Provided by: libbio-mage-utils-perl_20030502.0-5_all bug

NAME

       Bio::MAGE::XML::Writer - a module for exporting MAGE-ML

SYNOPSIS

         use Bio::MAGE::XMLUtils;

         my $writer = Bio::MAGE::XML::Writer->new(@args);
         $writer->write($mage);

         #
         # attributes to modify where the output is written
         #

         # set the output filehandle
         my $fh = \*STDOUT;
         $writer->fh($fh);

         # whether to write data cubes externally (default == FALSE)
         $writer->external_data($bool);

         # which directory to write external data cubes (default == /tmp)
         $writer->external_data_dir($path);

         # whether the to interpret the C<cube> as data or a file
         # path (default == FALSE)
         $writer->cube_holds_path($bool);

         #
         # attributes to modify the output format
         #

         # which format is the external data file
         $writer->data_format($dataformat);

         # to change the level of indent for each new tag (defaul == 2)
         $writer->indent_increment($num);

         # to change the beginning indent level (defaul == 0)
         $writer->indent_level($num);

         # set to true to not format attributes (default == FALSE)
         $writer->attrs_on_one_line($bool);

         # how many extra spaces attributes should be indented past start
         # tag end (default == 1)
         $writer->attr_indent($num);

         # whether to write all sub-tags on the same line (default == undef)
         $writer->collapse_tag($bool);

         #
         # attributes to modify the the document
         #

         # to change the encoding (default == ISO-8859-1)
         $writer->encoding($format);

         # to set the public id (default == undef)
         $writer->public_id($id);

         # to change the system id (default == MAGE-ML.dtd)
         $writer->system_id($id);

         # check to see that objects set more than just identifier (default == TRUE)
         $writer->empty_identifiable_check();

         #
         # attributes to handle identifiers
         #

         # whether to create identifiers if not specified (default == FALSE)
         $writer->generate_new_identifiers();

         # code reference to be invoked for creating new identifiers
         $writer->generate_identifier();

DESCRIPTION

       Methods for transforming information from a MAGE-OM objects into MAGE-ML.

METHODS

       write($MAGE_object);
           "write()"  prints  the  objects  contained  in $MAGE_object as MAGE-ML to the file handle used by the
           writer.

ATTRIBUTE METHODS

         The following methods must all be invoked using an instance of Bio::MAGE::XML::Writer;

       indent_level($num)
           This attribute controls the current level of indentation while writing a document. It should  not  be
           manipulated by users, unless for some reason you wanted to set the starting indent level to something
           other than zero.

           Default Value: 0 (zero)

       indent_increment($num)
           This  attribute  controls  the  the  number of spaces that added to the indent for every new level of
           elements.

           Default Value: 2

       attrs_on_one_line($bool)
           This attribute controls whether attribute values should be pretty-printed. If true,  attributes  will
           not pretty-printed, but will instead be written out all on one line.

           Default Value: false

       attr_indent($bool)
           Controls  how  many  spaces  past  the end start tag that attributes should be indented. This example
           shows an "attr_inden" of 1:

                 <Reporter identifier="Reporter:X Units Per Pixel"
                           name="X Units Per Pixel">

           The following illustrates and "attr_indent" of -2:

                 <Person firstName="John"
                      identifier="Person:John Smith"
                      name="John Smith"
                      lastName="Smith">

           Default Value: 1

       collapse_tag($bool)
           This attribute is not very useful at the moment. In the future it may be used to  specify  tags  that
           should have their contents all on a single line.

           Currently it controls whether or not to write a newline after each elements start tag, with no method
           to decide to write or not to write based on the name of the tag.

           Default Value: false

       encoding($string)
           This  is the value that value be written out as the encoding attribute for the XML Declaration of the
           output MAGE-ML document:

             <?xml version="1.0" encoding="ISO-8859-1" standalone="no"?>

           Default Value: ISO-8859-1

       public)_id($string)
           If defined, this value will be written out as the value of the PUBLIC attribute of the DOCTYPE tag in
           the output MAGE-ML document.

           Default Value: undef

       system_id($string)
           If defined, this value will be written out as the value of the SYSTEM attribute of the DOCTYPE tag in
           the output MAGE-ML document:

             <!DOCTYPE MAGE-ML  SYSTEM "MAGE-ML.dtd">

           Default Value: MAGE-ML.dtd

       generate_identifier($code_ref)
           This attribute stores a code reference that will be invoked to create a new identifier for any object
           that does not already have one defined. This  will  happen  only  if  the  "generate_new_identifiers"
           attribute is set to true.

           Default Value: \&identifier_generation

       generate_new_identifier($bool)
           If  this  attribute  is  set to true, the code reference store in the "generate_identifier" attribute
           will be invoked to create a new identifier for any object that does not already have one defined.

           Default Value: false

       fh($file_handle)
           This is the file handle to which the MAGE-ML document will be written.

           Default Value: undef

       external_data($bool)
           If defined, this will cause all BioAssayData objects to write themselves out using  the  DataExternal
           format.

           Default Value: false

       data_format($format)
           $format is either 'tab delimited' or 'space delimited'

           Default Value: 'tab delimited'

       external_data_dir($path)
           The  "fh"  attribute only controls where the main MAGE-ML document is written. If the "external_data"
           attribute is set, the writer will also create a separate external data file for each data cube.

           The "external_data_dir" controls what director those files are written to.

           Default Value: /tmp

       cube_holds_path($path)
           Sometimes, you already have your data written to an external file, and you simply want to  reuse  the
           file  without  any  extra  overhead.  The "cube_holds_path" attribute controls indicates that you are
           storing the path to the external file in the "cube" attribute of the "BioDataCube" objects.

           Default Value: false

       empty_identifiable_check($bool)
           If true, all objects that define an "identifier" attribute and  no  other  attributes  will  only  be
           included as <*_ref> elements.

           NOTE:  Currently no checking of association values is made, only attributes. So if you want to ensure
           that an Identifiable object is written, make sure that you set the "name" attribute as  well  as  the
           "identifier" attribute.

           Default Value: true

POD ERRORS

       Hey! The above document had some coding errors, which are explained below:

       Around line 147:
           '=item' outside of any '=over'

       Around line 656:
           You forgot a '=back' before '=head1'

       Around line 660:
           =over without closing =back

perl v5.32.0                                       2020-12-01                             MAGE::XML::Writer(3pm)