List of usage examples for java.io BufferedWriter write
public void write(int c) throws IOException
From source file:com.twentyn.chemicalClassifier.Runner.java
public static void main(String[] args) throws Exception { BufferedReader reader = new BufferedReader(new FileReader(args[0])); BufferedWriter writer = new BufferedWriter(new FileWriter(args[1])); try {//from w w w . j av a2s.com Oscar oscar = new Oscar(); String line = null; /* NOTE: this is exactly the wrong way to write a TSV reader. Caveat emptor. * See http://tburette.github.io/blog/2014/05/25/so-you-want-to-write-your-own-CSV-code/ * and then use org.apache.commons.csv.CSVParser instead. */ while ((line = reader.readLine()) != null) { // TSV means split on tabs! Nothing else will do. List<String> fields = Arrays.asList(line.split("\t")); // Choke if our invariants aren't satisfied. We expect ever line to have a name and an InChI. if (fields.size() != 2) { throw new RuntimeException( String.format("Found malformed line (all lines must have two fields: %s", line)); } String name = fields.get(1); List<ResolvedNamedEntity> entities = oscar.findAndResolveNamedEntities(name); System.out.println("**********"); System.out.println("Name: " + name); List<String> outputFields = new ArrayList<>(fields.size() + 1); outputFields.addAll(fields); if (entities.size() == 0) { System.out.println("No match"); outputFields.add("noMatch"); } else if (entities.size() == 1) { ResolvedNamedEntity entity = entities.get(0); NamedEntity ne = entity.getNamedEntity(); if (ne.getStart() != 0 || ne.getEnd() != name.length()) { System.out.println("Partial match"); printEntity(entity); outputFields.add("partialMatch"); } else { System.out.println("Exact match"); printEntity(entity); outputFields.add("exactMatch"); List<ChemicalStructure> structures = entity.getChemicalStructures(FormatType.STD_INCHI); for (ChemicalStructure s : structures) { outputFields.add(s.getValue()); } } } else { // Multiple matches found! System.out.println("Multiple matches"); for (ResolvedNamedEntity e : entities) { printEntity(e); } outputFields.add("multipleMatches"); } writer.write(String.join("\t", outputFields)); writer.newLine(); } } finally { writer.flush(); writer.close(); } }
From source file:com.era7.bioinfo.annotation.AutomaticQualityControl.java
public static void main(String[] args) { if (args.length != 4) { System.out.println("This program expects four parameters: \n" + "1. Gene annotation XML filename \n" + "2. Reference protein set (.fasta)\n" + "3. Output TXT filename\n" + "4. Initial Blast XML results filename (the one used at the very beginning of the semiautomatic annotation process)\n"); } else {//from w ww . j a v a 2s .c o m BufferedWriter outBuff = null; try { File inFile = new File(args[0]); File fastaFile = new File(args[1]); File outFile = new File(args[2]); File blastFile = new File(args[3]); //Primero cargo todos los datos del archivo xml del blast BufferedReader buffReader = new BufferedReader(new FileReader(blastFile)); StringBuilder stBuilder = new StringBuilder(); String line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); System.out.println("Creating blastoutput..."); BlastOutput blastOutput = new BlastOutput(stBuilder.toString()); System.out.println("BlastOutput created! :)"); stBuilder.delete(0, stBuilder.length()); HashMap<String, String> blastProteinsMap = new HashMap<String, String>(); ArrayList<Iteration> iterations = blastOutput.getBlastOutputIterations(); for (Iteration iteration : iterations) { blastProteinsMap.put(iteration.getQueryDef().split("\\|")[1].trim(), iteration.toString()); } //freeing some memory blastOutput = null; //------------------------------------------------------------------------ //Initializing writer for output file outBuff = new BufferedWriter(new FileWriter(outFile)); //reading gene annotation xml file..... buffReader = new BufferedReader(new FileReader(inFile)); stBuilder = new StringBuilder(); line = null; while ((line = buffReader.readLine()) != null) { stBuilder.append(line); } buffReader.close(); XMLElement genesXML = new XMLElement(stBuilder.toString()); //freeing some memory I don't need anymore stBuilder.delete(0, stBuilder.length()); //reading file with the reference proteins set ArrayList<String> proteinsReferenceSet = new ArrayList<String>(); buffReader = new BufferedReader(new FileReader(fastaFile)); while ((line = buffReader.readLine()) != null) { if (line.charAt(0) == '>') { proteinsReferenceSet.add(line.split("\\|")[1]); } } buffReader.close(); Element pGenes = genesXML.asJDomElement().getChild(PredictedGenes.TAG_NAME); List<Element> contigs = pGenes.getChildren(ContigXML.TAG_NAME); System.out.println("There are " + contigs.size() + " contigs to be checked... "); outBuff.write("There are " + contigs.size() + " contigs to be checked... \n"); outBuff.write("Proteins reference set: \n"); for (String st : proteinsReferenceSet) { outBuff.write(st + ","); } outBuff.write("\n"); for (Element elem : contigs) { ContigXML contig = new ContigXML(elem); //escribo el id del contig en el que estoy outBuff.write("Checking contig: " + contig.getId() + "\n"); outBuff.flush(); List<XMLElement> geneList = contig.getChildrenWith(PredictedGene.TAG_NAME); System.out.println("geneList.size() = " + geneList.size()); int numeroDeGenesParaAnalizar = geneList.size() / FACTOR; if (numeroDeGenesParaAnalizar == 0) { numeroDeGenesParaAnalizar++; } ArrayList<Integer> indicesUtilizados = new ArrayList<Integer>(); outBuff.write("\nThe contig has " + geneList.size() + " predicted genes, let's analyze: " + numeroDeGenesParaAnalizar + "\n"); for (int j = 0; j < numeroDeGenesParaAnalizar; j++) { int geneIndex; boolean geneIsDismissed = false; do { geneIsDismissed = false; geneIndex = (int) Math.round(Math.floor(Math.random() * geneList.size())); PredictedGene tempGene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); if (tempGene.getStatus().equals(PredictedGene.STATUS_DISMISSED)) { geneIsDismissed = true; } } while (indicesUtilizados.contains(new Integer(geneIndex)) && geneIsDismissed); indicesUtilizados.add(geneIndex); System.out.println("geneIndex = " + geneIndex); //Ahora hay que sacar el gen correspondiente al indice y hacer el control de calidad PredictedGene gene = new PredictedGene(geneList.get(geneIndex).asJDomElement()); outBuff.write("\nAnalyzing gene with id: " + gene.getId() + " , annotation uniprot id: " + gene.getAnnotationUniprotId() + "\n"); outBuff.write("eValue: " + gene.getEvalue() + "\n"); //--------------PETICION POST HTTP BLAST---------------------- PostMethod post = new