//The Java-Beanshell code would be similar to this:

import *;
GuiCfg.readCfgStudio();
System.setProperty("scriptingMode", "true");

//LOAD FILE WITH QUERY SEQUENCES
input0 = new prompt.importmenu.FastaFile();
filename = "lysate_new.fasta";
// 
C:/2_WZW_WEBCLU/w3/htdocs/prompt/casestudies/gravy_vs_protein_length/lysate_new.fasta
input0.setFormat("fasta");
input0.setAlphabet("protein");
input0.setFilename(filename);
input0.setDescription("lysate_new.fasta");
input0.run();

//LOAD FILE WITH DATABASE SEQUENCES
input1 = new prompt.importmenu.FastaFile();
filename = "fullgenome.fasta";
// 
C:/2_WZW_WEBCLU/w3/htdocs/prompt/casestudies/gravy_vs_protein_length/fullgenome.fasta
input1.setFormat("fasta");
input1.setAlphabet("protein");
input1.setFilename(filename);
input1.setDescription("fullgenome.fasta");
input1.run();

//BLAST
engine0 = new Blast();

//All warnings/errors/msgs of blastall will be ignored and only printed to the logfile
engine0.ignoreAllBlastErrors=true;

engine0.init(input0,input1);
engine0.setBlastParam("-q -3 -G -1 -E -1 -M BLOSUM62 -e 10.0 -r 1 -q -3");
engine0.setSequenceType(1);
engine0.setSwitchSets(false);
engine0.run();