Summary

Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies

Package variables

Included modules

Inherit

Bio::Matrix::IO

Synopsis

  use Bio::Matrix::IO;
  my $parser = new Bio::Matrix::IO(-format   => 'phylip'
                                   -file     => 't/data/phylipdist.out');
  my $matrix = $parser->next_matrix;

Description

This is a parser for PHYLIP distance matrix output.

Methods

Methods description

 Title   : new
 Usage   : my $obj = new Bio::Matrix::IO::phylip();
 Function: Builds a new Bio::Matrix::IO::phylip object 
 Returns : an instance of Bio::Matrix::IO::phylip
 Args    :

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

 Title   : write_matrix
 Usage   : $matio->write_matrix($matrix)
 Function: Write out a matrix in the phylip distance format
 Returns : none
 Args    : Bio::Matrix::PhylipDist

Methods code

sub new {

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

  my $self = $class->SUPER::new(@args);
  my ($prog) = $self->_rearrange([qw(PROGRAM)], @args);
  $self->{'_program'} = $prog || $DEFAULTPROGRAM;
  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
       (-matrix_name => $self->{'_program'},
	-matrix      =>\% dist,
	-names       =>\@ names,
	-values      =>\@ values);
    return $matrix;

}

sub write_matrix {

    my ($self,@matricies) = @_;
    foreach my $matrix ( @matricies ) {
	my @names = @{$matrix->names};
	my @values = @{$matrix->_values};
	my %matrix = %{$matrix->_matrix};
	my $str;
	$str.= (" "x 4). scalar(@names)."\n";
	foreach my $name (@names){
	    my $newname = $name. (" " x (15-length($name)));
	    if( length($name) >= 15 ) { $newname .= " " }
	    $str.=$newname;
	    my $count = 0;
	    foreach my $n (@names){
		my ($i,$j) = @{$matrix{$name}{$n}};
		if($count < $#names){
		    $str.= $values[$i][$j]. "  ";
		}
		else {
		    $str.= $values[$i][$j];
		}
		$count++;
	    }
	    $str.="\n";
	}
	$self->_print($str);
    }

}

General documentation

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