Source:
public void process(String[] argv){ printAboutMe(); for (int i = 0 ; i < argv.length; i++){ String arg = argv[i]; if(arg.equalsIgnoreCase("-h") || arg.equalsIgnoreCase("-help") || arg.equalsIgnoreCase("--help") ) { LOGGER.info(printHelp()); return; } if(arg.equalsIgnoreCase("-version") || arg.equalsIgnoreCase("--version")) { StructureAlignment alg = getAlgorithm(); LOGGER.info(alg.getAlgorithmName() + " v." + alg.getVersion() ); return; } String value = null; if ( i < argv.length -1) value = argv[i+1]; if (value != null && value.startsWith("-")) value = null; else i++; String[] tmp = {arg,value}; try { CliTools.configureBean(params, tmp); } catch (ConfigurationException e){ LOGGER.error("Error: "+e.getLocalizedMessage()); System.exit(1); return; } } if ( params.getPdbFilePath() != null){ System.setProperty(UserConfiguration.PDB_DIR,params.getPdbFilePath()); } if ( params.getCacheFilePath() != null){ System.setProperty(UserConfiguration.PDB_CACHE_DIR,params.getCacheFilePath()); } if ( params.isShowMenu()){ LOGGER.info("showing menu..."); try { GuiWrapper.showAlignmentGUI(); } catch (Exception e){ LOGGER.error(e.getMessage()); e.printStackTrace(); } } if ( params.getShowDBresult() != null){ LOGGER.info("showing DB results..."); try { GuiWrapper.showDBResults(params); } catch (Exception e){ LOGGER.error(e.getMessage()); e.printStackTrace(); } } String pdb1 = params.getPdb1(); String file1 = params.getFile1(); try { if (pdb1 != null || file1 != null){ runPairwise(); return; } if ( params.getAlignPairs() != null){ runDBSearch(); return; } if ( params.getSearchFile() != null){ runDBSearch(); return; } } catch (ConfigurationException e) { LOGGER.error(e.getLocalizedMessage()); System.exit(1); return; } LOGGER.info(printHelp()); LOGGER.error("Error: insufficient arguments."); System.exit(1); return; }

Target:
public void process(String[] argv){ printAboutMe(); for (int i = 0 ; i < argv.length; i++){ String arg = argv[i]; if(arg.equalsIgnoreCase("-h") || arg.equalsIgnoreCase("-help") || arg.equalsIgnoreCase("--help") ) { System.out.println(printHelp()); return; } if(arg.equalsIgnoreCase("-version") || arg.equalsIgnoreCase("--version")) { StructureAlignment alg = getAlgorithm(); LOGGER.info(alg.getAlgorithmName() + " v." + alg.getVersion() ); return; } String value = null; if ( i < argv.length -1) value = argv[i+1]; if (value != null && value.startsWith("-")) value = null; else i++; String[] tmp = {arg,value}; try { CliTools.configureBean(params, tmp); } catch (ConfigurationException e){ LOGGER.error("Error: "+e.getLocalizedMessage()); System.exit(1); return; } } if ( params.getPdbFilePath() != null){ System.setProperty(UserConfiguration.PDB_DIR,params.getPdbFilePath()); } if ( params.getCacheFilePath() != null){ System.setProperty(UserConfiguration.PDB_CACHE_DIR,params.getCacheFilePath()); } if ( params.isShowMenu()){ LOGGER.info("showing menu..."); try { GuiWrapper.showAlignmentGUI(); } catch (Exception e){ LOGGER.error(e.getMessage()); e.printStackTrace(); } } if ( params.getShowDBresult() != null){ LOGGER.info("showing DB results..."); try { GuiWrapper.showDBResults(params); } catch (Exception e){ LOGGER.error(e.getMessage()); e.printStackTrace(); } } String pdb1 = params.getPdb1(); String file1 = params.getFile1(); try { if (pdb1 != null || file1 != null){ runPairwise(); return; } if ( params.getAlignPairs() != null){ runDBSearch(); return; } if ( params.getSearchFile() != null){ runDBSearch(); return; } } catch (ConfigurationException e) { LOGGER.error(e.getLocalizedMessage()); System.exit(1); return; } LOGGER.info(printHelp()); LOGGER.error("Error: insufficient arguments."); System.exit(1); return; }