List of usage examples for java.io File listFiles
public File[] listFiles()
From source file:au.org.ala.layers.grid.GridClassBuilder.java
public static void main(String[] args) { logger.info("args[0]=diva grid input file (do not include .grd or .gri)\n\n"); if (args.length > 0) { //remove existing try {//from w w w .j ava 2 s . com File f; if ((f = new File(args[0] + ".classes.json")).exists()) { f.delete(); } if ((f = new File(args[0])).exists() && f.isDirectory()) { File[] fs = f.listFiles(); for (int i = 0; i < fs.length; i++) { if (fs[i].isFile()) { fs[i].delete(); } } } } catch (Exception e) { logger.error(e.getMessage(), e); } //build new try { buildFromGrid(args[0]); } catch (Exception e) { logger.error(e.getMessage(), e); } } }
From source file:mujava.cli.genmutes.java
public static void main(String[] args) throws Exception { // System.out.println("test"); genmutesCom jct = new genmutesCom(); String[] argv = { "-all", "-debug", "Flower" }; // development use, when release, // comment out this line JCommander jCommander = new JCommander(jct, args); // check session name if (jct.getParameters().size() > 1) { Util.Error("Has more parameters than needed."); return;// w w w . j a va 2 s.c o m } // set session name String sessionName = jct.getParameters().get(0); muJavaHomePath = Util.loadConfig(); // check if debug mode if (jct.isDebug()) { Util.debug = true; } // get all existing session name File folder = new File(muJavaHomePath); // check if the config file has defined the correct folder if (!folder.isDirectory()) { Util.Error("ERROR: cannot locate the folder specified in mujava.config"); return; } File[] listOfFiles = folder.listFiles(); // null checking // check the specified folder has files or not if (listOfFiles == null) { Util.Error("ERROR: no files in the muJava home folder: " + muJavaHomePath); return; } List<String> fileNameList = new ArrayList<>(); for (File file : listOfFiles) { fileNameList.add(file.getName()); } // check if session is already created. if (!fileNameList.contains(sessionName)) { Util.Error("Session does not exist."); return; } // get all files in the session String[] file_list = new String[1]; // if(jct.getD()) // { File sessionFolder = new File(muJavaHomePath + "/" + sessionName + "/src"); File[] listOfFilesInSession = sessionFolder.listFiles(); file_list = new String[listOfFilesInSession.length]; for (int i = 0; i < listOfFilesInSession.length; i++) { file_list[i] = listOfFilesInSession[i].getName(); } // get all mutation operators selected HashMap<String, List<String>> ops = new HashMap<String, List<String>>(); // used // for // add // random // percentage // and // maximum String[] paras = new String[] { "1", "0" }; if (jct.getAll()) // all is selected, add all operators { // if all is selected, all mutation operators are added ops.put("AORB", new ArrayList<String>(Arrays.asList(paras))); ops.put("AORS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODS", new ArrayList<String>(Arrays.asList(paras))); ops.put("ROR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COD", new ArrayList<String>(Arrays.asList(paras))); ops.put("COI", new ArrayList<String>(Arrays.asList(paras))); ops.put("SOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOI", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOD", new ArrayList<String>(Arrays.asList(paras))); ops.put("ASRS", new ArrayList<String>(Arrays.asList(paras))); ops.put("SDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("ODL", new ArrayList<String>(Arrays.asList(paras))); ops.put("VDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("CDL", new ArrayList<String>(Arrays.asList(paras))); // ops.put("SDL", jct.getAll()); } else { // if not all, add selected ops to the list if (jct.getAORB()) { ops.put("AORB", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAORS()) { ops.put("AORS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAOIU()) { ops.put("AOIU", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAOIS()) { ops.put("AOIS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAODU()) { ops.put("AODU", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getAODS()) { ops.put("AODS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getROR()) { ops.put("ROR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCOR()) { ops.put("COR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCOD()) { ops.put("COD", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCOI()) { ops.put("COI", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getSOR()) { ops.put("SOR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getLOR()) { ops.put("LOR", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getLOI()) { ops.put("LOI", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getLOD()) { ops.put("LOD", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getASRS()) { ops.put("ASRS", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getSDL()) { ops.put("SDL", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getVDL()) { ops.put("VDL", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getODL()) { ops.put("ODL", new ArrayList<String>(Arrays.asList(paras))); } if (jct.getCDL()) { ops.put("CDL", new ArrayList<String>(Arrays.asList(paras))); } } // add default option "all" if (ops.size() == 0) { ops.put("AORB", new ArrayList<String>(Arrays.asList(paras))); ops.put("AORS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AOIS", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODU", new ArrayList<String>(Arrays.asList(paras))); ops.put("AODS", new ArrayList<String>(Arrays.asList(paras))); ops.put("ROR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COR", new ArrayList<String>(Arrays.asList(paras))); ops.put("COD", new ArrayList<String>(Arrays.asList(paras))); ops.put("COI", new ArrayList<String>(Arrays.asList(paras))); ops.put("SOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOR", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOI", new ArrayList<String>(Arrays.asList(paras))); ops.put("LOD", new ArrayList<String>(Arrays.asList(paras))); ops.put("ASRS", new ArrayList<String>(Arrays.asList(paras))); ops.put("SDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("ODL", new ArrayList<String>(Arrays.asList(paras))); ops.put("VDL", new ArrayList<String>(Arrays.asList(paras))); ops.put("CDL", new ArrayList<String>(Arrays.asList(paras))); } // String[] tradional_ops = ops.toArray(new String[0]); // set system setJMutationStructureAndSession(sessionName); // MutationSystem.setJMutationStructureAndSession(sessionName); MutationSystem.recordInheritanceRelation(); // generate mutants generateMutants(file_list, ops); //System.exit(0); }
From source file:edu.wpi.khufnagle.webimagemanager.WebImageManager.java
/** * Defines information for the lighthouses, then runs the * photograph-collection process.//from w w w .ja v a 2 s.c o m * @param args Command-line arguments for this program (not used in this * implementation) */ // Auto-boxing done "on the fly" to show progress of downloading images @SuppressWarnings("boxing") public static void main(final String[] args) { final long startTime = System.nanoTime(); System.out.println("***BEGIN PHOTO TRANSFER PROCESS***"); // Add data for lighthouses (next 375 lines or so) final List<LighthouseInfo> lighthouseData = new ArrayList<LighthouseInfo>(); /* * lighthouseData.add(new LighthouseInfo("Statue of Liberty", 40.689348, * -74.044726)); */// Statue of Liberty = 2080 photos w/out restrictions lighthouseData.add(new LighthouseInfo("Portland Head Light", 43.623104, -70.207867)); lighthouseData.add(new LighthouseInfo("Pemaquid Point Light", 43.836970, -69.505997)); lighthouseData.add(new LighthouseInfo("Five Mile Point (New Haven Harbor) Light", 41.248958, -72.903766)); lighthouseData.add(new LighthouseInfo("Cape Neddick (Nubble) Light", 43.165211, -70.591102)); lighthouseData.add(new LighthouseInfo("Portland Breakwater Light", 43.655516, -70.234813)); lighthouseData.add(new LighthouseInfo("Beavertail Light", 41.449368, -71.399372)); lighthouseData.add(new LighthouseInfo("Bass Harbor Head Light", 44.221976, -68.337214)); lighthouseData.add(new LighthouseInfo("Nobska Point Light", 41.515792, -70.655116)); lighthouseData.add(new LighthouseInfo("Spring Point Ledge Light", 43.652108, -70.223922)); lighthouseData.add(new LighthouseInfo("Gay Head Light", 41.348450, -70.834956)); lighthouseData.add(new LighthouseInfo("Derby Wharf Light", 42.516566, -70.883536)); lighthouseData.add(new