PostMethod(BLAST_URL); post.addParameter("program", "blastx"); post.addParameter("sequence", gene.getSequence()); post.addParameter("database", "uniprotkb"); post.addParameter("email", "ppareja@era7.com"); post.addParameter("exp", "1e-10"); post.addParameter("stype", "dna"); // execute the POST HttpClient client = new HttpClient(); int status = client.executeMethod(post); System.out.println("status post = " + status); InputStream inStream = post.getResponseBodyAsStream(); String fileName = "jobid.txt"; FileOutputStream outStream = new FileOutputStream(new File(fileName)); byte[] buffer = new byte[1024]; int len; while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); String jobId = buffReader.readLine(); buffReader.close(); System.out.println("jobId = " + jobId); //--------------HTTP CHECK JOB STATUS REQUEST---------------------- GetMethod get = new GetMethod(CHECK_JOB_STATUS_URL + jobId); String jobStatus = ""; do { try { Thread.sleep(1000);//sleep for 1000 ms } catch (InterruptedException ie) { //If this thread was intrrupted by nother thread } status = client.executeMethod(get); //System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobStatus.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //Once the file is created I just have to read one line in order to extract the job id buffReader = new BufferedReader(new FileReader(new File(fileName))); jobStatus = buffReader.readLine(); //System.out.println("jobStatus = " + jobStatus); buffReader.close(); } while (!jobStatus.equals(FINISHED_JOB_STATUS)); //Once I'm here the blast should've already finished //--------------JOB RESULTS HTTP REQUEST---------------------- get = new GetMethod(JOB_RESULT_URL + jobId + "/out"); status = client.executeMethod(get); System.out.println("status get = " + status); inStream = get.getResponseBodyAsStream(); fileName = "jobResults.txt"; outStream = new FileOutputStream(new File(fileName)); while ((len = inStream.read(buffer)) != -1) { outStream.write(buffer, 0, len); } outStream.close(); //--------parsing the blast results file----- TreeSet<GeneEValuePair> featuresBlast = new TreeSet<GeneEValuePair>(); buffReader = new BufferedReader(new FileReader(new File(fileName))); while ((line = buffReader.readLine()) != null) { if (line.length() > 3) { String prefix = line.substring(0, 3); if (prefix.equals("TR:") || prefix.equals("SP:")) { String[] columns = line.split(" "); String id = columns[1]; //System.out.println("id = " + id); String e = ""; String[] arraySt = line.split("\\.\\.\\."); if (arraySt.length > 1) { arraySt = arraySt[1].trim().split(" "); int contador = 0; for (int k = 0; k < arraySt.length && contador <= 2; k++) { String string = arraySt[k]; if (!string.equals("")) { contador++; if (contador == 2) { e = string; } } } } else { //Number before e- String[] arr = arraySt[0].split("e-")[0].split(" "); String numeroAntesE = arr[arr.length - 1]; String numeroDespuesE = arraySt[0].split("e-")[1].split(" ")[0]; e = numeroAntesE + "e-" + numeroDespuesE; } double eValue = Double.parseDouble(e); //System.out.println("eValue = " + eValue); GeneEValuePair g = new GeneEValuePair(id, eValue); featuresBlast.add(g); } } } GeneEValuePair currentGeneEValuePair = new GeneEValuePair(gene.getAnnotationUniprotId(), gene.getEvalue()); System.out.println("currentGeneEValuePair.id = " + currentGeneEValuePair.id); System.out.println("currentGeneEValuePair.eValue = " + currentGeneEValuePair.eValue); boolean blastContainsGene = false; for (GeneEValuePair geneEValuePair : featuresBlast) { if (geneEValuePair.id.equals(currentGeneEValuePair.id)) { blastContainsGene = true; //le pongo la e que tiene en el wu-blast para poder comparar currentGeneEValuePair.eValue = geneEValuePair.eValue; break; } } if (blastContainsGene) { outBuff.write("The protein was found in the WU-BLAST result.. \n"); //Una vez que se que esta en el blast tengo que ver que sea la mejor GeneEValuePair first = featuresBlast.first(); outBuff.write("Protein with best eValue according to the WU-BLAST result: " + first.id + " , " + first.eValue + "\n"); if (first.id.equals(currentGeneEValuePair.id)) { outBuff.write("Proteins with best eValue match up \n"); } else { if (first.eValue == currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has the same eValue \n"); } else if (first.eValue > currentGeneEValuePair.eValue) { outBuff.write( "The one with best eValue is not the same protein but has a worse eValue :) \n"); } else { outBuff.write( "The best protein from BLAST has an eValue smaller than ours, checking if it's part of the reference set...\n"); //System.exit(-1); if (proteinsReferenceSet.contains(first.id)) { //The protein is in the reference set and that shouldn't happen outBuff.write( "The protein was found on the reference set, checking if it belongs to the same contig...\n"); String iterationSt = blastProteinsMap.get(gene.getAnnotationUniprotId()); if (iterationSt != null) { outBuff.write( "The protein was found in the BLAST used at the beginning of the annotation process.\n"); Iteration iteration = new Iteration(iterationSt); ArrayList<Hit> hits = iteration.getIterationHits(); boolean contigFound = false; Hit errorHit = null; for (Hit hit : hits) { if (hit.getHitDef().indexOf(contig.getId()) >= 0) { contigFound = true; errorHit = hit; break; } } if (contigFound) { outBuff.write( "ERROR: A hit from the same contig was find in the Blast file: \n" + errorHit.toString() + "\n"); } else { outBuff.write("There is no hit with the same contig! :)\n"); } } else { outBuff.write( "The protein is NOT in the BLAST used at the beginning of the annotation process.\n"); } } else { //The protein was not found on the reference set so everything's ok outBuff.write( "The protein was not found on the reference, everything's ok :)\n"); } } } } else { outBuff.write("The protein was NOT found on the WU-BLAST !! :( \n"); //System.exit(-1); } } } } catch (Exception ex) { ex.printStackTrace(); } finally { try { //closing outputfile outBuff.close(); } catch (IOException ex) { Logger.getLogger(AutomaticQualityControl.class.getName()).log(Level.SEVERE, null, ex); } } } }
From source file:TwitterClustering.java
