Bio::Matrix::IO - A factory for Matrix parsing


  use Bio::Matrix::IO;
  my $parser = Bio::Matrix::IO->new(-format => 'scoring',
                                    -file   => 'BLOSUMN50');

  my $matrix = $parser->next_matrix;


This is a general factory framework for writing parsers for Matricies. This includes parsing output from distance output like PHYLIP's ProtDist. Additionally it should be possible to fit parsers for PWM and PSSMs once their Matrix objects are written.


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AUTHOR - Jason Stajich

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


 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    :


 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    :


 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


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


 Title   : next_matrix
 Usage   : my $matrix = $matixio->next_matrix;
 Function: Parse the next matrix from the data stream
 Returns : L<Bio::Matrix::MatrixI> type object or undef when finished
 Args    : none


 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


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


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