LighthouseInfo("Rockland Breakwater Light", 44.104006, -69.077453)); lighthouseData.add(new LighthouseInfo("Sandy Neck Light", 41.722647, -70.280927)); lighthouseData.add(new LighthouseInfo("Marblehead Light", 42.505411, -70.833708)); lighthouseData.add(new LighthouseInfo("Portsmouth Harbor Light", 43.071061, -70.708634)); lighthouseData.add(new LighthouseInfo("Highland Light", 42.039122, -70.062025)); lighthouseData.add(new LighthouseInfo("Cape Elizabeth Light", 43.566058, -70.200042)); lighthouseData.add(new LighthouseInfo("Marshall Point Light", 43.917406, -69.261222)); lighthouseData.add(new LighthouseInfo("Chatham Light", 41.671407, -69.949884)); lighthouseData.add(new LighthouseInfo("Block Island Southeast Light", 41.153412, -71.552117)); lighthouseData.add(new LighthouseInfo("Edgartown Light", 41.390863, -70.503057)); lighthouseData.add(new LighthouseInfo("Watch Hill Light", 41.303884, -71.858575)); lighthouseData.add(new LighthouseInfo("Nauset Light", 41.858305, -69.951631)); lighthouseData .add(new LighthouseInfo("Fayerweather Island (Black Rock Harbor) Light", 41.142380, -73.217409)); lighthouseData.add(new LighthouseInfo("Owls Head Light", 44.092138, -69.044105)); lighthouseData.add(new LighthouseInfo("Point Judith Light", 41.361035, -71.481402)); lighthouseData.add(new LighthouseInfo("Sankaty Head Light", 41.284379, -69.966244)); lighthouseData.add(new LighthouseInfo("Eastern Point Light", 42.580229, -70.664537)); lighthouseData.add(new LighthouseInfo("Fort Pickering Light", 42.526473, -70.866465)); lighthouseData.add(new LighthouseInfo("Wood Island Light", 43.456788, -70.328976)); lighthouseData.add(new LighthouseInfo("Stonington Harbor Light", 41.328780, -71.905486)); lighthouseData.add(new LighthouseInfo("West Quoddy Head Light", 44.815073, -66.950742)); lighthouseData.add(new LighthouseInfo("Fort Point Light", 44.467265, -68.811717)); lighthouseData.add(new LighthouseInfo("Annisquam Light", 42.661874, -70.681488)); lighthouseData.add(new LighthouseInfo("Newport Harbor Light", 41.493299, -71.327038)); lighthouseData.add(new LighthouseInfo("Long Point Light", 42.033117, -70.168651)); lighthouseData.add(new LighthouseInfo("Castle Hill Light", 41.462116, -71.362919)); lighthouseData.add(new LighthouseInfo("Brant Point Light", 41.289918, -70.090287)); lighthouseData.add(new LighthouseInfo("Stratford Point Light", 41.151984, -73.103276)); lighthouseData.add(new LighthouseInfo("Boston Light", 42.327925, -70.890101)); lighthouseData.add(new LighthouseInfo("Lynde Point Light", 41.271452, -72.343142)); lighthouseData.add(new LighthouseInfo("Scituate Light", 42.204748, -70.715814)); lighthouseData.add(new LighthouseInfo("Prospect Harbor Light", 44.403285, -68.012922)); lighthouseData.add(new LighthouseInfo("Wood End Light", 42.021223, -70.193502)); lighthouseData.add(new LighthouseInfo("Rose Island Light", 41.495477, -71.342742)); lighthouseData.add(new LighthouseInfo("Saybrook Breakwater Light", 41.263158, -72.342813)); lighthouseData.add(new LighthouseInfo("Great Point Light", 41.390096, -70.048234)); lighthouseData.add(new LighthouseInfo("Cape Poge Light", 41.418798, -70.451923)); lighthouseData.add(new LighthouseInfo("Monhegan Light", 43.764779, -69.316204)); lighthouseData.add(new LighthouseInfo("Hendricks Head Light", 43.822589, -69.689761)); lighthouseData.add(new LighthouseInfo("Egg Rock Light", 44.354050, -68.138166)); lighthouseData.add(new LighthouseInfo("New London Ledge Light", 41.305826, -72.077448)); lighthouseData.add(new LighthouseInfo("Avery Point Lighthouse", 41.315245, -72.063579)); lighthouseData.add(new LighthouseInfo("Palmers Island Light", 41.626936, -70.909109)); lighthouseData.add(new LighthouseInfo("Cuckolds Light", 43.779663, -69.649982)); lighthouseData.add(new LighthouseInfo("Gull Rocks Light", 41.502451, -71.333140)); lighthouseData.add(new LighthouseInfo("Goat Island Light", 43.357826, -70.425109)); lighthouseData.add(new LighthouseInfo("East Chop Light", 41.470245, -70.567439)); lighthouseData.add(new LighthouseInfo("Neds Point Light", 41.650859, -70.795638)); lighthouseData.add(new LighthouseInfo("Sakonnet Point Light", 41.453090, -71.202382)); lighthouseData.add(new LighthouseInfo("Narrows (Bug) Light", 42.323137, -70.919158)); lighthouseData.add(new LighthouseInfo("Plum Island Light", 42.815119, -70.818981)); lighthouseData.add(new LighthouseInfo("Block Island North Light", 41.227639, -71.575811)); lighthouseData.add(new LighthouseInfo("Mount Desert Rock Light", 43.968582, -68.128306)); lighthouseData.add(new LighthouseInfo("Duxbury Pier Light", 41.987375, -70.648498)); lighthouseData.add(new LighthouseInfo("Long Island Head Light", 42.330197, -70.957712)); lighthouseData.add(new LighthouseInfo("Prudence Island Light", 41.605881, -71.303535)); lighthouseData.add(new LighthouseInfo("Plum Beach Light", 41.530248, -71.405202)); lighthouseData.add(new LighthouseInfo("Doubling Point Light", 43.882503, -69.806792)); lighthouseData.add(new LighthouseInfo("Dice Head Light", 44.382732, -68.819022)); lighthouseData.add(new LighthouseInfo("Ram Island Ledge Light", 43.631457, -70.187366)); lighthouseData.add(new LighthouseInfo("New London Harbor Light", 41.316619, -72.089743)); lighthouseData.add(new LighthouseInfo("Lime Rock Light", 41.477536, -71.325924)); lighthouseData.add(new LighthouseInfo("Ten Pound Island Light", 42.601865, -70.665556)); lighthouseData.add(new LighthouseInfo("Bristol Ferry Light", 41.642842, -71.260319)); lighthouseData.add(new LighthouseInfo("Musselbed Shoals Light", 41.636261, -71.259958)); lighthouseData.add(new LighthouseInfo("Conimicut Light", 41.716969, -71.345106)); lighthouseData.add(new LighthouseInfo("Tongue Point Light", 41.166590, -73.177497)); lighthouseData.add(new LighthouseInfo("Bass River Light", 41.651746, -70.169473)); lighthouseData.add(new LighthouseInfo("Hospital Point Light", 42.546413, -70.856164)); lighthouseData.add(new LighthouseInfo("Newburyport Range Light", 42.811524, -70.864838)); lighthouseData.add(new LighthouseInfo("Dutch Island Light", 41.496702, -71.404299)); lighthouseData.add(new LighthouseInfo("Heron Neck Light", 44.025216, -68.861966)); lighthouseData.add(new LighthouseInfo("Pumpkin Island Light", 44.309166, -68.742876)); lighthouseData.add(new LighthouseInfo("Whaleback Light", 43.058744, -70.696306)); lighthouseData.add(new LighthouseInfo("Hyannis Harbor Light", 41.636267, -70.288439)); lighthouseData.add(new LighthouseInfo("Stage Harbor Light", 41.658692, -69.983689)); lighthouseData.add(new LighthouseInfo("Lovells Island Range Light", 42.332440, -70.930214)); lighthouseData.add(new LighthouseInfo("Hog Island Shoal Light", 41.632338, -71.273198)); lighthouseData.add(new LighthouseInfo("Ram Island Light", 43.803935, -69.599349)); lighthouseData.add(new LighthouseInfo("Bridgeport Harbor Light", 41.156718, -73.179950)); lighthouseData.add(new LighthouseInfo("Straitsmouth Island Light", 42.662236, -70.588157)); lighthouseData.add(new LighthouseInfo("Squirrel Point Light", 43.816520, -69.802402)); lighthouseData.add(new LighthouseInfo("Mayos Beach Light", 41.930755, -70.032097)); lighthouseData.add(new LighthouseInfo("Race Point Light", 42.062314, -70.243084)); lighthouseData.add(new LighthouseInfo("Point Gammon Light", 41.609647, -70.266196)); lighthouseData.add(new LighthouseInfo("Wings Neck Light", 41.680235, -70.661250)); lighthouseData.add(new LighthouseInfo("West Chop Light", 41.480806, -70.599796)); lighthouseData.add(new LighthouseInfo("Bird Island Light", 41.669295, -70.717341)); lighthouseData.add(new LighthouseInfo("Clarks Point Light", 41.593176, -70.901416)); lighthouseData.add(new LighthouseInfo("Thacher Island Light", 42.639168, -70.574759)); lighthouseData.add(new LighthouseInfo("White Island Light", 42.967228, -70.623249)); lighthouseData.add(new LighthouseInfo("Wickford Harbor Light", 41.572618, -71.436831)); lighthouseData.add(new LighthouseInfo("Whale Rock Light", 41.444597, -71.423584)); lighthouseData.add(new LighthouseInfo("Burnt Island Light", 43.825133, -69.640262)); lighthouseData.add(new LighthouseInfo("Rockland Harbor Southwest Light", 44.082720, -69.096310)); lighthouseData.add(new LighthouseInfo("Saddleback Ledge Light", 44.014232, -68.726461)); lighthouseData.add(new LighthouseInfo("Grindle Point Light", 44.281451, -68.942967)); lighthouseData.add(new LighthouseInfo("Winter Harbor Light", 44.361421, -68.087742)); lighthouseData.add(new LighthouseInfo("Peck's Ledge Light", 