NAME

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

SYNOPSIS

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

         my $matrix = $parser->next_matrix;

DESCRIPTION

       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.

FEEDBACK

   Mailing Lists
       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
       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 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

AUTHOR - Jason Stajich

       Email jason-at-bioperl-dot-org

APPENDIX

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

   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    :

   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    :

   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

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

   next_matrix
        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

   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

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

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