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International
Tables for Crystallography Volume G Definition and exchange of crystallographic data Edited by S. R. Hall and B. McMahon © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. G. ch. 5.2, pp. 494-495
Section 5.2.5. Browser-based viewing with StarMarkUp
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School of Computer Science and Software Engineering, University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia,bSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia, and cInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England |
StarMarkUp is a Tcl/Tk program that takes any STAR File as input and outputs the contents as HTML. The output is a faithful copy of the input, and there is no reformatting or deletion of content.
During transformation, the contents can be cross-referenced against any other STAR File using HTML anchors. This feature is particularly useful when marking up a data file, since the data names contained within can be hyperlinked to their definition in their dictionary. Furthermore, the definitions contained within the dictionary can be hyperlinked to the DDL dictionary. StarMarkUp makes no presumptions about the version of DDL employed, the preferred dictionary structure or the specific application of the STAR File. The program understands only the rules of a legitimate STAR File.
StarMarkUp
provides a number of hyperlinking facilities. During markup, it automatically hyperlinks frame-code values to the internal save-frame block to which they point. As part of the same process, StarMarkUp inserts anchors in all data and save-frame blocks. It does this in anticipation that there may be the need to hyperlink to these anchors from another STAR File. The most obvious application for this is in the marking up of the DDL dictionary. The list of anchors generated from this process can be passed on to the discipline dictionary during its markup phase (Fig. 5.2.5.1![[link]](/graphics/greenarr.gif)
). In this way, the tags used in the discipline dictionary to define the data names can be made to point back to their entry in the DDL dictionary. At the same time that the discipline dictionary is being marked up, a list of its anchors is being generated (each anchor being to a data-item definition). This list is used when marking up an instance of the discipline STAR data file to hyperlink each data name back to its definition in the discipline dictionary.
![[Figure 5.2.5.1]](/figures/Gafig5o2o5o1thm.gif)
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Hyperlinking markup generated by StarMarkUp. The example is based on an extended relational dictionary definition language, StarDDL. |
StarMarkUp comprises a hand-crafted tokenizer employing a character buffer and one-character look-ahead to identify accepted tokens. StarMarkUp does not build an internal representation of the file, but functions as a streaming parser. The GetToken() function returns a structure consisting of the token type (an enumerated set) and the token value (the lexeme associated with that token). In most cases, the lexeme is marked up and injected into the output stream. If the token is associated with a STAR File block, the parser will recursively call a MarkUpBlock() function. A recursive descent parser makes it very easy to treat all STAR File blocks (global_, data_ and save_) in identical fashion.
StarMarkUp is implemented in Tcl/Tk for novelty and not because of any particular superior qualities of the language and its API. It is, however, fast and sufficiently flexible, and extensions to the program can be rapidly implemented and tested.