41.077298, -73.369811)); lighthouseData.add(new LighthouseInfo("Sheffield Island Light", 41.048251, -73.419931)); lighthouseData.add(new LighthouseInfo("Whitlocks Mill Light", 45.162793, -67.227395)); lighthouseData.add(new LighthouseInfo("Boon Island Light", 43.121183, -70.475845)); lighthouseData.add(new LighthouseInfo("Southwest Ledge Light", 41.234443, -72.912092)); lighthouseData.add(new LighthouseInfo("Broad Sound Channel Inner Range Light", 42.326933, -70.984649)); lighthouseData.add(new LighthouseInfo("Spectacle Island Light", 42.326898, -70.984772)); lighthouseData.add(new LighthouseInfo("Deer Island Light", 42.339836, -70.954525)); lighthouseData.add(new LighthouseInfo("Nayatt Point Light", 41.725120, -71.338926)); lighthouseData.add(new LighthouseInfo("Doubling Point Range Lights", 43.882860, -69.795652)); lighthouseData.add(new LighthouseInfo("Burkehaven Light", 43.371669, -72.065869)); lighthouseData.add(new LighthouseInfo("Loon Island Light", 43.392123, -72.059977)); lighthouseData.add(new LighthouseInfo("Curtis Island Light", 44.201372, -69.048865)); lighthouseData.add(new LighthouseInfo("Butler Flats Light", 41.603775, -70.894556)); lighthouseData.add(new LighthouseInfo("Graves Light", 42.365098, -70.869191)); lighthouseData.add(new LighthouseInfo("Stamford Harbor Light", 41.013643, -73.542577)); lighthouseData.add(new LighthouseInfo("Billingsgate Light", 41.871624, -70.068982)); lighthouseData.add(new LighthouseInfo("Monomoy Point Light", 41.559310, -69.993650)); lighthouseData.add(new LighthouseInfo("Bishop & Clerks Light", 41.574154, -70.249963)); lighthouseData.add(new LighthouseInfo("Plymouth Light", 42.003737, -70.600565)); lighthouseData.add(new LighthouseInfo("Cleveland Ledge Light", 41.630927, -70.694201)); lighthouseData.add(new LighthouseInfo("Tarpaulin Cove Light", 41.468822, -70.757514)); lighthouseData.add(new LighthouseInfo("Minots Ledge Light", 42.269678, -70.759136)); lighthouseData.add(new LighthouseInfo("Dumpling Rock Light", 41.538167, -70.921427)); lighthouseData.add(new LighthouseInfo("Bakers Island Light", 42.536470, -70.785995)); lighthouseData.add(new LighthouseInfo("Cuttyhunk Light", 41.414391, -70.949558)); lighthouseData.add(new LighthouseInfo("Egg Rock Light", 42.433346, -70.897386)); lighthouseData.add(new LighthouseInfo("Ipswich Range Light", 42.685360, -70.766128)); lighthouseData.add(new LighthouseInfo("Borden Flats Light", 41.704450, -71.174395)); lighthouseData.add(new LighthouseInfo("Bullocks Point Light", 41.737740, -71.364179)); lighthouseData.add(new LighthouseInfo("Pomham Rocks Light", 41.777618, -71.369594)); lighthouseData.add(new LighthouseInfo("Sabin Point Light", 41.762010, -71.374234)); lighthouseData.add(new LighthouseInfo("Fuller Rock Light", 41.794055, -71.379720)); lighthouseData.add(new LighthouseInfo("Gould Island Light", 41.537826, -71.344804)); lighthouseData.add(new LighthouseInfo("Warwick Light", 41.667111, -71.378413)); lighthouseData.add(new LighthouseInfo("Sassafras Point Light", 41.802496, -71.390272)); lighthouseData.add(new LighthouseInfo("Conanicut Light", 41.573484, -71.371767)); lighthouseData.add(new LighthouseInfo("Poplar Point Light", 41.571053, -71.439189)); lighthouseData.add(new LighthouseInfo("Halfway Rock Light", 43.655873, -70.037402)); lighthouseData.add(new LighthouseInfo("Seguin Island Light", 43.707554, -69.758118)); lighthouseData.add(new LighthouseInfo("Pond Island Light", 43.740031, -69.770273)); lighthouseData.add(new LighthouseInfo("Perkins Island Light", 43.786764, -69.785256)); lighthouseData.add(new LighthouseInfo("Latimer Reef Light", 41.304503, -71.933292)); lighthouseData.add(new LighthouseInfo("Morgan Point Light", 41.316669, -71.989327)); lighthouseData.add(new LighthouseInfo("Franklin Island Light", 43.892184, -69.374842)); lighthouseData.add(new LighthouseInfo("Matinicus Rock Light", 43.783605, -68.854898)); lighthouseData.add(new LighthouseInfo("Tenants Harbor Light", 43.961107, -69.184877)); lighthouseData.add(new LighthouseInfo("Whitehead Light", 43.978706, -69.124285)); lighthouseData.add(new LighthouseInfo("Two Bush Island Light", 43.964239, -69.073942)); lighthouseData.add(new LighthouseInfo("Indian Island Light", 44.165470, -69.061004)); lighthouseData.add(new LighthouseInfo("Browns Head Light", 44.111774, -68.909482)); lighthouseData.add(new LighthouseInfo("Goose Rocks Light", 44.135394, -68.830526)); lighthouseData.add(new LighthouseInfo("Sperry Light", 41.221221, -72.423110)); lighthouseData.add(new LighthouseInfo("Isle au Haut Light", 44.064733, -68.651339)); lighthouseData.add(new LighthouseInfo("Deer Island Thorofare Light", 44.134338, -68.703202)); lighthouseData.add(new LighthouseInfo("Herrick Cove Light", 43.411136, -72.041706)); lighthouseData.add(new LighthouseInfo("Eagle Island Light", 44.217634, -68.767743)); lighthouseData.add(new LighthouseInfo("Burnt Coat Harbor Light", 44.134176, -68.447258)); lighthouseData.add(new LighthouseInfo("Faulkner's Island Light", 41.211612, -72.655088)); lighthouseData.add(new LighthouseInfo("Blue Hill Bay Light", 44.248746, -68.497880)); lighthouseData.add(new LighthouseInfo("Great Duck Island Light", 44.142193, -68.245836)); lighthouseData.add(new LighthouseInfo("Bear Island Light", 44.283485, -68.269858)); lighthouseData.add(new LighthouseInfo("Baker Island Light", 44.241266, -68.198923)); lighthouseData.add(new LighthouseInfo("Crabtree Ledge Light", 44.475613, -68.199383)); lighthouseData.add(new LighthouseInfo("Statford Shoal Light", 41.059557, -73.101394)); lighthouseData.add(new LighthouseInfo("Petit Manan Light", 44.367574, -67.864129)); lighthouseData.add(new LighthouseInfo("Penfield Reef Light", 41.117101, -73.222070)); lighthouseData.add(new LighthouseInfo("Narraguagus Light", 44.462467, -67.837844)); lighthouseData.add(new LighthouseInfo("Nash Island Light", 44.464305, -67.747299)); lighthouseData.add(new LighthouseInfo("Moose Peak Light", 44.474244, -67.533471)); lighthouseData.add(new LighthouseInfo("Green's Ledge Light", 41.041551, -73.443974)); lighthouseData.add(new LighthouseInfo("Libby Island Light", 44.568236, -67.367339)); lighthouseData.add(new LighthouseInfo("Great Captain Island Light", 40.982478, -73.623706)); lighthouseData.add(new LighthouseInfo("Avery Rock Light", 44.654358, -67.344137)); lighthouseData.add(new LighthouseInfo("Little River Light", 44.650873, -67.192325)); lighthouseData.add(new LighthouseInfo("Lubec Channel Light", 44.841955, -66.976731)); lighthouseData.add(new LighthouseInfo("St. Croix River Light", 45.128762, -67.133594)); /* * "Clean out" photo directories before beginning photo transfer process. */ final File photosDir = new File("photos"); final File[] photoLighthouseDirsToDelete = photosDir.listFiles(); if (photoLighthouseDirsToDelete != null) { for (final File photoLighthouseDir : photoLighthouseDirsToDelete) { // Use Apache Commons IO (again) to recursively delete the directory // and all of the files within it if (photoLighthouseDir.exists() && photoLighthouseDir.isDirectory()) { try { FileUtils.deleteDirectory(photoLighthouseDir); System.out.println("Deleted directory \"" + photoLighthouseDir + "\" successfully."); } catch (final IOException ioe) { System.err.println( "Could not delete directory: \"" + photoLighthouseDir + "\" successfully!"); } } } } // Keep track of elapsed time long estimatedTime = System.nanoTime() - startTime; String elapsedTime = WebImageManager.calculateElapsedTime(estimatedTime); System.out.println("Estimated elapsed time: " + elapsedTime + "."); System.out.println(); /* * Keep track of total number of photographs transferred from Flickr * websites to disks across _all_ lighthouses */ int totalNumPhotosTransferred = 0; /* * Keep track of total number of photographs that _should_ be transferred * from Flickr for _all_ lighthouses */ int totalNumPhotos = 0; for (final LighthouseInfo lighthousePieceOfData : lighthouseData) { System.out.println("Processing photos of " + lighthousePieceOfData.getName() + "..."); /* * URL for accessing Flickr APIs. For a given lighthouse, this URL * provides an XML file in response that lists information about every * geotagged, Creative Commons-enabled photograph for that lighthouse * on Flickr. */ // GET Parameter Explanation: // method - Use the "search photos" method for the Flickr APIs // // api_key - A unique key that I use to get the results // // text - Find all lighthouses whose title, tags, or description // contains the word "lighthouse" // // license - Find all photos with a Creative Commons license _except_ // those that do not allow for modification on my part // // content_type - Find photos only (no videos) // // has_geo - Implicitly set to true; implies that all photos are // geotagged // // lat - The latitude of the center of the "search circle" // // lon - The longitude of the center of the "search circle" // // radius - The radius of the "search circle," in _kilometers_ (NOT // miles) // // extras - Also include a URL to the "raw" photo (small version) final String inputURLText = "http://ycpi.api.flickr.com/services/rest/?" + "method=flickr.photos.search" + "&api_key=3ea8366b020383eb91f170c6f41748f5" + "&text=lighthouse" + "&license=1,2,4,5,7" + "&content_type=1" + "&has_geo" + "&lat=" + lighthousePieceOfData.getLatitude() + "&lon=" + lighthousePieceOfData.getLongitude() + "&radius=1" + "&extras=url_s"; // Output file where XML web response will be stored temporarily final String outputFileName = "output.xml"; /* * Convert the name of the lighthouse to a "computer friendly" version * with all lower-case letters and underscores replacing spaces, * apostrophes, and parenthesis */ String lighthouseName = lighthousePieceOfData.getName(); lighthouseName = lighthouseName.toLowerCase(); lighthouseName = lighthouseName.replace(' ', '_'); lighthouseName = lighthouseName.replace('\'', '_'); lighthouseName = lighthouseName.replace('(', '_'); lighthouseName = lighthouseName.replace(')', '_'); // Will contain the textual links to each "raw" photo website Set<String> rawPhotoURLs = new HashSet<String>(); // Make sure file for XML output does not exist at first // (don't want to use an old, incorrect version accidentally) final File outputXMLFile = new File(outputFileName); if (outputXMLFile.exists()) { outputXMLFile.delete(); } System.out.println("Cleaned output XML file containing photo URLs on disk successfully."); /* * Access the list of photographs for a given lighthouse and copy them * to the XML file on disk */ final WebDataExtractor extractor = new WebDataExtractor(inputURLText, outputFileName); System.out.println("Looking for XML file containing lighthosue photo information..."); extractor.transferURLToFile(); System.out.println("Found XML file containing lighthouse photo URLs."); /* * Object for extracting the "raw" URLs from each piece of photo data * in the XML file */ final XMLParser parser = new FlickrXMLOutputParser(outputFileName); // Complete the extraction process rawPhotoURLs = parser.parseFile("//photo/@url_s"); final int numPhotos = rawPhotoURLs.size(); totalNumPhotos += numPhotos; int i = 0; // Counter for keeping track of progress /* * Keep track of photos transferred successfully (which might be less * than the total number of photos defined int the XML output from * Flickr, especially if connection issues occur */ int numPhotosTransferred = 0; for (final String photoURL : rawPhotoURLs) { System.out.print("Transferring photos..."); i++; /* * Go to a website containing a "raw" JPEG image file and save it * accordingly on disk in the photo folder corresponding to the * lighthouse name */ final WebDataExtractor rawPhotoExtractor = new WebDataExtractor(photoURL, "photos/" + lighthouseName + "/lighthouse_photo_" + Integer.toString(i) + ".jpg"); final boolean transferSuccessful = rawPhotoExtractor.transferURLToFile(); if (transferSuccessful) { numPhotosTransferred++; } // Simple progress tracker System.out.printf("%d of %d (%.1f%%) complete.\n", i, numPhotos, i * 1.0 / numPhotos * 100.0); } // Indicate number of photos successfully transferred to disk if (numPhotosTransferred == numPhotos && numPhotos > 0) { System.out.println("All photos transferred to disk successfully!"); } else if (numPhotos == 0) { System.out.println("It appears there are no photos available for this lighthouse..."); } else if (numPhotosTransferred == 1 && numPhotos > 1) { System.out.println("1 photo transferred to disk successfully."); } else if (numPhotosTransferred == 1 && numPhotos == 1) { System.out.println("The photo transferred to disk successfully!"); } else { System.out.println(numPhotosTransferred + " photos transferred to disk successfully."); } // Keep track of elapsed time estimatedTime = System.nanoTime() - startTime; elapsedTime = WebImageManager.calculateElapsedTime(estimatedTime); System.out.println("Estimated elapsed time: " + elapsedTime + "."); // Add extra line in between lighthouses in output stream System.out.println(); /* * Keep track of total number of photos transferred so far across * _all_lighthouses */ totalNumPhotosTransferred += numPhotosTransferred; } // Display "grand" total (which is hopefully greater than 0) System.out.println("***GRAND TOTAL: " + totalNumPhotosTransferred + " OF " + totalNumPhotos + " PHOTOS TRANSFERRED SUCCESSFULLY***"); estimatedTime = System.nanoTime() - startTime; elapsedTime = WebImageManager.calculateElapsedTime(estimatedTime); System.out.println("TOTAL ELAPSED TIME: " + elapsedTime.toUpperCase()); }
From source file:net.skyebook.zerocollada.ZeroCollada.java
/** * @param args//from w ww . jav a 2s .co m * @throws ParseException * @throws IOException * @throws JDOMException */ public static void main(String[] args) throws ParseException, JDOMException, IOException { // Setup Apache Commons CLI optionsSetup(); CommandLineParser parser = new PosixParser(); CommandLine cmd = parser.parse(options, args); if (args.length == 0 || cmd.hasOption(ZCOpts.help)) { showHelp(); } // was there a valid operation specified? if (hasValidOption(cmd)) { File fileFromCommandLine = new File(args[args.length - 1]); if (!fileFromCommandLine.exists()) { System.err.println( "The file located at " + fileFromCommandLine.toString() + " does not exist! Qutting."); return; } else if (fileFromCommandLine.isFile() && fileFromCommandLine.toString().endsWith(".dae")) { // we've been given a single file. Act on this single file doRequestedAction(fileFromCommandLine, cmd); } else if (fileFromCommandLine.isDirectory()) { // We've been given a directory of files process the ones that are .dae for (File file : fileFromCommandLine.listFiles()) { if (file.isFile() && file.toString().endsWith(".dae")) { doRequestedAction(file, cmd); } else { System.err.println(file.toString() + " does not seem to be a COLLADA file"); } } } } else { // Then why are we here? if (cmd.hasOption(ZCOpts.includeY)) { System.err.println( "You have used the " + ZCOpts.includeY + " option but have not asked for a transform (t)"); } else if (cmd.hasOption(ZCOpts.anchorCenter)) { System.err.println( "You have used the " + ZCOpts.includeY + " option but have not asked for a transform (t)"); } } }
From source file:com.clustercontrol.agent.Agent.java
/** * ?//from w ww. jav a2 s .c om * * @param args ?? */ public static void main(String[] args) throws Exception { // ? if (args.length != 1) { System.out.println("Usage : java Agent [Agent.properties File Path]"); System.exit(1); } try { // System m_log.info("starting Hinemos Agent..."); m_log.info("java.vm.version = " + System.getProperty("java.vm.version")); m_log.info("java.vm.vendor = " + System.getProperty("java.vm.vendor")); m_log.info("java.home = " + System.getProperty("java.home")); m_log.info("os.name = " + System.getProperty("os.name")); m_log.info("os.arch = " + System.getProperty("os.arch")); m_log.info("os.version = " + System.getProperty("os.version")); m_log.info("user.name = " + System.getProperty("user.name")); m_log.info("user.dir = " + System.getProperty("user.dir")); m_log.info("user.country = " + System.getProperty("user.country")); m_log.info("user.language = " + System.getProperty("user.language")); m_log.info("file.encoding = " + System.getProperty("file.encoding")); // System(SET) String limitKey = "jdk.xml.entityExpansionLimit"; // TODO JRE??????????????????? System.setProperty(limitKey, "0"); m_log.info(limitKey + " = " + System.getProperty(limitKey)); // TODO ???agentHome // ?????????? File file = new File(args[0]); agentHome = file.getParentFile().getParent() + "/"; m_log.info("agentHome=" + agentHome); // long startDate = HinemosTime.currentTimeMillis(); m_log.info("start date = " + new Date(startDate) + "(" + startDate + ")"); agentInfo.setStartupTime(startDate); // Agent?? m_log.info("Agent.properties = " + args[0]); // ? File scriptDir = new File(agentHome + "script/"); if (scriptDir.exists()) { File[] listFiles = scriptDir.listFiles(); if (listFiles != null) { for (File f : listFiles) { boolean ret = f.delete(); if (ret) { m_log.debug("delete script : " + f.getName()); } else { m_log.warn("delete script error : " + f.getName()); } } } else { m_log.warn("listFiles is null"); } } else { //???????? boolean ret = scriptDir.mkdir(); if (!ret) { m_log.warn("mkdir error " + scriptDir.getPath()); } } // queue? m_sendQueue = new SendQueue(); // Agent? Agent agent = new Agent(args[0]); //----------------- //-- //----------------- m_log.debug("exec() : create topic "); m_receiveTopic = new ReceiveTopic(m_sendQueue); m_receiveTopic.setName("ReceiveTopicThread"); m_log.info("receiveTopic start 1"); m_receiveTopic.start(); m_log.info("receiveTopic start 2"); // ? agent.exec(); m_log.info("Hinemos Agent started"); // ? agent.waitAwakeAgent(); } catch (Throwable e) { m_log.error("Agent.java: Runtime Exception Occurred. " + e.getClass().getName() + ", " + e.getMessage(), e); } }