public static void main(String[] args) throws FileNotFoundException, IOException { // TODO code application logic here File outFile = new File(args[3]); Scanner s = new Scanner(new File(args[1])).useDelimiter(","); JSONParser parser = new JSONParser(); Set<Cluster> clusterSet = new HashSet<Cluster>(); HashMap<String, Tweet> tweets = new HashMap(); FileWriter fw = new FileWriter(outFile.getAbsoluteFile()); BufferedWriter bw = new BufferedWriter(fw); // init/*www. j a v a2 s . c om*/ try { Object obj = parser.parse(new FileReader(args[2])); JSONArray jsonArray = (JSONArray) obj; for (int i = 0; i < jsonArray.size(); i++) { Tweet twt = new Tweet(); JSONObject jObj = (JSONObject) jsonArray.get(i); String text = jObj.get("text").toString(); long sum = 0; for (int y = 0; y < text.toCharArray().length; y++) { sum += (int) text.toCharArray()[y]; } String[] token = text.split(" "); String tID = jObj.get("id").toString(); Set<String> mySet = new HashSet<String>(Arrays.asList(token)); twt.setAttributeValue(sum); twt.setText(mySet); twt.setTweetID(tID); tweets.put(tID, twt); } // preparing initial clusters int i = 0; while (s.hasNext()) { String id = s.next();// id Tweet t = tweets.get(id.trim()); clusterSet.add(new Cluster(i + 1, t, new LinkedList())); i++; } Iterator it = tweets.entrySet().iterator(); for (int l = 0; l < 2; l++) { // limit to 25 iterations while (it.hasNext()) { Map.Entry me = (Map.Entry) it.next(); // calculate distance to each centroid Tweet p = (Tweet) me.getValue(); HashMap<Cluster, Float> distMap = new HashMap(); for (Cluster clust : clusterSet) { distMap.put(clust, jaccardDistance(p.getText(), clust.getCentroid().getText())); } HashMap<Cluster, Float> sorted = (HashMap<Cluster, Float>) sortByValue(distMap); sorted.keySet().iterator().next().getMembers().add(p); } // calculate new centroid and update Clusterset for (Cluster clust : clusterSet) { TreeMap<String, Long> tDistMap = new TreeMap(); Tweet newCentroid = null; Long avgSumDist = new Long(0); for (int j = 0; j < clust.getMembers().size(); j++) { avgSumDist += clust.getMembers().get(j).getAttributeValue(); tDistMap.put(clust.getMembers().get(j).getTweetID(), clust.getMembers().get(j).getAttributeValue()); } if (clust.getMembers().size() != 0) { avgSumDist /= (clust.getMembers().size()); } ArrayList<Long> listValues = new ArrayList<Long>(tDistMap.values()); if (tDistMap.containsValue(findClosestNumber(listValues, avgSumDist))) { // found closest newCentroid = tweets .get(getKeyByValue(tDistMap, findClosestNumber(listValues, avgSumDist))); clust.setCentroid(newCentroid); } } } // create an iterator Iterator iterator = clusterSet.iterator(); // check values while (iterator.hasNext()) { Cluster c = (Cluster) iterator.next(); bw.write(c.getId() + "\t"); System.out.print(c.getId() + "\t"); for (Tweet t : c.getMembers()) { bw.write(t.getTweetID() + ", "); System.out.print(t.getTweetID() + ","); } bw.write("\n"); System.out.println(""); } System.out.println(""); System.out.println("SSE " + sumSquaredErrror(clusterSet)); } catch (Exception e) { e.printStackTrace(); } finally { bw.close(); fw.close(); } }
From source file:apps.Source2XML.java
public static void main(String[] args) { Options options = new Options(); options.addOption("i", null, true, "input file"); options.addOption("o", null, true, "output file"); options.addOption("reparse_xml", null, false, "reparse each XML entry to ensure the parser doesn't fail"); Joiner commaJoin = Joiner.on(','); options.addOption("source_type", null, true, "document source type: " + commaJoin.join(SourceFactory.getDocSourceList())); Joiner spaceJoin = Joiner.on(' '); CommandLineParser parser = new org.apache.commons.cli.GnuParser(); BufferedWriter outputFile = null; int docNum = 0; if (USE_LEMMATIZER && USE_STEMMER) { System.err.println("Bug/inconsistent code: cann't use the stemmer and lemmatizer at the same time!"); System.exit(1);//from ww w.j a va2 s . c o m } //Stemmer stemmer = new Stemmer(); KrovetzStemmer stemmer = new KrovetzStemmer(); System.out.println("Using Stanford NLP? " + USE_STANFORD); System.out.println("Using Stanford lemmatizer? " + USE_LEMMATIZER); System.out.println("Using stemmer? " + USE_STEMMER + (USE_STEMMER ? " (class: " + stemmer.getClass().getCanonicalName() + ")" : "")); try { CommandLine cmd = parser.parse(options, args); String inputFileName = null, outputFileName = null; if (cmd.hasOption("i")) { inputFileName = cmd.getOptionValue("i"); } else { Usage("Specify 'input file'", options); } if (cmd.hasOption("o")) { outputFileName = cmd.getOptionValue("o"); } else { Usage("Specify 'output file'", options); } outputFile = new BufferedWriter( new OutputStreamWriter(CompressUtils.createOutputStream(outputFileName))); String sourceName = cmd.getOptionValue("source_type"); if (sourceName == null) Usage("Specify document source type", options); boolean reparseXML = options.hasOption("reparse_xml"); DocumentSource inpDocSource = SourceFactory.createDocumentSource(sourceName, inputFileName); DocumentEntry inpDoc = null; TextCleaner textCleaner = new TextCleaner( new DictNoComments(new File("data/stopwords.txt"), true /* lower case */), USE_STANFORD, USE_LEMMATIZER); Map<String, String> outputMap = new HashMap<String, String>(); outputMap.put(UtilConst.XML_FIELD_DOCNO, null); outputMap.put(UtilConst.XML_FIELD_TEXT, null); XmlHelper xmlHlp = new XmlHelper(); if (reparseXML) System.out.println("Will reparse every XML entry to verify correctness!"); while ((inpDoc = inpDocSource.next()) != null) { ++docNum; ArrayList<String> toks = textCleaner.cleanUp(inpDoc.mDocText); ArrayList<String> goodToks = new ArrayList<String>(); for (String s : toks) if (s.length() <= MAX_WORD_LEN && // Exclude long and short words s.length() >= MIN_WORD_LEN && isGoodWord(s)) goodToks.add(USE_STEMMER ? stemmer.stem(s) : s); String partlyCleanedText = spaceJoin.join(goodToks); String cleanText = XmlHelper.removeInvaildXMLChars(partlyCleanedText); // isGoodWord combiend with Stanford tokenizer should be quite restrictive already //cleanText = replaceSomePunct(cleanText); outputMap.replace(UtilConst.XML_FIELD_DOCNO, inpDoc.mDocId); outputMap.replace(UtilConst.XML_FIELD_TEXT, cleanText); String xml = xmlHlp.genXMLIndexEntry(outputMap); if (reparseXML) { try { XmlHelper.parseDocWithoutXMLDecl(xml); } catch (Exception e) { System.err.println("Error re-parsing xml for document ID: " + inpDoc.mDocId); System.exit(1); } } /* { System.out.println(inpDoc.mDocId); System.out.println("====================="); System.out.println(partlyCleanedText); System.out.println("====================="); System.out.println(cleanText); } */ try { outputFile.write(xml); outputFile.write(NL); } catch (Exception e) { e.printStackTrace(); System.err.println("Error processing/saving a document!"); } if (docNum % 1000 == 0) System.out.println(String.format("Processed %d documents", docNum)); } } catch (ParseException e) { e.printStackTrace(); Usage("Cannot parse arguments" + e, options); } catch (Exception e) { System.err.println("Terminating due to an exception: " + e); System.exit(1); } finally { System.out.println(String.format("Processed %d documents", docNum)); try { if (null != outputFile) { outputFile.close(); System.out.println("Output file is closed! all seems to be fine..."); } } catch (IOException e) { System.err.println("IO exception: " + e); e.printStackTrace(); } } }
