Using more existing Java libraries

[claczny]

VizBin has evolved organically over time and has multiple contributing authors. The underlying Java code could thus benefit from a rewrite, at least by the increased use of existing Java libraries (that have been tested exhaustively over time). Accordingly, some of the parts may be substituted by existing Java libraries instead of currently used custom-written code.

This issue will keep track of libraries that appear to be interesting and related points.

Operation	Suggestions
Input/Output of fasta files	http://biojava.org/wiki/BioJava:CookBook:Core:FastaReadWrite
Compression/Decompression of fasta sequences to save memory during runtime	https://docs.oracle.com/javase/7/docs/api/java/util/zip/Deflater.html -> Seems applicable to individual strings -> foreach seq: compute kmer frequency; seq = compress(seq)

Feel free to extend/modify the list.

Best,

Cedric