From source file:edu.harvard.hul.ois.drs.pdfaconvert.PdfaConvert.java
public static void main(String[] args) throws IOException { if (logger == null) { System.out.println("About to initialize Log4j"); logger = LogManager.getLogger(); System.out.println("Finished initializing Log4j"); }//from w w w . java2 s . c om logger.debug("Entering main()"); // WIP: the following command line code was pulled from FITS Options options = new Options(); Option inputFileOption = new Option(PARAM_I, true, "input file"); options.addOption(inputFileOption); options.addOption(PARAM_V, false, "print version information"); options.addOption(PARAM_H, false, "help information"); options.addOption(PARAM_O, true, "output sub-directory"); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args, true); } catch (ParseException e) { System.err.println(e.getMessage()); System.exit(1); } // print version info if (cmd.hasOption(PARAM_V)) { if (StringUtils.isEmpty(applicationVersion)) { applicationVersion = "<not set>"; System.exit(1); } System.out.println("Version: " + applicationVersion); System.exit(0); } // print help info if (cmd.hasOption(PARAM_H)) { displayHelp(); System.exit(0); } // input parameter if (cmd.hasOption(PARAM_I)) { String input = cmd.getOptionValue(PARAM_I); boolean hasValue = cmd.hasOption(PARAM_I); logger.debug("Has option {} value: [{}]", PARAM_I, hasValue); String paramVal = cmd.getOptionValue(PARAM_I); logger.debug("value of option: [{}] ****", paramVal); File inputFile = new File(input); if (!inputFile.exists()) { logger.warn("{} does not exist or is not readable.", input); System.exit(1); } String subDir = cmd.getOptionValue(PARAM_O); PdfaConvert convert; if (!StringUtils.isEmpty(subDir)) { convert = new PdfaConvert(subDir); } else { convert = new PdfaConvert(); } if (inputFile.isDirectory()) { if (inputFile.listFiles() == null || inputFile.listFiles().length < 1) { logger.warn("Input directory is empty, nothing to process."); System.exit(1); } else { logger.debug("Have directory: [{}] with file count: {}", inputFile.getAbsolutePath(), inputFile.listFiles().length); DirectoryStream<Path> dirStream = null; dirStream = Files.newDirectoryStream(inputFile.toPath()); for (Path filePath : dirStream) { logger.debug("Have file name: {}", filePath.toString()); // Note: only handling files, not recursively going into sub-directories if (filePath.toFile().isFile()) { // Catch possible exception for each file so can handle other files in directory. try { convert.examine(filePath.toFile()); } catch (Exception e) { logger.error("Problem processing file: {} -- Error message: {}", filePath.getFileName(), e.getMessage()); } } else { logger.warn("Not a file so not processing: {}", filePath.toString()); // could be a directory but not recursing } } dirStream.close(); } } else { logger.debug("About to process file: {}", inputFile.getPath()); try { convert.examine(inputFile); } catch (Exception e) { logger.error("Problem processing file: {} -- Error message: {}", inputFile.getName(), e.getMessage()); logger.debug("Problem processing file: {} -- Error message: {}", inputFile.getName(), e.getMessage(), e); } } } else { System.err.println("Missing required option: " + PARAM_I); displayHelp(); System.exit(-1); } System.exit(0); }
From source file:edu.isi.karma.research.modeling.ModelLearner_LOD.java
public static void main(String[] args) throws Exception { ServletContextParameterMap contextParameters = ContextParametersRegistry.getInstance().getDefault(); contextParameters.setParameterValue(ContextParameter.USER_CONFIG_DIRECTORY, "/Users/mohsen/karma/config"); OntologyManager ontologyManager = new OntologyManager(contextParameters.getId()); File ff = new File(Params.ONTOLOGY_DIR); File[] files = ff.listFiles(); if (files == null) { logger.error("no ontology to import at " + ff.getAbsolutePath()); return;/* w ww . j av a 2s . c om*/ } for (File f : files) { if (f.getName().endsWith(".owl") || f.getName().endsWith(".rdf") || f.getName().endsWith(".n3") || f.getName().endsWith(".ttl") || f.getName().endsWith(".xml")) { logger.info("Loading ontology file: " + f.getAbsolutePath()); ontologyManager.doImport(f, "UTF-8"); } } ontologyManager.updateCache(); String outputPath = Params.OUTPUT_DIR; String graphPath = Params.GRAPHS_DIR; FileUtils.cleanDirectory(new File(graphPath)); List<SemanticModel> semanticModels = ModelReader.importSemanticModelsFromJsonFiles(Params.MODEL_DIR, Params.MODEL_MAIN_FILE_EXT); ModelLearner_LOD modelLearner = null; boolean onlyGenerateSemanticTypeStatistics = false; boolean onlyUseOntology = false; boolean useCorrectType = false; int numberOfCandidates = 4; boolean onlyEvaluateInternalLinks = false; int maxPatternSize = 3; if (onlyGenerateSemanticTypeStatistics) { getStatistics(semanticModels); return; } String filePath = Params.RESULTS_DIR + "temp/"; String filename = ""; filename += "lod-results"; filename += useCorrectType ? "-correct" : "-k=" + numberOfCandidates; filename += onlyUseOntology ? "-ontology" : "-p" + maxPatternSize; filename += onlyEvaluateInternalLinks ? "-internal" : "-all"; filename += ".csv"; PrintWriter resultFile = new PrintWriter(new File(filePath + filename)); resultFile.println("source \t p \t r \t t \n"); for (int i = 0; i < semanticModels.size(); i++) { // for (int i = 0; i <= 10; i++) { // int i = 1; { int newSourceIndex = i; SemanticModel newSource = semanticModels.get(newSourceIndex); logger.info("======================================================"); logger.info(newSource.getName() + "(#attributes:" + newSource.getColumnNodes().size() + ")"); System.out.println(newSource.getName() + "(#attributes:" + newSource.getColumnNodes().size() + ")"); logger.info("======================================================"); SemanticModel correctModel = newSource; List<ColumnNode> columnNodes = correctModel.getColumnNodes(); List<Node> steinerNodes = new LinkedList<Node>(columnNodes); String graphName = graphPath + "lod" + Params.GRAPH_FILE_EXT; if (onlyUseOntology) { modelLearner = new ModelLearner_LOD(new GraphBuilder(ontologyManager, false), steinerNodes); } else if (new File(graphName).exists()) { // read graph from file try { logger.info("loading the graph ..."); DirectedWeightedMultigraph<Node, DefaultLink> graph = GraphUtil.importJson(graphName); modelLearner = new ModelLearner_LOD(new GraphBuilderTopK(ontologyManager, graph), steinerNodes); } catch (Exception e) { e.printStackTrace(); resultFile.close(); return; } } else { logger.info("building the graph ..."); // create and save the graph to file // GraphBuilder_Popularity b = new GraphBuilder_Popularity(ontologyManager, // Params.LOD_OBJECT_PROPERIES_FILE, // Params.LOD_DATA_PROPERIES_FILE); GraphBuilder_LOD_Pattern b = new GraphBuilder_LOD_Pattern(ontologyManager, Params.PATTERNS_DIR, maxPatternSize); modelLearner = new ModelLearner_LOD(b.getGraphBuilder(), steinerNodes); } long start = System.currentTimeMillis(); List<SortableSemanticModel> hypothesisList = modelLearner.hypothesize(useCorrectType, numberOfCandidates); long elapsedTimeMillis = System.currentTimeMillis() - start; float elapsedTimeSec = elapsedTimeMillis / 1000F; List<SortableSemanticModel> topHypotheses = null; if (hypothesisList != null) { // for (SortableSemanticModel sss : hypothesisList) { // ModelEvaluation mmm = sss.evaluate(correctModel); // System.out.println(mmm.getPrecision() + ", " + mmm.getRecall()); // } topHypotheses = hypothesisList.size() > 10 ? hypothesisList.subList(0, 10) : hypothesisList; } Map<String, SemanticModel> models = new TreeMap<String, SemanticModel>(); ModelEvaluation