DETECTER
NodesBlock
| No package variables defined. |
my $nodes_block = new NodesBlock();
$nodes_block->parse_file('ABC.Redo.CFTRsubtree.Crop.txt');
|
NodesBlock parses the PAML input and stores all the data as nodes and the site
objects. Refer to Node and Site object for more details.
|
Methods description
Title : add_node
Usage : $nodes_block_obj->add_node()
Function : adds node object to the nodes array
Returns : none
Argument : $node_obj
Title : delete_node
Usage : $nodes_block_obj->delete_node
Function : undefines the node object in the nodes array. This can be
used to remove large amounts of node data in memory.
Returns : none
Argument : position of node object in the nodes array
Title : get_node
Usage : $nodes_block_obj->get_node()
Function : get the node object from the nodes array
Returns : $node_obj
Argument : position of node object in the nodes array
Title : get_numb_of_nodes
Usage : $no_of_nodes = $node_blocks_obj->get_number_of_nodes
Function : returns the number of nodes stored in the nodes_block_obj
Returns : number of nodes
Argument : none
Title : new
Usage : $nodes_block_obj = new NodesBlock()
Function : creates new object for storing NodesBlock data
Returns : NodesBlock Object
Argument : none
Title : Parses the Input (PAML) File
Usage : my $nodes_block = new NodesBlock($file_name);
Function : creates a new NodesBlock object by parsing files
Returns : NodesBlock object
Argument : $file_name
Methods code
sub add_node
{ my $class = shift;
my $node = shift;
push(@{$class->{_nodes_array}},$node);}
sub delete_node
{ my $class = shift;
$class->{_nodes_array}->[$_[0]] = undef;}
sub get_node
{ my $class = shift;
return $class->{_nodes_array}->[$_[0]];}
sub get_numb_of_nodes
{ my $class = shift;
my $numbOfnodes = @{$class->{_nodes_array}};
return $numbOfnodes;}
sub new
{
my $class = shift;
my $data = {
'_nodes_array' => []
};
bless ($data,$class);
return $data;}
sub parse_file
{ my $class = shift;
my $file_name = shift;
my ($freq,$line,$data);
open (IF, $file_name) or die $!;
$line = <IF>;
my $node;
my $site_id;
while ($line !~ /Prob/) { $line = <IF> }
while ($line = <IF>) {
$line =~ s/\\par//; ##get rid of all the /par's
chomp $line;
$line =~ s/^\s*//g;
if ( $line =~ /^Prob/ ) {
print "$line\n";
$class->add_node($node) if (defined($node)); ### Adding nodes to the NodesBlock
##last if $count++ == 2;
$node = new Node();
(my $node_no = $line) =~s/[^\d]//g;
$node->set_node_no($node_no);
$line = <IF>; $line = <IF>; $line = <IF>;
}
elsif ($line =~ /^\d+/) {
($header, $footer) = split(/:/, $line);
$header =~s/^\s*//g;
($site_id, $freq, $data) = split(/\s+/,$header);
$site_id = sprintf("%04d",$site_id);
my $site_obj = new Site();
$site_obj->set_site($site_id,$data,$footer);
$node->add_site($site_obj); ## Sites are added to the node
}
}}
General documentation