Summary

Bio::Tools::Phylo::Phylip::ProtDist - DESCRIPTION of Object

Package variables

Included modules

Inherit

Bio::Root::IO Bio::Root::Root

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
           -program  => 'programname' # name of the program

 Title   : next_matrix
 Usage   : my $matrix = $parser->next_matrix
 Function: Get the next result set from parser data
 Returns : Bio::Matrix::PhylipDist
 Args    : none

Methods code

sub new {

  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  $self->_initialize_io(@args);
  my ($prog) = $self->_rearrange([qw(PROGRAM)], @args);
  $self->{'_program'} = $prog;
  return $self;

}

sub next_matrix {

   my ($self) = @_;
   my @names;
   my @values;
   my $entry;
   my $size = 0;
   while ($entry=$self->_readline) {
       if($#names >=0 && $entry =~/^\s+\d+\n$/){
	   $self->_pushback($_);
	   last;
       } elsif($entry=~/^\s+(\d+)\n$/){	   
	   $size = $1;
	   next;
       } elsif( $entry =~ s/^\s+(\-?\d+\.\d+)/$1/ ) {
	   my (@line) = split( /\s+/,$entry);
	   push @{$values[-1]}, @line;
	   next;
       }
       my ($n,@line) = split( /\s+/,$entry);
       
       push @names, $n;
       push @values, [@line];
   }
   if( scalar @names != $size ) {
       $self->warn("The number of entries ".(scalar @names).
		   " is not the same $size");
   }
   $#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(-program => $self->{'_program'},
					     -matrix  =>\% dist,
					     -names   =>\@ names,
					     -values  =>\@ values);
    return $matrix;

}

General documentation

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Email shawnh@fugu-sg.org
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Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _