Bio::Matrix IO
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Summary
Bio::Matrix::IO - A factory for Matrix parsing
Package variables
No package variables defined.
Inherit
Bio::Root::IO
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.
Methods
newDescriptionCode
newFhDescriptionCode
fhDescriptionCode
next_matrixDescriptionCode
write_matrixDescriptionCode
_initialize
No description
Code
_load_format_moduleDescriptionCode
_guess_formatDescriptionCode
DESTROY
No description
Code
TIEHANDLE
No description
Code
READLINE
No description
Code
PRINT
No description
Code
Methods description
newcode    nextTop
 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 :
newFhcodeprevnextTop
 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 :
fhcodeprevnextTop
 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_matrixcodeprevnextTop
 Title   : next_matrix
Usage : my $matrix = $matixio->next_matrix;
Function: Parse the next matrix from the data stream
Returns : Bio::Matrix::MatrixI type object or undef when finished
Args : none
write_matrixcodeprevnextTop
 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_modulecodeprevnextTop
 Title   : _load_format_module
Usage : *INTERNAL Matrix::IO stuff*
Function: Loads up (like use) a module at run time on demand
_guess_formatcodeprevnextTop
 Title   : _guess_format
Usage : $obj->_guess_format($filename)
Returns : guessed format of filename (lower case)
Args : filename
Methods code
newdescriptionprevnextTop
sub new {
   my($caller,@args) = @_;
  my $class = ref($caller) || $caller;
    
    # or do we want to call SUPER on an object if $caller is an
# object?
if( $class =~ /Bio::Matrix::IO::(\S+)/ ) { my ($self) = $class->SUPER::new(@args); $self->_initialize(@args); return $self; } else { my %param = @args; @param{ map { lc $_ } keys %param } = values %param; # lowercase keys
my $format = $param{'-format'} || $class->_guess_format( $param{'-file'} || $ARGV[0] ) || 'scoring'; $format = "\L$format"; # normalize capitalization to lower case
# normalize capitalization
return unless( $class->_load_format_module($format) ); return "Bio::Matrix::IO::$format"->new(@args); }
}
newFhdescriptionprevnextTop
sub newFh {
  my $class = shift;
  return unless my $self = $class->new(@_);
  return $self->fh;
}
fhdescriptionprevnextTop
sub fh {
  my $self = shift;
  my $class = ref($self) || $self;
  my $s = Symbol::gensym;
  tie $$s,$class,$self;
  return $s;
}
next_matrixdescriptionprevnextTop
sub next_matrix {
   my ($self) = @_;
   $self->throw_not_implemented();
}
write_matrixdescriptionprevnextTop
sub write_matrix {
   my ($self) = @_;
   $self->throw_not_implemented();
}
_initializedescriptionprevnextTop
sub _initialize {
    my ($self,@args) = @_;
    $self->_initialize_io(@args);
}
_load_format_moduledescriptionprevnextTop
sub _load_format_module {
  my ($self,$format) = @_;
  my $module = "Bio::Matrix::IO::" . $format;
  my $ok;
  
  eval {
      $ok = $self->_load_module($module);
  };
  if ( $@ ) {
    print STDERR <<END;
$self: $format cannot be found
Exception $@
For more information about the Matrix::IO system please see the
Matrix::IO docs. This includes ways of checking for formats at
compile time, not run time
END
; } return $ok;
}
_guess_formatdescriptionprevnextTop
sub _guess_format {
   my $class = shift;
   return unless $_ = shift;
   return 'scoring'   if /BLOSUM|PAM$/i;
   return 'phylip'   if /\.dist$/i;
}
DESTROYdescriptionprevnextTop
sub DESTROY {
    my $self = shift;
    $self->close();
}
TIEHANDLEdescriptionprevnextTop
sub TIEHANDLE {
  my $class = shift;
  return bless {'matrixio' => shift},$class;
}
READLINEdescriptionprevnextTop
sub READLINE {
  my $self = shift;
  return $self->{'matrixio'}->next_tree() unless wantarray;
  my (@list,$obj);
  push @list,$obj  while $obj = $self->{'treeio'}->next_tree();
  return @list;
}
PRINTdescriptionprevnextTop
sub PRINT {
  my $self = shift;
  $self->{'matrixio'}->write_tree(@_);
}

1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl-dot-org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
formatTop
 Title   : format
Usage : $format = $obj->format()
Function: Get the matrix format
Returns : matrix format
Args : none