I think this is not a problem of identification, but of export.
Other export methods might allow exporting special characters correctly
(e.g., the SQL export), but the target formats of CSV or mzTab export
cannot accept them.
Best,
Tomas
On Fri, Feb 6, 2015 at 8:59 PM, TFRD (Thomas Franck Dyrlund) <t...@steno.dk>
wrote:
> Well spotted! I have fixed the issue for the mzTab export. But why not fix
> this in all the identification modules instead?
>
> /Thomas
>
> -----Original Message-----
> From: Tomas Pluskal [mailto:plus...@oist.jp]
> Sent: 6. februar 2015 08:40
> To: Developer discussion
> Subject: [Mzmine-devel] mzTab export - stripping special characters
>
> Hi Thomas,
>
> I added a new method escapeStringForCSV to CSVExportTask. The purpose of
> this method is to strip control characters from the exported strings
> (particularly things like EOL \n). It basically calls
> inputString.replaceAll("[\\p{Cntrl}]", " “);
>
> It is possible that some peak identity data might contain such special
> characters. I recommend to also check your mzTab export module how it
> behaves in such case. Perhaps you might also need to remove any special
> characters before exporting the strings. I mean, for example, what happens
> if the peak identity contains the \t (tab) character? Maybe the jmztab
> library can handle this, but we should make sure it works.
>
> Cheers,
>
> Tomas
>
>
> ===============================================
> Tomas Pluskal
> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
> University
> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
> WWW: https://groups.oist.jp/g0
> TEL: +81-98-966-8684
> Fax: +81-98-966-2890
>
>
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leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
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