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SBMLWrite - HTML output


In this mode SBMLWrite will read an SBML file and generate an interpretive listing - similar to the verbose output of SBMLRead - that is formatted in html.

SBMLWrite html format new in version 1.0. Modified in version 2.3.6 (style sheets added); 2.3.24 (notes option).


Verbose options for SBMLRead, such as verboseStoichiometryMatrix, etc, can be used, as well as the following options.

Option
Description

inputfile

The (string) name of the file to be read. This option is required, and its format is system dependent.

outputfile

The name of the file to be written. If this option is not specified, the output will be written to the currently active Mathematica notebook.

format

String indicating the type of output to write. format->"HTML" is the required option to return the html interpretive listing of the model

notes

notes->True: write Model notes to html file.

notes->False (default): do not write Model notes to html file.

stylesheet

stylesheet->string-filename - include the line <link rel="stylesheet" href="string-filename " type="text/css"> in the header of the html file.

stylesheet->"Inline" (default) - include a complete style sheet in the header of the html file and make no reference to any external style sheet.

stylesheet->"None" - do not include either a reference to an external style sheet or any internal style sheet in the header of the html file.


Example

SBMLWrite[inputfile -> "rep.xml", 
          format -> html, 
          outputfile -> "foo.html", 
          stylesheet -> "foo.css"]

Sample Style Sheets

These examples are illustrated on the sbml file rep.xml, which can be downloaded as zipped XML | HTML Encapsulated XML | Raw XML (Note that most browsers will not display raw xml files correctly). The MathSBML commands that were used to create this XML file are here.

Style Sheet Elements

The following style sheet elements are defined by this option. For more details one should consult the examples files listed above.

Style
Description
p.file-information File name, SBML version, model id and name
span.file-information-label Lablels in file-information
table.sbml-table Overall styles for tables
td.sbml-tag-title Table data styles for SBML tag label such as "compartment", "unit", etc.
td.sbml-model-notes Table data styles for the model notes
td.sbml-column-data Table data styles for the column contents
td.sbml-column-head Table data styles for the column headers
divThe entire body is encapsulated in a single div
body Default styles for entire body of the file.

This page last modified 5 July 2004