;
if ($self->is_selected($parent_coords, 'show_kids')) {
return 1;
}
}
}
}
return 0;
}
sub close_below {
my $self = shift;
my $closed_array = $self->{"closed_below"};
foreach my $closed (@$closed_array) {
$self->{'selected_array'} = $self->delete_array($closed);
}
foreach my $closed (@$closed_array) {
$self->{'show_kids'} = $self->delete_array($closed, 'show_kids');
}
}
sub delete_array {
my $self = shift;
my $parent_array = shift;
my $array_to_test_against = shift || 'selected_array';
my $selected_array = $self->{$array_to_test_against};
my @two_d_array;
foreach my $arr(@$selected_array) {
my $test = 1;
if (scalar(@$arr) >= scalar(@$parent_array)) {
my $i = 0;
while ($i < scalar(@$parent_array)) {
if ($parent_array->[$i] ne $arr->[$i]) {
$test = 0;
}
} continue {
$i++;
}
} else {
$test = 0;
}
if ($test != 1) {
push @two_d_array, $arr;
} else {
}
}
return \@two_d_array;
}
sub is_selected {
my $self = shift;
my $parent_array = shift;
my $array_to_test_against = shift || 'selected_array';
my $selected_array = $self->{$array_to_test_against};
foreach my $arr(@$selected_array) {
if (scalar(@$arr) eq scalar(@$parent_array)) {
my $i = 0;
my $test = 1;
while ($i < scalar(@$arr)) {
if ($parent_array->[$i] ne $arr->[$i]) {
$test = 0;
}
} continue {
$i++;
}
if ($test == 1) {
return 1;
}
}
}
return 0;
}
sub reltype_filter {
my $self = shift;
$self->{'nit'}->reltype_filter(@_);
}
1;
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