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PRIDE-Archive / jmzIdentML

A java library to parse and read mzIdentML files
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new changes to improve performance #3

Closed UKQIDA closed 6 years ago

UKQIDA commented 7 years ago

replaced the SimpleXmlElementExtractor with FastXmlElementExtractor

UKQIDA commented 7 years ago

Would it also possible to merge this please?

julianu commented 7 years ago

I just updated my dependencies to version 1.2.7 (which is the least stable, as far as I know). The performance dropped drastically and I am not sure why, there must be anything with indexing or something. So, is there any reason for not merging this, if it makes the parser fast again?

ypriverol commented 7 years ago

@UKQIDA can you take a look to this.. performance issues are important in jmzIdentML. The last updates are coming from @UKQIDA using the new xindex.

UKQIDA commented 7 years ago

I dont think my pull request was merged in release 1.2.7 which occurred in July.

julianu commented 7 years ago

Ok, I will test Da's version with my tool and report back. Probably won't have time until end of next week, though.

ypriverol commented 7 years ago

That would be great, if it works let me know we can do the release and propagate this to other libraries

andrewrobertjones commented 6 years ago

@julianu did you ever get a chance to test Da's version. I also think it is running much faster, and would like to get it integrated into the main maven build process.

julianu commented 6 years ago

No, not yet, sorry. But I put it back on my agenda and will hopefully do so soon.

julianu commented 6 years ago

I finally checked the pull request: It works and is much faster than the current 1.2.7 version and finally allows to export 1.2 files natively. I vote for merging this!