Bio::Matrix::IO(3pm)					User Contributed Perl Documentation				      Bio::Matrix::IO(3pm)

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://redmine.open-bio.org/projects/bioperl/

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

   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

perl v5.14.2							    2012-03-02						      Bio::Matrix::IO(3pm)