Bio::Tools::Phylo::Phylip ProtDist
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Summary
Bio::Tools::Phylo::Phylip::ProtDist - parser for ProtDist output
Package variables
No package variables defined.
Included modules
Bio::Matrix::PhylipDist
Inherit
Bio::Root::IO Bio::Root::Root
Synopsis
    use Bio::Tools::Phylo::Phylip::ProtDist;
my $parser = Bio::Tools::Phylo::Phylip::ProtDist->new(-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
newDescriptionCode
next_matrixDescriptionCode
Methods description
newcode    nextTop
 Title   : new
Usage : my $obj = Bio::Tools::Phylo::Phylip::ProtDist->new();
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
next_matrixcodeprevnextTop
 Title   : next_matrix
Usage : my $matrix = $parser->next_matrix
Function: Get the next result set from parser data
Returns : Bio::Matrix::PhylipDist
Args : none
Methods code
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

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

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 - Shawn Hoon Top
Email shawnh@fugu-sg.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _