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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.

=head2 Reporting Bugs

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://github.com/bioperl/bioperl-live/issues

=head1 AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

=head1 APPENDIX

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

=cut


# Let the code begin...


package Bio::Matrix::IO;
use strict;


use base qw(Bio::Root::IO);

=head2 new

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


=cut

sub new { 
  my($caller,@args) = @_;
  my $class = ref($caller) || $caller;
    
    # or do we want to call SUPER on an object if $caller is an
    # object?
    if( $class =~ /Bio::Matrix::IO::(\S+)/ ) {
	my ($self) = $class->SUPER::new(@args);	
	$self->_initialize(@args);
	return $self;
    } else { 

	my %param = @args;
	@param{ map { lc $_ } keys %param } = values %param; # lowercase keys
	my $format = $param{'-format'} || 
	    $class->_guess_format( $param{'-file'} || $ARGV[0] ) ||
		'scoring';
	$format = "\L$format";	# normalize capitalization to lower case

	# normalize capitalization
	return unless( $class->_load_format_module($format) );
	return "Bio::Matrix::IO::$format"->new(@args);
    }
}

=head2 newFh

 Title   : newFh
 Usage   : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format')
 Function: does a new() followed by an fh()
 Example : $fh = Bio::Matrix::IO->newFh(-file=>$filename,-format=>'Format')
           $matrix = <$fh>;   # read a matrix object
           print $fh $matrix; # write a matrix object
 Returns : filehandle tied to the Bio::SeqIO::Fh class
 Args    :

=cut

sub newFh {
  my $class = shift;
  return unless my $self = $class->new(@_);
  return $self->fh;
}

=head2 fh

 Title   : fh
 Usage   : $obj->fh
 Function: Get a filehandle type access to the matrix parser
 Example : $fh = $obj->fh;      # make a tied filehandle
           $matrix = <$fh>;     # read a matrix object
           print $fh $matrix;   # write a matrix object
 Returns : filehandle tied to Bio::Matrix::IO class
 Args    : none

=cut


sub fh {
  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;
}


=head2 format

 Title   : format
 Usage   : $format = $obj->format()
 Function: Get the matrix format
 Returns : matrix format
 Args    : none

=cut

Bio/Matrix/IO.pm  view on Meta::CPAN

=cut

sub next_matrix{
   my ($self) = @_;
   $self->throw_not_implemented();
}

=head2 write_matrix

 Title   : write_matrix
 Usage   : $io->write_matrix($matrix)
 Function: Writes a matrix out to the data stream
 Returns : none
 Args    : Array of Bio::Matrix::MatrixI object
          - note that not all matricies can be converted to 
            each format, beware with mixing matrix types and output formats

=cut

sub write_matrix{
   my ($self) = @_;
   $self->throw_not_implemented();
}

sub _initialize {
    my ($self,@args) = @_;
    $self->_initialize_io(@args);
}

=head2 _load_format_module

 Title   : _load_format_module
 Usage   : *INTERNAL Matrix::IO stuff*
 Function: Loads up (like use) a module at run time on demand

=cut

sub _load_format_module {
  my ($self,$format) = @_;
  my $module = "Bio::Matrix::IO::" . $format;
  my $ok;
  
  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the Matrix::IO system please see the
Matrix::IO docs.  This includes ways of checking for formats at
compile time, not run time
END
  ;
  }
  return $ok;
}


=head2 _guess_format

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Returns : guessed format of filename (lower case)
 Args    : filename

=cut

sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'scoring'   if /BLOSUM|PAM$/i;
   return 'phylip'   if /\.dist$/i;
}

sub DESTROY {
    my $self = shift;
    $self->close();
}

sub TIEHANDLE {
  my $class = shift;
  return bless {'matrixio' => shift},$class;
}

sub READLINE {
  my $self = shift;
  return $self->{'matrixio'}->next_tree() || undef unless wantarray;
  my (@list,$obj);
  push @list,$obj  while $obj = $self->{'treeio'}->next_tree();
  return @list;
}

sub PRINT {
  my $self = shift;
  $self->{'matrixio'}->write_tree(@_);
}

1;