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.\" ========================================================================
.\"
.IX Title "MAGE::XML::Reader 3pm"
.TH MAGE::XML::Reader 3pm "2020-12-01" "perl v5.32.0" "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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.nh
.SH "NAME"
Bio::MAGE::XML::Reader \- a module for exporting MAGE\-ML
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::MAGE::XML::Reader;
\&
\&  my $reader = Bio::MAGE::XML::Reader\->new(handler=>$handler,
\&                                         sax1=>$sax1,
\&                                         verbose=>$verbose,
\&                                         log_file=>\e*STDERR,
\&                                        );
\&
\&  # set the sax1 attribute
\&  $reader\->sax1($bool);
\&
\&  # get the current value
\&  $value = $reader\->sax1();
\&
\&  # set the content/document handler \- this method is provided for completeness
\&  # the value should be set in the call to the constructor to be effective
\&  $reader\->handler($HANDLER);
\&
\&  # get the current handler
\&  $handler = $reader\->handler();
\&
\&  # set the attribute
\&  $reader\->verbose($integer);
\&
\&  # get the current value
\&  $value = $reader\->verbose();
\&
\&  # set the attribute
\&  $reader\->log_file($filename);
\&
\&  # get the current value
\&  $value = $reader\->log_file();
\&
\&  # whether to read data cubes externally (default == FALSE)
\&  $writer\->external_data($bool);
\&
\&  my $fh = \e*STDOUT;
\&  my $mage = $reader\->read($file_name);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Methods for transforming information from a MAGE-OM objects into
MAGE-ML.
.SS "\s-1ATTRIBUTE METHODS\s0"
.IX Subsection "ATTRIBUTE METHODS"
These methods have a polymorphic setter/getter method that sets an
attribute which affects the parsing of MAGE-ML. If given a value, the
method will save the value to the attribute, if invoked with no
argument it will return the current value of the attribute.
.PP
These attributes can all be set in the call to the constructor using
the named parameter style.
.IP "sax1" 4
.IX Item "sax1"
This attribute determines whether a \s-1SAX1\s0 parser and DocumentHandler or
a SAX2XMLReader and a ContentHandler will be used for parsing. The
default is to use a \s-1SAX2\s0 parser.
.IP "handler" 4
.IX Item "handler"
If an application needs a custom handler it can set this attribute in
the call to the constructor. It is advised that the object use inherit
either from Bio::MAGE::XML::Handler::ContentHandler (if using \s-1SAX2\s0) or
Bio::MAGE::DocumentHandler if using \s-1SAX1.\s0 In particular, whatever
class is used, it needs to implement the following methods:
.RS 4
.IP "\(bu" 4
verbose
.Sp
called with the integer parameter that specifies the desired level of
output
.IP "\(bu" 4
log_file
.Sp
called with the file handle to which output should be sent
.IP "\(bu" 4
init
.Sp
called during the constructor for any needed work
.RE
.RS 4
.RE
.SS "parser"
.IX Subsection "parser"
.Vb 6
\& Title   : parser
\& Usage   : $obj\->parser($newval)
\& Function: 
\& Example : 
\& Returns : value of parser (a scalar)
\& Args    : on set, new value (a scalar or undef, optional)
.Ve
.IP "verbose" 4
.IX Item "verbose"
This attribute determines the desired level of output during the
parse. The default is no output. A positive value increases the amount
of information.
.IP "log_file" 4
.IX Item "log_file"
This attribute specifies a file handle to which parse output will be
directed. It is only needed if verbose is positive.
.IP "external_data($bool)" 4
.IX Item "external_data($bool)"
If defined, this will cause all BioAssayData objects to read
themselves out using the DataExternal format.
.Sp
\&\fBDefault Value:\fR false
.IP "resolve_identifiers" 4
.IX Item "resolve_identifiers"
This attribute specifies whether the reader should attempt to track
unhandled identifiers in the document, and then resolve them when
parsing is over. This can be a huge performance hit if you know that
all identifiers wil not resolve.
.Sp
\&\fBDefault Value:\fR false
.SS "\s-1INSTANCE METHODS\s0"
.IX Subsection "INSTANCE METHODS"
.ie n .IP "$self\->read($file_name)" 4
.el .IP "\f(CW$self\fR\->read($file_name)" 4
.IX Item "$self->read($file_name)"
This method will open the MAGE-ML file specified by \f(CW$file_name\fR and if
the \f(CW\*(C`handler\*(C'\fR attribute is not set, it will create either a \s-1SAX2\s0
parser or a \s-1SAX1\s0 parser (depending on the value of the C <sax1>
attribute) and parse the file.
.Sp
\&\f(CW\*(C`read()\*(C'\fR can read from \s-1STDIN\s0 by specifying '\-' as the filename. This
enables you to handle compressed \s-1XML\s0 files:
.Sp
.Vb 1
\&  gzip \-dc file.xml.gz | read.pl [options]
.Ve
.SH "POD ERRORS"
.IX Header "POD ERRORS"
Hey! \fBThe above document had some coding errors, which are explained below:\fR
.IP "Around line 172:" 4
.IX Item "Around line 172:"
You forgot a '=back' before '=head2'
.IP "Around line 190:" 4
.IX Item "Around line 190:"
\&'=item' outside of any '=over'