Hi all,
I found an annoying bug in MZmine (up to last version 2.5). If you create a
batch with two steps of the same mass detector (e.g. Centroid), then the
instance of the parameter set of this mass detector is shared for both steps
and it is not possible to set different parameters to them. This bug was
probably caused by a general confusion in how many instances of ParameterSet
should exist: the MZmineModule interface had a getParameterSet() method, but
the runModule() method had another ParameterSet as its parameter. To make the
story short, I decided to fix this by changing the MZmineModule interface and
took this as an opportunity to cleanup some old code.
The MZmineModule interface now defines the modules's parameter class using this
method:
public Class<? extends ParameterSet> getParameterSetClass();
There is a new interface MZmineConfiguration that stores the global (main)
parameter set for each module.
During startup, one instance of each module's parameter set is created and
stored in the configuration class.
I moved the code for loading/saving configuration to the configuration class,
so the MZmineCore class is now a bit shorter.
Additionally, I created a new interface MZmineProcessingStep, which represents
a pair of a module and its parameter set.
For example, this is used for each step of the batch mode processing.
Please update your sources from the trunk and let me know if have any
questions/problems.
Cheers,
Tomas
===============================================
Tomas Pluskal
G0 Cell Unit, Okinawa Institute of Science and Technology Graduate University
1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
TEL: +81-98-966-8684
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