From source file:com.yahoo.labs.yamall.local.Yamall.java
public static void main(String[] args) { String[] remainingArgs = null; String inputFile = null;/*from ww w.java 2s .com*/ String predsFile = null; String saveModelFile = null; String initialModelFile = null; String lossName = null; String parserName = null; String linkName = null; String invertHashName = null; double learningRate = 1; String minPredictionString = null; String maxPredictionString = null; String fmNumberFactorsString = null; int bitsHash; int numberPasses; int holdoutPeriod = 10; boolean testOnly = false; boolean exponentialProgress; double progressInterval; options.addOption("h", "help", false, "displays this help"); options.addOption("t", false, "ignore label information and just test"); options.addOption(Option.builder().hasArg(false).required(false).longOpt("binary") .desc("reports loss as binary classification with -1,1 labels").build()); options.addOption( Option.builder().hasArg(false).required(false).longOpt("solo").desc("uses SOLO optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pcsolo") .desc("uses Per Coordinate SOLO optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pistol") .desc("uses PiSTOL optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("kt") .desc("(EXPERIMENTAL) uses KT optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pckt") .desc("(EXPERIMENTAL) uses Per Coordinate KT optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("pccocob") .desc("(EXPERIMENTAL) uses Per Coordinate COCOB optimizer").build()); options.addOption(Option.builder().hasArg(false).required(false).longOpt("cocob") .desc("(EXPERIMENTAL) uses COCOB optimizer").build()); options.addOption( Option.builder().hasArg(false).required(false).longOpt("fm").desc("Factorization Machine").build()); options.addOption(Option.builder("f").hasArg(true).required(false).desc("final regressor to save") .type(String.class).longOpt("final_regressor").build()); options.addOption(Option.builder("p").hasArg(true).required(false).desc("file to output predictions to") .longOpt("predictions").type(String.class).build()); options.addOption( Option.builder("i").hasArg(true).required(false).desc("initial regressor(s) to load into memory") .longOpt("initial_regressor").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc( "specify the loss function to be used. Currently available ones are: absolute, squared (default), hinge, logistic") .longOpt("loss_function").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc( "specify the link function used in the output of the predictions. Currently available ones are: identity (default), logistic") .longOpt("link").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("output human-readable final regressor with feature names").longOpt("invert_hash") .type(String.class).build()); options.addOption( Option.builder("l").hasArg(true).required(false).desc("set (initial) learning Rate, default = 1.0") .longOpt("learning_rate").type(String.class).build()); options.addOption(Option.builder("b").hasArg(true).required(false) .desc("number of bits in the feature table, default = 18").longOpt("bit_precision") .type(String.class).build()); options.addOption(Option.builder("P").hasArg(true).required(false) .desc("progress update frequency, integer: additive; float: multiplicative, default = 2.0") .longOpt("progress").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("smallest prediction to output, before the link function, default = -50") .longOpt("min_prediction").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("smallest prediction to output, before the link function, default = 50") .longOpt("max_prediction").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("ignore namespaces beginning with the characters in <arg>").longOpt("ignore") .type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc("number of training passes") .longOpt("passes").type(String.class).build()); options.addOption( Option.builder().hasArg(true).required(false).desc("holdout period for test only, default = 10") .longOpt("holdout_period").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("number of factors for Factorization Machines default = 8").longOpt("fmNumberFactors") .type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false) .desc("specify the parser to use. Currently available ones are: vw (default), libsvm, tsv") .longOpt("parser").type(String.class).build()); options.addOption(Option.builder().hasArg(true).required(false).desc("schema file for the TSV input") .longOpt("schema").type(String.class).build()); CommandLineParser parser = new DefaultParser(); CommandLine cmd = null; try { cmd = parser.parse(options, args); } catch (ParseException e) { System.out.println("Unrecognized option"); help(); } if (cmd.hasOption("h")) help(); if (cmd.hasOption("t")) testOnly = true; if (cmd.hasOption("binary")) { binary = true; System.out.println("Reporting binary loss"); } initialModelFile = cmd.getOptionValue("i"); predsFile = cmd.getOptionValue("p"); lossName = cmd.getOptionValue("loss_function", "squared"); linkName = cmd.getOptionValue("link", "identity"); saveModelFile = cmd.getOptionValue("f"); learningRate = Double.parseDouble(cmd.getOptionValue("l", "1.0")); bitsHash = Integer.parseInt(cmd.getOptionValue("b", "18")); invertHashName = cmd.getOptionValue("invert_hash"); minPredictionString = cmd.getOptionValue("min_prediction", "-50"); maxPredictionString = cmd.getOptionValue("max_prediction", "50"); fmNumberFactorsString = cmd.getOptionValue("fmNumberFactors", "8"); parserName = cmd.getOptionValue("parser", "vw"); numberPasses = Integer.parseInt(cmd.getOptionValue("passes", "1")); System.out.println("Number of passes = " + numberPasses); if (numberPasses > 1) { holdoutPeriod = Integer.parseInt(cmd.getOptionValue("holdout_period", "10")); System.out.println("Holdout period = " + holdoutPeriod); } remainingArgs = cmd.getArgs(); if (remainingArgs.length == 1) inputFile = remainingArgs[0]; InstanceParser instanceParser = null; if (parserName.equals("vw")) instanceParser = new VWParser(bitsHash, cmd.getOptionValue("ignore"), (invertHashName != null)); else if (parserName.equals("libsvm")) instanceParser = new LIBSVMParser(bitsHash, (invertHashName != null)); else if (parserName.equals("tsv")) { String schema = cmd.getOptionValue("schema"); if (schema == null) { System.out.println("TSV parser requires a schema file."); System.exit(0); } else { String spec = null; try { spec = new String(Files.readAllBytes(Paths.get(schema))); } catch (IOException e) { System.out.println("Error reading the TSV schema file."); e.printStackTrace(); System.exit(0); } instanceParser = new TSVParser(bitsHash, cmd.getOptionValue("ignore"), (invertHashName != null), spec); } } else { System.out.println("Unknown parser."); System.exit(0); } System.out.println("Num weight bits = " + bitsHash); // setup progress String progress = cmd.getOptionValue("P", "2.0"); if (progress.indexOf('.') >= 0) { exponentialProgress = true; progressInterval = (double) Double.parseDouble(progress); } else { exponentialProgress = false; progressInterval = (double) Integer.parseInt(progress); } // min and max predictions minPrediction = (double) Double.parseDouble(minPredictionString); maxPrediction = (double) Double.parseDouble(maxPredictionString); // number of factors for Factorization Machines fmNumberFactors = (int) Integer.parseInt(fmNumberFactorsString); // configure the learner Loss lossFnc = null; LinkFunction link = null; if (initialModelFile == null) { if (cmd.hasOption("kt")) { learner = new KT(bitsHash); } else if (cmd.hasOption("pckt")) { learner = new PerCoordinateKT(bitsHash); } else if (cmd.hasOption("pcsolo")) { learner = new PerCoordinateSOLO(bitsHash); } else if (cmd.hasOption("solo")) { learner = new SOLO(bitsHash); } else if (cmd.hasOption("pccocob")) { learner = new PerCoordinateCOCOB(bitsHash); } else if (cmd.hasOption("cocob")) { learner = new COCOB(bitsHash); } else if (cmd.hasOption("pistol")) { learner = new PerCoordinatePiSTOL(bitsHash); } else if (cmd.hasOption("fm")) { learner = new SGD_FM(bitsHash, fmNumberFactors); } else learner = new SGD_VW(bitsHash); } else { learner = IOLearner.loadLearner(initialModelFile); } // setup link function if (linkName.equals("identity")) { link = new IdentityLinkFunction(); } else if (linkName.equals("logistic")) { link = new LogisticLinkFunction(); } else { System.out.println("Unknown link function."); System.exit(0); } // setup loss function if (lossName.equals("squared")) { lossFnc = new SquareLoss(); } else if (lossName.equals("hinge")) { lossFnc = new HingeLoss(); } else if (lossName.equals("logistic")) { lossFnc = new LogisticLoss(); } else if (lossName.equals("absolute")) { lossFnc = new AbsLoss(); } else { System.out.println("Unknown loss function."); System.exit(0); } learner.setLoss(lossFnc); learner.setLearningRate(learningRate); // maximum range predictions System.out.println("Max prediction = " + maxPrediction + ", Min Prediction = " + minPrediction); // print information about the learner System.out.println(learner.toString()); // print information about the link function System.out.println(link.toString()); // print information about the parser System.out.println(instanceParser.toString()); // print information about ignored namespaces System.out.println("Ignored namespaces = " + cmd.getOptionValue("ignore", "")); long start = System.nanoTime(); FileInputStream fstream; try { BufferedReader br = null; if (inputFile != null) { fstream = new FileInputStream(inputFile); System.out.println("Reading datafile = " + inputFile); br = new BufferedReader(new InputStreamReader(fstream)); } else { System.out.println("Reading from console"); br = new BufferedReader(new InputStreamReader(System.in)); } File fout = null; FileOutputStream fos = null; BufferedWriter bw = null; if (predsFile != null) { fout = new File(predsFile); fos = new FileOutputStream(fout); bw = new BufferedWriter(new OutputStreamWriter(fos)); } try { System.out.println("average example current current current"); System.out.println("loss counter label predict features"); int iter = 0; double cumLoss = 0; double weightedSampleSum = 0; double sPlus = 0; double sMinus = 0; Instance sample = null; boolean justPrinted = false; int pass = 0; ObjectOutputStream ooutTr = null; ObjectOutputStream ooutHO = null; ObjectInputStream oinTr = null; double pred = 0; int limit = 1; double hError = Double.MAX_VALUE; double lastHError = Double.MAX_VALUE; int numTestSample = 0; int numTrainingSample = 0; int idx = 0; if (numberPasses > 1) { ooutTr = new ObjectOutputStream(new FileOutputStream("cache_training.bin")); ooutHO = new ObjectOutputStream(new FileOutputStream("cache_holdout.bin")); oinTr = new ObjectInputStream(new FileInputStream("cache_training.bin")); } do { while (true) { double score; if (pass > 0 && numberPasses > 1) { Instance tmp = (Instance) oinTr.readObject(); if (tmp != null) sample = tmp; else break; } else { String strLine = br.readLine(); if (strLine != null) sample = instanceParser.parse(strLine); else break; } justPrinted = false; idx++; if (numberPasses > 1 && pass == 0 && idx % holdoutPeriod == 0) { // store the current sample for the holdout set ooutHO.writeObject(sample); ooutHO.reset(); numTestSample++; } else { if (numberPasses > 1 && pass == 0) { ooutTr.writeObject(sample); ooutTr.reset(); numTrainingSample++; } iter++; if (testOnly) { // predict the sample score = learner.predict(sample); } else { // predict the sample and update the classifier using the sample score = learner.update(sample); } score = Math.min(Math.max(score, minPrediction), maxPrediction); pred = link.apply(score); if (!binary) cumLoss += learner.getLoss().lossValue(score, sample.getLabel()) * sample.getWeight(); else if (Math.signum(score) != sample.getLabel()) cumLoss += sample.getWeight(); weightedSampleSum += sample.getWeight(); if (sample.getLabel() > 0) sPlus = sPlus + sample.getWeight(); else sMinus = sMinus + sample.getWeight(); // output predictions to file if (predsFile != null) { bw.write(String.format("%.6f %s", pred, sample.getTag())); bw.newLine(); } // print statistics to screen if (iter == limit) { justPrinted = true; System.out.printf("%.6f %12d % .4f % .4f %d\n", cumLoss / weightedSampleSum, iter, sample.getLabel(), pred, sample.getVector().size()); if (exponentialProgress) limit *= progressInterval; else limit += progressInterval; } } } if (numberPasses > 1) { if (pass == 0) { // finished first pass of many // write a null at the end of the files ooutTr.writeObject(null); ooutHO.writeObject(null); ooutTr.flush(); ooutHO.flush(); ooutTr.close(); ooutHO.close(); System.out.println("finished first epoch"); System.out.println(numTrainingSample + " training samples"); System.out.println(numTestSample + " holdout samples