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Index a protein database (FASTA file) for fast searching.

Usage: java -Xmx3500M -cp MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA
	    -d DatabaseFile (*.fasta or *.fa or *.faa; if a directory path, index all FASTA files)
	    [-tda 0/1/2] (0: Target database only, 1: Concatenated target-decoy database only, 2: Both (Default))
	    [-o OutputDir] (Directory to save index files; default is the same as the input file)
	    [-decoy DecoyPrefix] (Prefix for decoy protein names; default is XXX)


BuildSA creates a suffix array of the protein database. For an input database file DBFileName.fasta, BuildSA will generate 4 auxiliary files:

BuildSA only needs to be executed once for each protein database file.