Summary

Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output

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) {
      # do something with it
    }

Description

A parser for ProtDist output into a Bio::Matrix::PhylipDist object.
See also Bio::Matrix::IO::phylip this module may go away.

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;
   for my $name (@names){
       my $j=0;
       for my $n (@names) {
	   $dist{$name}{$n} = [$i,$j];
	   $j++;
       }
       $i++;
   }
   return Bio::Matrix::PhylipDist->new(-program => $self->{'_program'},
					     -matrix  =>\% dist,
					     -names   =>\@ names,
					     -values  =>\@ values);

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:

  http://bugzilla.open-bio.org/

Email shawnh@fugu-sg.org

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