saved"); } lastHError = hError; hError = evalHoldoutError(); } if (numberPasses > 1) { System.out.printf("Weighted loss on holdout on epoch %d = %.6f\n", pass + 1, hError); oinTr.close(); oinTr = new ObjectInputStream(new FileInputStream("cache_training.bin")); if (hError > lastHError) { System.out.println("Early stopping"); break; } } pass++; } while (pass < numberPasses); if (justPrinted == false) { System.out.printf("%.6f %12d % .4f % .4f %d\n", cumLoss / weightedSampleSum, iter, sample.getLabel(), pred, sample.getVector().size()); } System.out.println("finished run"); System.out.println(String.format("average loss best constant predictor: %.6f", lossFnc.lossConstantBinaryLabels(sPlus, sMinus))); if (saveModelFile != null) IOLearner.saveLearner(learner, saveModelFile); if (invertHashName != null) IOLearner.saveInvertHash(learner.getWeights(), instanceParser.getInvertHashMap(), invertHashName); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } catch (ClassNotFoundException e) { // TODO Auto-generated catch block e.printStackTrace(); } // close the input stream try { br.close(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } // close the output stream if (predsFile != null) { try { bw.close(); } catch (IOException e) { // TODO Auto-generated catch block e.printStackTrace(); } } long millis = System.nanoTime() - start; System.out.printf("Elapsed time: %d min, %d sec\n", TimeUnit.NANOSECONDS.toMinutes(millis), TimeUnit.NANOSECONDS.toSeconds(millis) - 60 * TimeUnit.NANOSECONDS.toMinutes(millis)); } catch ( FileNotFoundException e) { System.out.println("Error opening the input file"); e.printStackTrace(); } }
From source file:com.cws.esolutions.security.main.PasswordUtility.java
public static void main(final String[] args) { final String methodName = PasswordUtility.CNAME + "#main(final String[] args)"; if (DEBUG) {//from ww w. ja va 2s . c om DEBUGGER.debug("Value: {}", methodName); } if (args.length == 0) { HelpFormatter usage = new HelpFormatter(); usage.printHelp(PasswordUtility.CNAME, options, true); System.exit(1); } BufferedReader bReader = null; BufferedWriter bWriter = null; try { // load service config first !! SecurityServiceInitializer.initializeService(PasswordUtility.SEC_CONFIG, PasswordUtility.LOG_CONFIG, false); if (DEBUG) { DEBUGGER.debug("Options options: {}", options); for (String arg : args) { DEBUGGER.debug("Value: {}", arg); } } CommandLineParser parser = new PosixParser(); CommandLine commandLine = parser.parse(options, args); if (DEBUG) { DEBUGGER.debug("CommandLineParser parser: {}", parser); DEBUGGER.debug("CommandLine commandLine: {}", commandLine); DEBUGGER.debug("CommandLine commandLine.getOptions(): {}", (Object[]) commandLine.getOptions()); DEBUGGER.debug("CommandLine commandLine.getArgList(): {}", commandLine.getArgList()); } final SecurityConfigurationData secConfigData = PasswordUtility.svcBean.getConfigData(); final SecurityConfig secConfig = secConfigData.getSecurityConfig(); final PasswordRepositoryConfig repoConfig = secConfigData.getPasswordRepo(); final SystemConfig systemConfig = secConfigData.getSystemConfig(); if (DEBUG) { DEBUGGER.debug("SecurityConfigurationData secConfig: {}", secConfigData); DEBUGGER.debug("SecurityConfig secConfig: {}", secConfig); DEBUGGER.debug("RepositoryConfig secConfig: {}", repoConfig); DEBUGGER.debug("SystemConfig systemConfig: {}", systemConfig); } if (commandLine.hasOption("encrypt")) { if ((StringUtils.isBlank(repoConfig.getPasswordFile())) || (StringUtils.isBlank(repoConfig.getSaltFile()))) { System.err.println("The password/salt files are not configured. Entries will not be stored!"); } File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile()); File saltFile = FileUtils.getFile(repoConfig.getSaltFile()); if (DEBUG) { DEBUGGER.debug("File passwordFile: {}", passwordFile); DEBUGGER.debug("File saltFile: {}", saltFile); } final String entryName = commandLine.getOptionValue("entry"); final String username = commandLine.getOptionValue("username"); final String password = commandLine.getOptionValue("password"); final String salt = RandomStringUtils.randomAlphanumeric(secConfig.getSaltLength()); if (DEBUG) { DEBUGGER.debug("String entryName: {}", entryName); DEBUGGER.debug("String username: {}", username); DEBUGGER.debug("String password: {}", password); DEBUGGER.debug("String salt: {}", salt); } final String encodedSalt = PasswordUtils.base64Encode(salt); final String encodedUserName = PasswordUtils.base64Encode(username); final String encryptedPassword = PasswordUtils.encryptText(password, salt, secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(), secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(), systemConfig.getEncoding()); final String encodedPassword = PasswordUtils.base64Encode(encryptedPassword); if (DEBUG) { DEBUGGER.debug("String encodedSalt: {}", encodedSalt); DEBUGGER.debug("String encodedUserName: {}", encodedUserName); DEBUGGER.debug("String encodedPassword: {}", encodedPassword); } if (commandLine.hasOption("store")) { try { new File(passwordFile.getParent()).mkdirs(); new File(saltFile.getParent()).mkdirs(); boolean saltFileExists = (saltFile.exists()) ? true : saltFile.createNewFile(); if (DEBUG) { DEBUGGER.debug("saltFileExists: {}", saltFileExists); } // write the salt out first if (!(saltFileExists)) { throw new IOException("Unable to create salt file"); } boolean passwordFileExists = (passwordFile.exists()) ? true : passwordFile.createNewFile(); if (!(passwordFileExists)) { throw new IOException("Unable to create password file"); } if (commandLine.hasOption("replace")) { File[] files = new File[] { saltFile, passwordFile }; if (DEBUG) { DEBUGGER.debug("File[] files: {}", (Object) files); } for (File file : files) { if (DEBUG) { DEBUGGER.debug("File: {}", file); } String currentLine = null; File tmpFile = new File(FileUtils.getTempDirectory() + "/" + "tmpFile"); if (DEBUG) { DEBUGGER.debug("File tmpFile: {}", tmpFile); } bReader = new BufferedReader(new FileReader(file)); bWriter = new BufferedWriter(new FileWriter(tmpFile)); while ((currentLine = bReader.readLine()) != null) { if (!