[Animl-develop] Sequence of info in AnIML documents

[Prof. R. J. L. <rob...@uw...>]

Hi all,

Please excuse me while I try to come to grips with the design of
AnIML documents. I need some pointers.....

I have been looking at a method of parsing info out of AnIML
files using StAX (the Streaming API for XML that uses pull-based methods).
This allows the user to read large documents with minimal overhead
which I figured was going to be an essential ingredient when we have
nD spectra or hyphenated spectral data.

I originally started with DOM routines (courtesy of Stuart) for reading
AnIML files for the JSpecView project but now find that there are issues
when using the Applet on a web page that seem to stop the document being
parsed even for small files. I am still not totally clear as to what the issue
is but think it may be due to having to hold the whole file in memory at once.
Anyway this led me to look at StAX as an alternative. (We already use
streaming methods for reading JCAMP-DX files)

When attempting to process the document to find all the essential
variables and information needed to be able to plot the data, it seems
that the first thing that needs to be known is NOT what the SAMPLE
is but rather what the TECHNIQUE is. This then determines which
critical technique dependent parameters we need to look for.

StAX parses through in one direction only and does not allow you to move
backwards so it would suggest that if the MEASUREMENTDATA and in
particular the EXPERIMENTSTEP came first then it would make it easier
to parse through the file to find things like NMR Frequencies etc.
Otherwise you need to store all the info somewhere and read it again.

What this implies is that the SAMPLESET node needs to come after
the MEASUREMENTDATA node.

This would solve the problem I have with SAMPLE info as well in that
at present there is no way of knowing which is SAMPLE/BLANK/REFERENCE
etc when processing the SAMPLESET since that information is in the
MEASUREMENTDATA under the SAMPLESUSED/SAMPLESET. It still needs
to be welll defined and I am not sure whether
role="SampleMeasurement" is a predefined STRING or free TEXT.

Any help appreciated

Robert






-- 
Prof. Robert J. Lancashire   mailto:rob...@uw...
Department of Chemistry                           Tel (876) 512 3026
University of the West Indies, Kingston 7     Fax (876) 9771835
Mona Campus, JAMAICA.  http://wwwchem.uwimona.edu.jm/chrl.html