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|
package ReadCoverageNode;
use strict;
use warnings;
use Carp;
use base qw (GenericNode);
## static vars
my %READ_TRACKER;
my $READ_COUNTER = 0;
sub new {
my $packagename = shift;
my ($node_name, $read_acc) = @_;
my $self = $packagename->SUPER::new($node_name); # sets _value
$self->{_reads} = {};
$self->{_count} = 0;
bless ($self, $packagename);
$self->add_read($read_acc);
return($self);
}
####
sub get_count {
my $self = shift;
return($self->{_count});
}
sub set_count {
my $self = shift;
my $count = shift;
$self->{_count} = $count;
return;
}
####
sub add_read {
my $self = shift;
my $read_acc = shift;
my $node_name = $self->get_value();
unless ((defined $read_acc) && $read_acc =~ /\w/) {
confess "Error, need read accession";
}
my $read_tracking_no = $self->_get_or_create_tracking_number($read_acc);
if (exists $self->{_reads}->{$read_tracking_no}) {
#print "Already got read $read_acc for $node_name, count:" . $self->get_count() . "\n";
}
else {
$self->{_reads}->{$read_tracking_no} = 1;
$self->{_count}++;
#print "-incrementing count for $read_acc for $node_name => $self->{_count}\n";
}
return;
}
####
sub get_reads {
my $self = shift;
my @reads = keys %{$self->{_reads}};
return(@reads);
}
###
sub has_read {
my $self = shift;
my $read_acc = shift;
if (exists $self->{_reads}->{$read_acc}) {
return(1);
}
else {
return(0);
}
}
####
sub count_reads_in_common {
my $self = shift;
my $other_node = shift;
my $count = 0;
foreach my $read ($self->get_reads()) {
if ($other_node->has_read($read)) {
$count++;
}
}
return($count);
}
####
sub toString {
my $self = shift;
my @prev_nodes = $self->get_all_prev_nodes();
my @next_nodes = $self->get_all_next_nodes();
my $text = "";
foreach my $prev_node (@prev_nodes) {
$text .= "P " . $prev_node->get_value() . "(" . $prev_node->get_count() . ")\n";
}
$text .= "X " . $self->get_value() . "(" . $self->get_count() . ")\n";
foreach my $next_node (@next_nodes) {
$text .= "N " . $next_node->get_value() . "(" . $self->get_count() . ")\n";
}
return($text);
}
#### Private read tracking ## this should probably be a separate class at some point, with a singleton class object.
sub _read_is_tracked {
my $self = shift;
my $read_acc = shift;
if (exists $READ_TRACKER{$read_acc}) {
return(1);
}
else {
return(0);
}
}
sub _get_read_tracking_number {
my $self = shift;
my $read_acc = shift;
if (! $self->_read_is_tracked($read_acc)) {
die "Error, read $read_acc is not tracked";
}
my $tracking_number = $READ_TRACKER{$read_acc};
return($tracking_number);
}
sub _get_or_create_tracking_number {
my $self = shift;
my $read_acc = shift;
if ($self->_read_is_tracked($read_acc)) {
return($self->_get_read_tracking_number($read_acc));
}
else {
## track this new read:
$READ_COUNTER++;
$READ_TRACKER{$read_acc} = $READ_COUNTER;
return($self->_get_read_tracking_number($read_acc));
}
}
1; # EOM
|