me; models.put("1-correct model", correctModel); if (topHypotheses != null) for (int k = 0; k < topHypotheses.size(); k++) { SortableSemanticModel m = topHypotheses.get(k); me = m.evaluate(correctModel, onlyEvaluateInternalLinks, false); String label = "candidate " + k + "\n" + // (m.getSteinerNodes() == null ? "" : m.getSteinerNodes().getScoreDetailsString()) + "link coherence:" + (m.getLinkCoherence() == null ? "" : m.getLinkCoherence().getCoherenceValue()) + "\n"; label += (m.getSteinerNodes() == null || m.getSteinerNodes().getCoherence() == null) ? "" : "node coherence:" + m.getSteinerNodes().getCoherence().getCoherenceValue() + "\n"; label += "confidence:" + m.getConfidenceScore() + "\n"; label += m.getSteinerNodes() == null ? "" : "mapping score:" + m.getSteinerNodes().getScore() + "\n"; label += "cost:" + roundDecimals(m.getCost(), 6) + "\n" + // "-distance:" + me.getDistance() + "-precision:" + me.getPrecision() + "-recall:" + me.getRecall(); models.put(label, m); if (k == 0) { // first rank model System.out.println("precision: " + me.getPrecision() + ", recall: " + me.getRecall() + ", time: " + elapsedTimeSec); logger.info("precision: " + me.getPrecision() + ", recall: " + me.getRecall() + ", time: " + elapsedTimeSec); String s = newSource.getName() + "\t" + me.getPrecision() + "\t" + me.getRecall() + "\t" + elapsedTimeSec; resultFile.println(s); } } String outName = outputPath + newSource.getName() + Params.GRAPHVIS_OUT_DETAILS_FILE_EXT; GraphVizUtil.exportSemanticModelsToGraphviz(models, newSource.getName(), outName, GraphVizLabelType.LocalId, GraphVizLabelType.LocalUri, true, true); } resultFile.close(); }
From source file:DIA_Umpire_Quant.DIA_Umpire_ProtQuant.java
/** * @param args the command line arguments *//*w ww . ja v a2s. co m*/ public static void main(String[] args) throws FileNotFoundException, IOException, Exception { System.out.println( "================================================================================================="); System.out.println( "DIA-Umpire protein quantitation module (version: " + UmpireInfo.GetInstance().Version + ")"); if (args.length != 1) { System.out.println( "command format error, the correct format should be: java -jar -Xmx10G DIA_Umpire_PortQuant.jar diaumpire_module.params"); return; } try { ConsoleLogger.SetConsoleLogger(Level.INFO); ConsoleLogger.SetFileLogger(Level.DEBUG, FilenameUtils.getFullPath(args[0]) + "diaumpire_orotquant.log"); } catch (Exception e) { } Logger.getRootLogger().info("Version: " + UmpireInfo.GetInstance().Version); Logger.getRootLogger().info("Parameter file:" + args[0]); BufferedReader reader = new BufferedReader(new FileReader(args[0])); String line = ""; String WorkFolder = ""; int NoCPUs = 2; String Combined_Prot = ""; boolean DefaultProtFiltering = true; float Freq = 0f; int TopNPep = 6; int TopNFrag = 6; String FilterWeight = "GW"; float MinWeight = 0.9f; TandemParam tandemPara = new TandemParam(DBSearchParam.SearchInstrumentType.TOF5600); HashMap<String, File> AssignFiles = new HashMap<>(); boolean ExportSaint = false; boolean SAINT_MS1 = false; boolean SAINT_MS2 = true; HashMap<String, String[]> BaitList = new HashMap<>(); HashMap<String, String> BaitName = new HashMap<>(); HashMap<String, String[]> ControlList = new HashMap<>(); HashMap<String, String> ControlName = new HashMap<>(); //<editor-fold defaultstate="collapsed" desc="Reading parameter file"> while ((line = reader.readLine()) != null) { line = line.trim(); Logger.getRootLogger().info(line); if (!"".equals(line) && !line.startsWith("#")) { //System.out.println(line); if (line.equals("==File list begin")) { do { line = reader.readLine(); line = line.trim(); if (line.equals("==File list end")) { continue; } else if (!"".equals(line)) { File newfile = new File(line); if (newfile.exists()) { AssignFiles.put(newfile.getAbsolutePath(), newfile); } else { Logger.getRootLogger().info("File: " + newfile + " does not exist."); } } } while (!line.equals("==File list end")); } if (line.split("=").length < 2) { continue; } String type = line.split("=")[0].trim(); String value = line.split("=")[1].trim(); switch (type) { case "Path": { WorkFolder = value; break; } case "path": { WorkFolder = value; break; } case "Thread": { NoCPUs = Integer.parseInt(value); break; } case "Fasta": { tandemPara.FastaPath = value; break; } case "Combined_Prot": { Combined_Prot = value; break; } case "DefaultProtFiltering": { DefaultProtFiltering = Boolean.parseBoolean(value); break; } case "DecoyPrefix": { if (!"".equals(value)) { tandemPara.DecoyPrefix = value; } break; } case "ProteinFDR": { tandemPara.ProtFDR = Float.parseFloat(value); break; } case "FilterWeight": { FilterWeight = value; break; } case "MinWeight": { MinWeight = Float.parseFloat(value); break; } case "TopNFrag": { TopNFrag = Integer.parseInt(value); break; } case "TopNPep": { TopNPep = Integer.parseInt(value); break; } case "Freq": { Freq = Float.parseFloat(value); break; } //<editor-fold defaultstate="collapsed" desc="SaintOutput"> case "ExportSaintInput": { ExportSaint = Boolean.parseBoolean(value); break; } case "QuantitationType": { switch (value) { case "MS1": { SAINT_MS1 = true; SAINT_MS2 = false; break; } case "MS2": { SAINT_MS1 = false; SAINT_MS2 = true; break; } case "BOTH": { SAINT_MS1 = true; SAINT_MS2 = true; break; } } break; } // case "BaitInputFile": { // SaintBaitFile = value; // break; // } // case "PreyInputFile": { // SaintPreyFile = value; // break; // } // case "InterationInputFile": { // SaintInteractionFile = value; // break; // } default: { if (type.startsWith("BaitName_")) { BaitName.put(type.substring(9), value); } if (type.startsWith("BaitFile_")) { BaitList.put(type.substring(9), value.split("\t")); } if (type.startsWith("ControlName_")) { ControlName.put(type.substring(12), value); } if (type.startsWith("ControlFile_")) { ControlList.put(type.substring(12), value.split("\t")); } break; } //</editor-fold> } } } //</editor-fold> //Initialize PTM manager using compomics library PTMManager.GetInstance(); //Check if the fasta file can be found if (!new File(tandemPara.FastaPath).exists()) { Logger.getRootLogger().info("Fasta file :" + tandemPara.FastaPath + " cannot be found, the process will be terminated, please check."); System.exit(1); } //Check if the prot.xml file can be found if (!new File(Combined_Prot).exists()) { Logger.getRootLogger().info("ProtXML file: " + Combined_Prot + " cannot be found, the export protein summary table will be empty."); } LCMSID protID = null; //Parse prot.xml and generate protein master list given an FDR if (Combined_Prot != null && !Combined_Prot.equals("")) { protID = LCMSID.ReadLCMSIDSerialization(Combined_Prot); if (!"".equals(Combined_Prot) && protID == null) { protID = new LCMSID(Combined_Prot, tandemPara.DecoyPrefix, tandemPara.FastaPath); ProtXMLParser protxmlparser = new ProtXMLParser(protID, Combined_Prot, 0f); //Use DIA-Umpire default protein FDR calculation if (DefaultProtFiltering) { protID.RemoveLowLocalPWProtein(0.8f); protID.RemoveLowMaxIniProbProtein(0.9f); protID.FilterByProteinDecoyFDRUsingMaxIniProb(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } //Get protein FDR calculation without other filtering else { protID.FilterByProteinDecoyFDRUsingLocalPW(tandemPara.DecoyPrefix, tandemPara.ProtFDR); } protID.LoadSequence(); protID.WriteLCMSIDSerialization(Combined_Prot); } Logger.getRootLogger().info("Protein No.:" + protID.ProteinList.size()); } HashMap<String, HashMap<String, FragmentPeak>> IDSummaryFragments = new HashMap<>(); //Generate DIA file list ArrayList<DIAPack> FileList = new ArrayList<>(); try { File folder = new File(WorkFolder); if (!folder.exists()) { Logger.getRootLogger().info("The path : " + WorkFolder + " cannot be found."); System.exit(1); } for (final File fileEntry : folder.listFiles()) { if (fileEntry.isFile() && (fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry.getAbsolutePath(), fileEntry); } if (fileEntry.isDirectory()) { for (final File fileEntry2 : fileEntry.listFiles()) { if (fileEntry2.isFile() && (fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzxml") | fileEntry2.getAbsolutePath().toLowerCase().endsWith(".mzml")) && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q1.