Bio::Matrix::IO phylip
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Summary
Bio::Matrix::IO::phylip - A parser for PHYLIP distance matricies
Package variables
No package variables defined.
Included modules
Bio::Matrix::PhylipDist
Inherit
Bio::Matrix::IO
Synopsis
  use Bio::Matrix::IO;
my $parser = Bio::Matrix::IO->new(-format => 'phylip',
-file => 't/data/phylipdist.out');
my $matrix = $parser->next_matrix;
Description
This is a parser for PHYLIP distance matrix output.
Methods
newDescriptionCode
next_matrixDescriptionCode
write_matrixDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Matrix::IO::phylip->new();
Function: Builds a new Bio::Matrix::IO::phylip object
Returns : an instance of Bio::Matrix::IO::phylip
Args :
next_matrixcodeprevnextTop
 Title   : next_matrix
Usage : my $matrix = $parser->next_matrix
Function: Get the next result set from parser data
Returns : Bio::Matrix::PhylipDist
Args : none
write_matrixcodeprevnextTop
 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
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  my ($prog) = $self->_rearrange([qw(PROGRAM)], @args);
  $self->{'_program'} = $prog || $DEFAULTPROGRAM;
  return $self;
}
next_matrixdescriptionprevnextTop
sub next_matrix {
   my ($self) = @_;
   my @names;
   my @values;
   my $entry;
   my $size = 0;
   while ($entry=$self->_readline) {
       if($#names >=0 && $entry =~/^\s+\d+\n$/){
	   $self->_pushback($entry);
	   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 $matrix;
}
write_matrixdescriptionprevnextTop
sub write_matrix {
    my ($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);
    }
}


1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
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:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason StajichTop
Email jason-at-bioperl-dot.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _