I have updated the mzTab import module and everything should work. Please let
me know if you find any issues with the module. My experience with the mzTab
format so far is very good and I hope that you and the community will enjoy
using the format and that we can help push to have this open format the new
standard in metabolomics.
I have also updated the PeakListTableModel to allow for empty values in the
following fields: average RT, peak RT and peak height. Please let me know if
you see any problems with this.
/Thomas
From: Tomas Pluskal [mailto:plus...@oist.jp]
Sent: 27. januar 2015 09:48
To: Developer discussion
Subject: Re: [Mzmine-devel] MZmine - importing mzTab files
Hi Thomas,
I have added a mzTab import module
(r3627<http://sourceforge.net/p/mzmine/code/3627/>) to MZmine but have a
problem. After adding peaks to the row using newRow.addPeak(rawData, peak); I
get a NullPointerException in SimplePeakListRow.java:104 because
peak.getRawDataPointsIntensityRange() is null. I’m guessing this is because I’m
not defining any DataPoint for my peak. But how can I get around this for the
following two cases:
a. the raw data file is available for the sample
b. only an empty dummy raw file is available for the sample
It doesn’t matter if the raw data is available or not, because anyway, you
don’t know from what scans and what data points the peak was formed.
So I think you should not set any data points to the peak. This is exactly why
we need a new data model :)
With the current data model, I think the easiest solution is to add a single
data point to the peak, something like
new DataPoint(peak.getMz(), peak.getHeight())
I would also like to discuss the following with regards to supporting import of
mzTab files:
1.
mzTab files pr. standard only include the average m/z and rt values and not
individual values for all samples. I suggest that we use these values for the
individual peaks for all samples in the peak list in case the individual values
are not available. What do you think?
If the individual m/z values are not available, this seems to be the only
solution.
2.
Duration, height and peak shape is not included in mzTab files. Should we leave
these empty in the peak lists or should we calculate these values for the
samples for which raw files are available?
Same as I mentioned above, I think it does not matter if raw data is available
or not. You will never know how exactly was peak detection performed to produce
the mzTab file.
I think that leaving this data empty (or providing some dummy values) is a
reasonable solution.
3.
I think that the placement of the export/import modules could be improved. I
would suggest that we place the export and import modules as separate sub-menus
under project. I think that this would be the place most people would look
first for import and export functions. Also, the new mzTab import module
imports both raw files and peak lists. This change could wait until MZmine 3
but I think it is important that we think of how to structure the menus in the
next big version to see if we can make things more intuitive.
I agree the menu needs improving.
If you have a specific idea how to structure it better, could you write down
your vision of the menu structure in another email? Then we can discuss it.
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
------------------------------------------------------------------------------
Dive into the World of Parallel Programming. The Go Parallel Website,
sponsored by Intel and developed in partnership with Slashdot Media, is your
hub for all things parallel software development, from weekly thought
leadership blogs to news, videos, case studies, tutorials and more. Take a
look and join the conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Mzmine-devel mailing list
Mzmine-devel@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/mzmine-devel