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q2.mzxml") && !fileEntry2.getAbsolutePath().toLowerCase().endsWith("q3.mzxml")) { AssignFiles.put(fileEntry2.getAbsolutePath(), fileEntry2); } } } } Logger.getRootLogger().info("No. of files assigned :" + AssignFiles.size()); for (File fileEntry : AssignFiles.values()) { Logger.getRootLogger().info(fileEntry.getAbsolutePath()); } for (File fileEntry : AssignFiles.values()) { String mzXMLFile = fileEntry.getAbsolutePath(); if (mzXMLFile.toLowerCase().endsWith(".mzxml") | mzXMLFile.toLowerCase().endsWith(".mzml")) { DIAPack DiaFile = new DIAPack(mzXMLFile, NoCPUs); Logger.getRootLogger().info( "================================================================================================="); Logger.getRootLogger().info("Processing " + mzXMLFile); if (!DiaFile.LoadDIASetting()) { Logger.getRootLogger().info("Loading DIA setting failed, job is incomplete"); System.exit(1); } if (!DiaFile.LoadParams()) { Logger.getRootLogger().info("Loading parameters failed, job is incomplete"); System.exit(1); } Logger.getRootLogger().info("Loading identification results " + mzXMLFile + "...."); //If the serialization file for ID file existed if (DiaFile.ReadSerializedLCMSID()) { DiaFile.IDsummary.ReduceMemoryUsage(); DiaFile.IDsummary.ClearAssignPeakCluster(); FileList.add(DiaFile); HashMap<String, FragmentPeak> FragMap = new HashMap<>(); IDSummaryFragments.put(FilenameUtils.getBaseName(mzXMLFile), FragMap); } } } //<editor-fold defaultstate="collapsed" desc="Peptide and fragment selection"> Logger.getRootLogger().info("Peptide and fragment selection across the whole dataset"); ArrayList<LCMSID> SummaryList = new ArrayList<>(); for (DIAPack diafile : FileList) { if (protID != null) { //Generate protein list according to mapping of peptide ions for each DIA file to the master protein list diafile.IDsummary.GenerateProteinByRefIDByPepSeq(protID, true); diafile.IDsummary.ReMapProPep(); } if ("GW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByGroupWeight(); } else if ("PepW".equals(FilterWeight)) { diafile.IDsummary.SetFilterByWeight(); } SummaryList.add(diafile.IDsummary); } FragmentSelection fragselection = new FragmentSelection(SummaryList); fragselection.freqPercent = Freq; fragselection.GeneratePepFragScoreMap(); fragselection.GenerateTopFragMap(TopNFrag); fragselection.GenerateProtPepScoreMap(MinWeight); fragselection.GenerateTopPepMap(TopNPep); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="Writing general reports"> ExportTable export = new ExportTable(WorkFolder, SummaryList, IDSummaryFragments, protID, fragselection); export.Export(TopNPep, TopNFrag, Freq); //</editor-fold> //<editor-fold defaultstate="collapsed" desc="//<editor-fold defaultstate="collapsed" desc="Generate SAINT input files"> if (ExportSaint && protID != null) { HashMap<String, DIAPack> Filemap = new HashMap<>(); for (DIAPack DIAfile : FileList) { Filemap.put(DIAfile.GetBaseName(), DIAfile); } FileWriter baitfile = new FileWriter(WorkFolder + "SAINT_Bait_" + DateTimeTag.GetTag() + ".txt"); FileWriter preyfile = new FileWriter(WorkFolder + "SAINT_Prey_" + DateTimeTag.GetTag() + ".txt"); FileWriter interactionfileMS1 = null; FileWriter interactionfileMS2 = null; if (SAINT_MS1) { interactionfileMS1 = new FileWriter( WorkFolder + "SAINT_Interaction_MS1_" + DateTimeTag.GetTag() + ".txt"); } if (SAINT_MS2) { interactionfileMS2 = new FileWriter( WorkFolder + "SAINT_Interaction_MS2_" + DateTimeTag.GetTag() + ".txt"); } HashMap<String, String> PreyID = new HashMap<>(); for (String samplekey : ControlName.keySet()) { String name = ControlName.get(samplekey); for (String file : ControlList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "C\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } for (String samplekey : BaitName.keySet()) { String name = BaitName.get(samplekey); for (String file : BaitList.get(samplekey)) { baitfile.write(FilenameUtils.getBaseName(file) + "\t" + name + "\t" + "T\n"); LCMSID IDsummary = Filemap.get(FilenameUtils.getBaseName(file)).IDsummary; if (SAINT_MS1) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS1, file, name, PreyID, 1); } if (SAINT_MS2) { SaintOutput(protID, IDsummary, fragselection, interactionfileMS2, file, name, PreyID, 2); } } } baitfile.close(); if (SAINT_MS1) { interactionfileMS1.close(); } if (SAINT_MS2) { interactionfileMS2.close(); } for (String AccNo : PreyID.keySet()) { preyfile.write(AccNo + "\t" + PreyID.get(AccNo) + "\n"); } preyfile.close(); } //</editor-fold> Logger.getRootLogger().info("Job done"); Logger.getRootLogger().info( "================================================================================================="); } catch (Exception e) { Logger.getRootLogger().error(ExceptionUtils.getStackTrace(e)); throw e; } }
From source file:net.iiit.siel.analysis.lang.LanguageIdentifier.java
/** * The main method.//from ww w. j av a 2 s . co m * * @param args the arguments */ public static void main(String args[]) { String usage = "Usage: LanguageIdentifier " + "[-identifyrows filename maxlines] " + "[-identifyfile charset filename] " + "[-identifyfileset charset files] " + "[-identifytext text] " + "[-identifyurl url]"; int command = 0; final int IDFILE = 1; final int IDTEXT = 2; final int IDURL = 3; final int IDFILESET = 4; final int IDROWS = 5; Vector fileset = new Vector(); String filename = ""; String charset = ""; String url = ""; String text = ""; int max = 0; // TODO niket writing test args here.. /* args = new String[2]; args[0] = "-identifyurl"; args[1] = "file:/home1/niket/TamilSamplePage.html"; //args[2] = "/home1/niket/nutch-clia/input.txt"; */ // TODO niket end here if (args.length == 0) { System.err.println(usage); System.exit(-1); } for (int i = 0; i < args.length; i++) { // parse command line if (args[i].equals("-identifyfile")) { command = IDFILE; charset = args[++i]; filename = args[++i]; } if (args[i].equals("-identifyurl")) { command = IDURL; filename = args[++i]; } if (args[i].equals("-identifyrows")) { command = IDROWS; filename = args[++i]; max = Integer.parseInt(args[++i]); } if (args[i].equals("-identifytext")) { command = IDTEXT; for (i++; i < args.length - 1; i++) text += args[i] + " "; } if (args[i].equals("-identifyfileset")) { command = IDFILESET; charset = args[++i]; for (i++; i < args.length; i++) { File[] files = null; File f = new File(args[i]); if (f.isDirectory()) { files = f.listFiles(); } else { files = new File[] { f }; } for (int j = 0; j < files.length; j++) { fileset.add(files[j].getAbsolutePath()); } } } } Configuration conf = NutchConfiguration.create(); String lang = null; LanguageIdentifier idfr = new LanguageIdentifier(conf); File f; FileInputStream fis; try { switch (command) { case IDTEXT: lang = idfr.identify(text); System.out.println("Lang :" + lang); break; case IDFILE: f = new File(filename); fis = new FileInputStream(f); lang = idfr.identify(fis, charset); fis.close(); break; case IDURL: lang = LangIdentifierUtility.IdentifyLangFromURLDirectly(filename); /* * our url identifier is confused or couldn't identify lang from * URL */ if (lang == null || lang.equalsIgnoreCase("en")) { System.out.println("Ambuguity in identifying language from URL"); } else { System.out.println("Lang was identified(using URL) as: " + lang); } break; case IDROWS: f = new File(filename); BufferedReader br = new BufferedReader(new InputStreamReader(new FileInputStream(f))); String line; while (max > 0 && (line = br.readLine()) != null) { line = line.trim(); if (line.length() > 2) { max--; lang = idfr.identify(line); System.out.println("R=" + lang + ":" + line); } } br.close(); System.exit(0); break; case IDFILESET: /* * used for benchs for (int j=128; j<=524288; j*=2) { long start * = System.currentTimeMillis(); idfr.analyzeLength = j; */ System.out.println("FILESET"); Iterator i = fileset.iterator(); while (i.hasNext()) { try { filename = (String) i.next(); f = new File(filename); fis = new FileInputStream(f); lang = idfr.identify(fis, charset); fis.close(); } catch (Exception e) { System.out.println(e); } System.out.println(filename + " was identified as " + lang); } /* * used for benchs System.out.println(j + "/" + * (System.currentTimeMillis()-start)); } */ System.exit(0); break; } } catch (Exception e) { System.out.println(e); System.out.println("lang could not be identified properly"); e.printStackTrace(); } System.out.println("text was identified as " + lang); /* * DONOT delete the next few lines, they should be enabled, when a lang. * mapping map needs to be generated. TODO this is for printing * the hashMapRangeLangIDTable only * * idfr.langMarkerObject.printHashmapTableWithFormatting(); * * System.out * .println("\n\n\n Printing english text contents in this file:\n"); * System.out.println(idfr.langMarkerObject.getLangCharacters( * LanguageIdentifierConstants.LangShortNames.ENGLISH * .langShortName()).toString()); * * System.out * .println("\n\n\n Printing telugu text contents in this file:\n"); * System.out.println(idfr.langMarkerObject.getLangCharacters( * LanguageIdentifierConstants.LangShortNames.TELUGU * .langShortName()).toString()); * * System.out * .println("\n\n\n Printing unknown text contents in this file:\n"); * System.out.println(idfr.langMarkerObject.getLangCharacters( * LanguageIdentifierConstants.LangShortNames.UNKNOWN_LANG * .langShortName()).toString()); */ }
