this.outputFile = outputFile;
this.confidenceScore = confidenceScore;
}
public void run() throws Exception {
VirtualProteinMascotLocationGenerator locationGenerator = new VirtualProteinMascotLocationGenerator(
searchResultsPaths, translationTableFile, genomeFile,
chromosomeDir, confidenceScore);
List<ProteinLocation> locations = locationGenerator.generateLocations();
Collections.sort(locations);
GffOutputterGenerator outputterGenerator = new GffOutputterGenerator(genomeFile.getName());
ProteinLocationFileGenerator.generateFile(locations, outputFile, outputterGenerator, "##gff-version 3");
}