--- name: "Bio::MAGE::XML::Writer" section: "3pm" platform: "linux" package: "libbio-mage-utils-perl" version: "20030502.0-5" release: "Debian 13 (Trixie)" platforms: ["linux"] url: "https://new.carta.tech/Bio::MAGE::XML::Writer" --- # Bio::MAGE::XML::Writer(3pm) a module for exporting MAGE-ML ## 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 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($bool) Controls how many spaces past the end start tag that attributes should be indented. This example shows an `"attr_inden"` of 1: ``` ``` The following illustrates and `"attr_indent"` of -2: ``` ``` **Default Value:** 1 - collapse\_tag($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($string) This is the value that value be written out as the encoding attribute for the XML Declaration of the output MAGE-ML document: ``` ``` **Default Value:** ISO-8859-1 - public)\_id($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($string) If defined, this value will be written out as the value of the SYSTEM attribute of the DOCTYPE tag in the output MAGE-ML document: ``` ``` **Default Value:** MAGE-ML.dtd - generate\_identifier($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