Provided by: libbio-perl-perl_1.7.6-3_all bug


       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

       Email jason-at-bioperl-dot-org


       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