A core of banchelor thesis of Bc. Josef Havranek DiS.

Code in this repository is a core of work of me author of this repository Bc. Josef Havranek DiS. a Banchelor thesis. Topic of this thesis was a Optimalization and refactoring of DNA analyser Its purpose is prepocesing of FASTA and plain (only nucleic character as ACTGU etc.) sequences. it was part of procesing of uploaded files (during upload and in batch later)

About code

Code has been partialy redacted since it is not oficialy open source but what it here is sensible cutdown version of code(with alowance ) it only contains things that are related all package names was redacted. Everything i wrote compleetly or clases that i changed and it had big inpact on speed was denoted with not redacted and vere not redacted.

Code was put publicly as demonstration of my abilities and as tribute to scientific comunity for further use outside of my school. It contains as far as I know only format extensible multithreaded preprocesor of DNA sequences in Java with most likely fastest vectorizing DNA string uppercaser in Java. Faster than comon implementation of string.toUppercase() (with proof)

It even employ cash size to improve cache hit ratio since chunks of data are read/writen multiple times.. not dooing so had regresive efect on speed (unrecorded).

it also implements custom spinlock since it was faster (unrecorded)

noteworthy (unredacted) code

• THE preprocesor that contains fast uppercaser and paralel preprocesor of data
• Parallel nucleic counter with custom spinlock
• Pre-PreProcesor and datastorage handling this is where uploaded data goes first this is where "cache aligning" happens
• Streamed database downloader allows process data swiftly from external NCBI database.

UppercaserSpeed

Time of uppercaser mesured with visualVM with profiling
on 2 cores 4 thread i5-7200U with 3.1GHZ

note: Even time seems miniscule this will mater when you account that DNA sequences can go up to 2GB (currently longest chromosome is a chromosome of Axolotl Mexicana)

Size/Version	string.toUpperCase()	Custom
MB	time (ms)	time (ms)
3	18.1	12.7
5	29.4	17.4
10	63.3	35.2
50	364	163

Achivements/graphs

speed up preprocesor by $3\times$

in all graphs blue is oreginal implementation

diamonds are mesurement

Speed of pre-preprocesor

speed of preprocesor

arrow indicate crash of oreginal implementation