/** Sets the path configuration. */
private void setPathConfiguration() throws IOException {
File pathConfigurationFile =
new File(PeptideShaker.getJarFilePath(), UtilitiesPathPreferences.configurationFileName);
if (pathConfigurationFile.exists()) {
PeptideShakerPathPreferences.loadPathPreferencesFromFile(pathConfigurationFile);
}
}
/** Loads the species from the species file into the species factory. */
private void loadSpecies() {
try {
SpeciesFactory speciesFactory = SpeciesFactory.getInstance();
speciesFactory.initiate(PeptideShaker.getJarFilePath());
} catch (Exception e) {
System.out.println("An error occurred while loading the species.");
e.printStackTrace();
}
}