Bio::Tools::Phylo::Phylip
ProtDist
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Summary
Bio::Tools::Phylo::Phylip::ProtDist - DESCRIPTION of Object
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Tools::Phylo::Phylip::ProtDist;
my $parser = new Bio::Tools::Phylo::Phylip::ProtDist(-file => 'outfile');
while( my $result = $parser->next_matrix) {
}
Description
A parser for ProtDist output into a Bio::Matrix::PhylipDist object
Methods
Methods description
Title : new
Usage : my $obj = new Bio::Tools::Phylo::Phylip::ProtDist();
Function: Builds a new Bio::Tools::Phylo::Phylip::ProtDist object
Returns : Bio::Tools::ProtDist
Args : -fh/-file => $val, # for initing input, see Bio::Root::IO |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->_initialize_io(@args);
return $self; } | sub next_matrix
{ my ($self) = @_;
my @names;
my @values;
my $entry;
while ($entry=$self->_readline) {
if($#names >=0 && $entry =~/^\s+\d+$/){
last;
}
elsif($entry=~/^\s+\d+\n$/){
next;
}
my ($n,@line) = split( /\s+/,$entry);
push @names, $n;
push @values, [@line];
}
$#names>=0 || return;
my %dist;
my $i=0;
foreach my $name(@names){
my $j=0;
foreach my $n(@names) {
$dist{$name}{$n} = [$i,$j];
$j++;
}
$i++;
}
my $matrix = Bio::Matrix::PhylipDist->new(-matrix=>\%dist,
-names =>\@names,
-values=>\@values);
return $matrix;
}
1;} | General documentation
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The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : next_result
Usage : my $matrix = $parser->next_result
Function: Get the next result set from parser data
Returns : Bio::Matrix::PhylipDist
Args : none