(StringUtils.equals(currentLine.trim().split(",")[0], entryName))) { bWriter.write(currentLine + System.getProperty("line.separator")); bWriter.flush(); } } bWriter.close(); FileUtils.deleteQuietly(file); FileUtils.copyFile(tmpFile, file); FileUtils.deleteQuietly(tmpFile); } } FileUtils.writeStringToFile(saltFile, entryName + "," + encodedUserName + "," + encodedSalt + System.getProperty("line.separator"), true); FileUtils.writeStringToFile(passwordFile, entryName + "," + encodedUserName + "," + encodedPassword + System.getProperty("line.separator"), true); } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); } } System.out.println("Entry Name " + entryName + " stored."); } if (commandLine.hasOption("decrypt")) { String saltEntryName = null; String saltEntryValue = null; String decryptedPassword = null; String passwordEntryName = null; if ((StringUtils.isEmpty(commandLine.getOptionValue("entry")) && (StringUtils.isEmpty(commandLine.getOptionValue("username"))))) { throw new ParseException("No entry or username was provided to decrypt."); } if (StringUtils.isEmpty(commandLine.getOptionValue("username"))) { throw new ParseException("no entry provided to decrypt"); } String entryName = commandLine.getOptionValue("entry"); String username = commandLine.getOptionValue("username"); if (DEBUG) { DEBUGGER.debug("String entryName: {}", entryName); DEBUGGER.debug("String username: {}", username); } File passwordFile = FileUtils.getFile(repoConfig.getPasswordFile()); File saltFile = FileUtils.getFile(repoConfig.getSaltFile()); if (DEBUG) { DEBUGGER.debug("File passwordFile: {}", passwordFile); DEBUGGER.debug("File saltFile: {}", saltFile); } if ((!(saltFile.canRead())) || (!(passwordFile.canRead()))) { throw new IOException( "Unable to read configured password/salt file. Please check configuration and/or permissions."); } for (String lineEntry : FileUtils.readLines(saltFile, systemConfig.getEncoding())) { saltEntryName = lineEntry.split(",")[0]; if (DEBUG) { DEBUGGER.debug("String saltEntryName: {}", saltEntryName); } if (StringUtils.equals(saltEntryName, entryName)) { saltEntryValue = PasswordUtils.base64Decode(lineEntry.split(",")[2]); break; } } if (StringUtils.isEmpty(saltEntryValue)) { throw new SecurityException("No entries were found that matched the provided information"); } for (String lineEntry : FileUtils.readLines(passwordFile, systemConfig.getEncoding())) { passwordEntryName = lineEntry.split(",")[0]; if (DEBUG) { DEBUGGER.debug("String passwordEntryName: {}", passwordEntryName); } if (StringUtils.equals(passwordEntryName, saltEntryName)) { String decodedPassword = PasswordUtils.base64Decode(lineEntry.split(",")[2]); decryptedPassword = PasswordUtils.decryptText(decodedPassword, saltEntryValue, secConfig.getSecretAlgorithm(), secConfig.getIterations(), secConfig.getKeyBits(), secConfig.getEncryptionAlgorithm(), secConfig.getEncryptionInstance(), systemConfig.getEncoding()); break; } } if (StringUtils.isEmpty(decryptedPassword)) { throw new SecurityException("No entries were found that matched the provided information"); } System.out.println(decryptedPassword); } else if (commandLine.hasOption("encode")) { System.out.println(PasswordUtils.base64Encode((String) commandLine.getArgList().get(0))); } else if (commandLine.hasOption("decode")) { System.out.println(PasswordUtils.base64Decode((String) commandLine.getArgList().get(0))); } } catch (IOException iox) { ERROR_RECORDER.error(iox.getMessage(), iox); System.err.println("An error occurred during processing: " + iox.getMessage()); System.exit(1); } catch (ParseException px) { ERROR_RECORDER.error(px.getMessage(), px); System.err.println("An error occurred during processing: " + px.getMessage()); System.exit(1); } catch (SecurityException sx) { ERROR_RECORDER.error(sx.getMessage(), sx); System.err.println("An error occurred during processing: " + sx.getMessage()); System.exit(1); } catch (SecurityServiceException ssx) { ERROR_RECORDER.error(ssx.getMessage(), ssx); System.exit(1); } finally { try { if (bReader != null) { bReader.close(); } if (bWriter != null) { bReader.close(); } } catch (IOException iox) { } } System.exit(0); }
From source file:graticules2wld.Main.java
/** * @param args/*from w w w . j a va 2 s .c o m*/ * @throws Exception */ public static void main(String[] args) throws Exception { /* parse the command line arguments */ // create the command line parser CommandLineParser parser = new PosixParser(); // create the Options Options options = new Options(); options.addOption("x", "originx", true, "x component of projected coordinates of upper left pixel"); options.addOption("y", "originy", true, "y component of projected coordinates of upper left pixel"); options.addOption("u", "tometers", true, "multiplication factor to get source units into meters"); options.addOption("h", "help", false, "prints this usage page"); options.addOption("d", "debug", false, "prints debugging information to stdout"); double originNorthing = 0; double originEasting = 0; String inputFileName = null; String outputFileName = null; try { // parse the command line arguments CommandLine line = parser.parse(options, args); if (line.hasOption("help")) printUsage(0); // print usage then exit using a non error exit status if (line.hasOption("debug")) debug = true; // these arguments are required if (!line.hasOption("originy") || !line.hasOption("originx")) printUsage(1); originNorthing = Double.parseDouble(line.getOptionValue("originy")); originEasting = Double.parseDouble(line.getOptionValue("originx")); if (line.hasOption("tometers")) unitsToMeters = Double.parseDouble(line.getOptionValue("tometers")); // two args should be left. the input csv file name and the output wld file name. String[] iofiles = line.getArgs(); if (iofiles.length < 2) { printUsage(1); } inputFileName = iofiles[0]; outputFileName = iofiles[1]; } catch (ParseException exp) { System.err.println("Unexpected exception:" + exp.getMessage()); System.exit(1); } // try to open the input file for reading and the output file for writing File graticulesCsvFile; BufferedReader csvReader = null; File wldFile; BufferedWriter wldWriter = null; try { graticulesCsvFile = new File(inputFileName); csvReader = new BufferedReader(new FileReader(graticulesCsvFile)); } catch (IOException exp) { System.err.println("Could not open input file for reading: " + inputFileName); System.exit(1); } try { wldFile = new File(outputFileName); wldWriter = new BufferedWriter(new FileWriter(wldFile)); } catch (IOException exp) { System.err.println("Could not open output file for writing: " + outputFileName); System.exit(1); } // list of lon graticules and lat graticules ArrayList<Graticule> lonGrats = new ArrayList<Graticule>(); ArrayList<Graticule> latGrats = new ArrayList<Graticule>(); // read the source CSV and convert its information into the two ArrayList<Graticule> data structures readCSV(csvReader, lonGrats, latGrats); // we now need to start finding the world file paramaters DescriptiveStatistics stats = new DescriptiveStatistics(); // find