From source file:org.silverpeas.dbbuilder.DBBuilder.java
/** * @param args//ww w . j av a 2s .c o m * @see */ public static void main(String[] args) { ClassPathXmlApplicationContext springContext = new ClassPathXmlApplicationContext( "classpath:/spring-jdbc-datasource.xml"); try { // Ouverture des traces Date startDate = new Date(); System.out.println( MessageFormat.format(messages.getString("dbbuilder.start"), DBBuilderAppVersion, startDate)); console = new Console(DBBuilder.class); console.printMessage("*************************************************************"); console.printMessage( MessageFormat.format(messages.getString("dbbuilder.start"), DBBuilderAppVersion, startDate)); // Lecture des variables d'environnement partir de dbBuilderSettings dbBuilderResources = FileUtil .loadResource("/org/silverpeas/dbBuilder/settings/dbBuilderSettings.properties"); // Lecture des paramtres d'entre params = new CommandLineParameters(console, args); if (params.isSimulate() && DatabaseType.ORACLE == params.getDbType()) { throw new Exception(messages.getString("oracle.simulate.error")); } console.printMessage(messages.getString("jdbc.connection.configuration")); console.printMessage(ConnectionFactory.getConnectionInfo()); console.printMessage("\tAction : " + params.getAction()); console.printMessage("\tVerbose mode : " + params.isVerbose()); console.printMessage("\tSimulate mode : " + params.isSimulate()); if (Action.ACTION_CONNECT == params.getAction()) { // un petit message et puis c'est tout console.printMessage(messages.getString("connection.success")); System.out.println(messages.getString("connection.success")); } else { // Modules en place sur la BD avant install console.printMessage("DB Status before build :"); List<String> packagesIntoDB = checkDBStatus(); // initialisation d'un vecteur des instructions SQL passer en fin d'upgrade // pour mettre niveau les versions de modules en base MetaInstructions sqlMetaInstructions = new MetaInstructions(); File dirXml = new File(params.getDbType().getDBContributionDir()); DBXmlDocument destXml = loadMasterContribution(dirXml); UninstallInformations processesToCacheIntoDB = new UninstallInformations(); File[] listeFileXml = dirXml.listFiles(); Arrays.sort(listeFileXml); List<DBXmlDocument> listeDBXmlDocument = new ArrayList<DBXmlDocument>(listeFileXml.length); int ignoredFiles = 0; // Ouverture de tous les fichiers de configurations console.printMessage(messages.getString("ignored.contribution")); for (File xmlFile : listeFileXml) { if (xmlFile.isFile() && "xml".equals(FileUtil.getExtension(xmlFile)) && !(FIRST_DBCONTRIBUTION_FILE.equalsIgnoreCase(xmlFile.getName())) && !(MASTER_DBCONTRIBUTION_FILE.equalsIgnoreCase(xmlFile.getName()))) { DBXmlDocument fXml = new DBXmlDocument(dirXml, xmlFile.getName()); fXml.load(); // vrification des dpendances et prise en compte uniquement si dependences OK if (hasUnresolvedRequirements(listeFileXml, fXml)) { console.printMessage( '\t' + xmlFile.getName() + " (because of unresolved requirements)."); ignoredFiles++; } else if (ACTION_ENFORCE_UNINSTALL == params.getAction()) { console.printMessage('\t' + xmlFile.getName() + " (because of " + ACTION_ENFORCE_UNINSTALL + " mode)."); ignoredFiles++; } else { listeDBXmlDocument.add(fXml); } } } if (0 == ignoredFiles) { console.printMessage("\t(none)"); } // prpare une HashMap des modules prsents en fichiers de contribution Map packagesIntoFile = new HashMap(); int j = 0; console.printMessage(messages.getString("merged.contribution")); console.printMessage(params.getAction().toString()); if (ACTION_ENFORCE_UNINSTALL != params.getAction()) { console.printMessage('\t' + FIRST_DBCONTRIBUTION_FILE); j++; } for (DBXmlDocument currentDoc : listeDBXmlDocument) { console.printMessage('\t' + currentDoc.getName()); j++; } if (0 == j) { console.printMessage("\t(none)"); } // merge des diffrents fichiers de contribution ligibles : console.printMessage("Build decisions are :"); // d'abord le fichier dbbuilder-contribution ... DBXmlDocument fileXml; if (ACTION_ENFORCE_UNINSTALL != params.getAction()) { try { fileXml = new DBXmlDocument(dirXml, FIRST_DBCONTRIBUTION_FILE); fileXml.load(); } catch (Exception e) { // contribution de dbbuilder non trouve -> on continue, on est certainement en train // de desinstaller la totale fileXml = null; } if (null != fileXml) { DBBuilderFileItem dbbuilderItem = new DBBuilderFileItem(fileXml); packagesIntoFile.put(dbbuilderItem.getModule(), null); mergeActionsToDo(dbbuilderItem, destXml, processesToCacheIntoDB, sqlMetaInstructions); } } // ... puis les autres for (DBXmlDocument currentDoc : listeDBXmlDocument) { DBBuilderFileItem tmpdbbuilderItem = new DBBuilderFileItem(currentDoc); packagesIntoFile.put(tmpdbbuilderItem.getModule(), null); mergeActionsToDo(tmpdbbuilderItem, destXml, processesToCacheIntoDB, sqlMetaInstructions); } // ... et enfin les pices BD dsinstaller // ... attention, l'ordonnancement n'tant pas dispo, on les traite dans // l'ordre inverse pour faire passer busCore a la fin, de nombreuses contraintes // des autres modules referencant les PK de busCore List<String> itemsList = new ArrayList<String>(); boolean foundDBBuilder = false; for (String dbPackage : packagesIntoDB) { if (!packagesIntoFile.containsKey(dbPackage)) { // Package en base et non en contribution -> candidat desinstallation if (DBBUILDER_MODULE.equalsIgnoreCase(dbPackage)) { foundDBBuilder = true; } else if (ACTION_ENFORCE_UNINSTALL == params.getAction()) { if (dbPackage.equals(params.getModuleName())) { itemsList.add(0, dbPackage); } } else { itemsList.add(0, dbPackage); } } } if (foundDBBuilder) { if (ACTION_ENFORCE_UNINSTALL == params.getAction()) { if (DBBUILDER_MODULE.equals(params.getModuleName())) { itemsList.add(itemsList.size(), DBBUILDER_MODULE); } } else { itemsList.add(itemsList.size(), DBBUILDER_MODULE); } } for (String item : itemsList) { console.printMessage("**** Treating " + item + " ****"); DBBuilderDBItem tmpdbbuilderItem = new DBBuilderDBItem(item); mergeActionsToDo(tmpdbbuilderItem, destXml, processesToCacheIntoDB, sqlMetaInstructions); } destXml.setName("res.txt"); destXml.save(); console.printMessage("Build parts are :"); // Traitement des pices slectionnes // remarque : durant cette phase, les erreurs sont traites -> on les catche en // retour sans les retraiter if (ACTION_INSTALL == params.getAction()) { processDB(destXml, processesToCacheIntoDB, sqlMetaInstructions, TAGS_TO_MERGE_4_INSTALL); } else if (ACTION_UNINSTALL == params.getAction() || ACTION_ENFORCE_UNINSTALL == params.getAction()) { processDB(destXml, processesToCacheIntoDB, sqlMetaInstructions, TAGS_TO_MERGE_4_UNINSTALL); } else if (ACTION_OPTIMIZE == params.getAction()) { processDB(destXml, processesToCacheIntoDB, sqlMetaInstructions, TAGS_TO_MERGE_4_OPTIMIZE); } else if (ACTION_ALL == params.getAction()) { processDB(destXml, processesToCacheIntoDB, sqlMetaInstructions, TAGS_TO_MERGE_4_ALL); } // Modules en place sur la BD en final console.printMessage("Finally DB Status :"); checkDBStatus(); } Date endDate = new Date(); console.printMessage(MessageFormat.format(messages.getString("dbbuilder.success"), endDate)); System.out.println("*******************************************************************"); System.out.println(MessageFormat.format(messages.getString("dbbuilder.success"), endDate)); } catch (Exception e) { e.printStackTrace(); console.printError(e.getMessage(), e); Date endDate = new Date(); console.printError(MessageFormat.format(messages.getString("dbbuilder.failure"), endDate)); System.out.println("*******************************************************************"); System.out.println(MessageFormat.format(messages.getString("dbbuilder.failure"), endDate)); System.exit(1); } finally { springContext.close(); console.close(); } }