Re: [chemclipse-dev] Question about AbstractVendorMassSpectrumProxy clas

[Trig Chen <trigchen@xxxxxxxxx>]

Hi Philip,

Yes, your consideration is reasonable. Since the isProxy is a private
field and has no method to modify it, I did not extend
AbstractVendorMassSpectrumProxy class. I just copy it to my package
and add a setter for isProxy field. After I have calibrated the m/z
conversion factors, I iteratively set all scan's isProxy to true to
force them to reload if them are reaccess later. :)

Best regards,

Trig


2016-10-20 15:30 GMT+08:00 Philip Wenig <philip.wenig@xxxxxxxxxxxxx>:
> Hi Trig,
>
> this could cause some implications which would decrease the performance
> tremendously.
> Think of a loop where one looks for a certain m/z values. Each time, the
> scan would be loaded and discarded and the loaded again and again. If it
> stays in memory, no further I/O operation is needed.
>
> I don't want to activate additional in the core platform where I'm not sure
> if there are unwanted side-effects. Anyhow, feel free to overwrite the
> methods in your own class and add your specific functionality. If that works
> fine, let's see if we can refactor the core.
>
>
> Best,
> Philip
>
>
> Am 20.10.2016 um 09:23 schrieb Trig Chen:
>
> Hi Philip,
>
> In most cases, such as processing data in OpenChrom, it would be good
> loading once data from file through proxy and thereafter access this data in
> memory. In my case, my data is acquired from spectrometer and then written
> to file and sent to GUI for display. That means all scans are gotten access
> and loaded! I prefer to release the scan after it was shown. If user clicks
> the TIC plot and recall the related scan, I can reload it from file again.
> So, it would be good if AbstractVendorMassSpectrumProxy class has the
> ability to access data through proxy always, not just once.
>
>
>
>
>
>
> Best regards,
>
> Trig
>
> 2016-10-19 17:08 GMT+08:00 Philip Wenig <philip.wenig@xxxxxxxxxxxxx>:
>>
>> Hi Trig,
>>
>> that's correct.
>>
>> When analyzing huge files > 1 GB, the performance would be miserable if
>> each scan is loaded in advance. Hence, it shall be loaded only when it is
>> needed. Each vendor supplier best knows on his own ho to extract the data
>> from a scan, when it's needed (e.g. only he knows the byte position in the
>> file where the requested scan is located). The member variable is set to
>> true after successfully loading the file. I've explicitly not added a method
>> to set this to false again, cause the scan is loaded after running the
>> "checkProxyAndImportOnDemand()" method. So it's not a proxy anymore
>> afterwards.
>>
>>
>> Best,
>> Philip
>>
>>
>>
>> Am 19.10.2016 um 10:57 schrieb Trig Chen:
>>
>> Hi all,
>>
>> The class
>> org.eclipse.chemclipse.msd.model.core.AbstractVendorMassSpectrumProxy has
>> one private boolean type field "isProxy" with true initial value. This value
>> is changed to false as method checkProxyAndImportOnDemand() called.
>> checkProxyAndImportOnDemand method does the import ions job and then set
>> isProxy to false. Then isProxy stays false always and will never change to
>> true again. That means I can't import ions again.
>>
>> private void checkProxyAndImportOnDemand() {
>>
>> if(isProxy) {
>> isProxy = false;
>> importIons();
>> }
>> }
>>
>> In my case, I firstly import ions and find the m/z values incorrect, so I
>> make a m/z calibration on current mass spectrum. Here comes the problem, I
>> can't reimport ions for current mass spectrum or any other spectra because
>> isProxy is false. There is not a way to set isProxy to true in
>> AbstractVendorMassSpectrumProxy class.
>>
>>
>> Best regards,
>>
>> Trig
>>
>>
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>> --
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>> OpenChrom - the open source alternative for chromatography / mass
>> spectrometry
>> Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx »
>> http://www.openchrom.net
>> ~~~~~~~~~~~~~~~~~~~~~~~~
>>
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> Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx »
> http://www.openchrom.net
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