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.\" ========================================================================
.\"
.IX Title "Bio::Matrix::IO 3pm"
.TH Bio::Matrix::IO 3pm "2020-10-28" "perl v5.30.3" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Bio::Matrix::IO \- A factory for Matrix parsing
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 3
\&  use Bio::Matrix::IO;
\&  my $parser = Bio::Matrix::IO\->new(\-format => \*(Aqscoring\*(Aq,
\&                                    \-file   => \*(AqBLOSUMN50\*(Aq);
\&
\&  my $matrix = $parser\->next_matrix;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a general factory framework for writing parsers for Matricies.
This includes parsing output from distance output like \s-1PHYLIP\s0's
ProtDist.  Additionally it should be possible to fit parsers for \s-1PWM\s0
and PSSMs once their Matrix objects are written.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  https://github.com/bioperl/bioperl\-live/issues
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason-at-bioperl-dot-org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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    :
.Ve
.SS "newFh"
.IX Subsection "newFh"
.Vb 8
\& Title   : newFh
\& Usage   : $fh = Bio::Matrix::IO\->newFh(\-file=>$filename,\-format=>\*(AqFormat\*(Aq)
\& Function: does a new() followed by an fh()
\& Example : $fh = Bio::Matrix::IO\->newFh(\-file=>$filename,\-format=>\*(AqFormat\*(Aq)
\&           $matrix = <$fh>;   # read a matrix object
\&           print $fh $matrix; # write a matrix object
\& Returns : filehandle tied to the Bio::SeqIO::Fh class
\& Args    :
.Ve
.SS "fh"
.IX Subsection "fh"
.Vb 8
\& 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
.Ve
.SS "format"
.IX Subsection "format"
.Vb 5
\& Title   : format
\& Usage   : $format = $obj\->format()
\& Function: Get the matrix format
\& Returns : matrix format
\& Args    : none
.Ve
.SS "next_matrix"
.IX Subsection "next_matrix"
.Vb 5
\& 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
.Ve
.SS "write_matrix"
.IX Subsection "write_matrix"
.Vb 7
\& 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
.Ve
.SS "_load_format_module"
.IX Subsection "_load_format_module"
.Vb 3
\& Title   : _load_format_module
\& Usage   : *INTERNAL Matrix::IO stuff*
\& Function: Loads up (like use) a module at run time on demand
.Ve
.SS "_guess_format"
.IX Subsection "_guess_format"
.Vb 4
\& Title   : _guess_format
\& Usage   : $obj\->_guess_format($filename)
\& Returns : guessed format of filename (lower case)
\& Args    : filename
.Ve