Re: [chemclipse-dev] Question about AbstractVendorMassSpectrumProxy clas

[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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-- 
~~~~~~~~~~~~~~~~~~~~~~~~
OpenChrom - the open source alternative for chromatography / mass spectrometry
Dr. Philip Wenig » Founder » philip.wenig@xxxxxxxxxxxxx » http://www.openchrom.net
~~~~~~~~~~~~~~~~~~~~~~~~