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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
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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.
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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 |
| div | The entire body is encapsulated in a single div |
| body | Default styles for entire body of the file. |
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