theta and phi for (Graticule g : latGrats) { stats.addValue(g.angle()); } double theta = stats.getMean(); // we use the mean of the lat angles as theta if (debug) System.out.println("theta range = " + Math.toDegrees(stats.getMax() - stats.getMin())); stats.clear(); for (Graticule g : lonGrats) { stats.addValue(g.angle()); } double phi = stats.getMean(); // ... and the mean of the lon angles for phi if (debug) System.out.println("phi range = " + Math.toDegrees(stats.getMax() - stats.getMin())); stats.clear(); // print these if in debug mode if (debug) { System.out.println("theta = " + Math.toDegrees(theta) + "deg"); System.out.println("phi = " + Math.toDegrees(phi) + "deg"); } // find x and y (distance beteen pixels in map units) Collections.sort(latGrats); Collections.sort(lonGrats); int prevMapValue = 0; //fixme: how to stop warning about not being initilised? Line2D prevGratPixelSys = new Line2D.Double(); boolean first = true; for (Graticule g : latGrats) { if (!first) { int deltaMapValue = Math.abs(g.realValue() - prevMapValue); double deltaPixelValue = (g.l.ptLineDist(prevGratPixelSys.getP1()) + (g.l.ptLineDist(prevGratPixelSys.getP2()))) / 2; double delta = deltaMapValue / deltaPixelValue; stats.addValue(delta); } else { first = false; prevMapValue = g.realValue(); prevGratPixelSys = (Line2D) g.l.clone(); } } double y = stats.getMean(); if (debug) System.out.println("y range = " + (stats.getMax() - stats.getMin())); stats.clear(); first = true; for (Graticule g : lonGrats) { if (!first) { int deltaMapValue = g.realValue() - prevMapValue; double deltaPixelValue = (g.l.ptLineDist(prevGratPixelSys.getP1()) + (g.l.ptLineDist(prevGratPixelSys.getP2()))) / 2; double delta = deltaMapValue / deltaPixelValue; stats.addValue(delta); } else { first = false; prevMapValue = g.realValue(); prevGratPixelSys = (Line2D) g.l.clone(); } } double x = stats.getMean(); if (debug) System.out.println("x range = " + (stats.getMax() - stats.getMin())); stats.clear(); if (debug) { System.out.println("x = " + x); System.out.println("y = " + y); } SimpleRegression regression = new SimpleRegression(); // C, F are translation terms: x, y map coordinates of the center of the upper-left pixel for (Graticule g : latGrats) { // find perp dist to pixel space 0,0 Double perpPixelDist = g.l.ptLineDist(new Point2D.Double(0, 0)); // find the map space distance from this graticule to the center of the 0,0 pixel Double perpMapDist = perpPixelDist * y; // perpMapDist / perpPixelDist = y regression.addData(perpMapDist, g.realValue()); } double F = regression.getIntercept(); regression.clear(); for (Graticule g : lonGrats) { // find perp dist to pixel space 0,0 Double perpPixelDist = g.l.ptLineDist(new Point2D.Double(0, 0)); // find the map space distance from this graticule to the center of the 0,0 pixel Double perpMapDist = perpPixelDist * x; // perpMapDist / perpPixelDist = x regression.addData(perpMapDist, g.realValue()); } double C = regression.getIntercept(); regression.clear(); if (debug) { System.out.println("Upper Left pixel has coordinates " + C + ", " + F); } // convert to meters C *= unitsToMeters; F *= unitsToMeters; // C,F store the projected (in map units) coordinates of the upper left pixel. // originNorthing,originEasting is the offset we need to apply to 0,0 to push the offsets into our global coordinate system C = originEasting + C; F = originNorthing + F; // calculate the affine transformation matrix elements double D = -1 * x * unitsToMeters * Math.sin(theta); double A = x * unitsToMeters * Math.cos(theta); double B = y * unitsToMeters * Math.sin(phi); // if should be negative, it'll formed by negative sin double E = -1 * y * unitsToMeters * Math.cos(phi); /* * Line 1: A: pixel size in the x-direction in map units/pixel * Line 2: D: rotation about y-axis * Line 3: B: rotation about x-axis * Line 4: E: pixel size in the y-direction in map units, almost always negative[3] * Line 5: C: x-coordinate of the center of the upper left pixel * Line 6: F: y-coordinate of the center of the upper left pixel */ if (debug) { System.out.println("A = " + A); System.out.println("D = " + D); System.out.println("B = " + B); System.out.println("E = " + E); System.out.println("C = " + C); System.out.println("F = " + F); // write the world file System.out.println(); System.out.println("World File:"); System.out.println(A); System.out.println(D); System.out.println(B); System.out.println(E); System.out.println(C); System.out.println(F); } // write to the .wld file wldWriter.write(A + "\n"); wldWriter.write(D + "\n"); wldWriter.write(B + "\n"); wldWriter.write(E + "\n"); wldWriter.write(C + "\n"); wldWriter.write(F + "\n"); wldWriter.close(); }
From source file:net.cloudkit.enterprises.ws.SuperPassQueryTest.java
public static void main(String[] args) throws Exception { List<String> params = new ArrayList<>(); // System.out.println(SuperPassQueryTest.class.getResource("/list.dat").toURI()); Path path = Paths.get(SuperPassQueryTest.class.getResource("/list.dat").toURI()); try (BufferedReader reader = Files.newBufferedReader(path, Charset.forName("UTF-8"))) { // System.out.println(reader.readLine().length()); String line;/*from w w w .j av a2 s . c o m*/ while ((line = reader.readLine()) != null) { // System.out.println("TEXT LINE:" + line); params.add(line); } } Path succeededFile = Paths.get(SuperPassQueryTest.class.getResource("/succeeded.dat").toURI()); BufferedWriter succeededWriter = Files.newBufferedWriter(succeededFile, StandardCharsets.UTF_8, StandardOpenOption.APPEND); Path failedFile = Paths.get(SuperPassQueryTest.class.getResource("/failed.dat").toURI()); BufferedWriter failedWriter = Files.newBufferedWriter(failedFile, StandardCharsets.UTF_8, StandardOpenOption.APPEND); for (String param : params) { try { /* StringTokenizer stringTokenizer = new StringTokenizer(param, ","); while(stringTokenizer.hasMoreTokens()){ System.out.println("COUNT:" + stringTokenizer.countTokens()); System.out.println("VALUE:" + stringTokenizer.nextToken()); System.out.println("COUNT:" + stringTokenizer.countTokens()); } */ System.out.println("QUERY PARAMS:" + param); String[] paramArray = param.split(","); // System.out.println("VALUE:" + paramArray[0]); // System.out.println("VALUE:" + paramArray[1]); // System.out.println("VALUE:" + paramArray[2]); String value_1 = paramArray[0]; String value_2 = paramArray[1]; String value_3 = paramArray[2]; String serviceName = "eport.superpass.spdec.DecQueryListService"; byte[] requestContext = ("<?xml version=\"1.0\" encoding=\"utf-8\" standalone=\"yes\"?>\n" + "<RequestContext>\n" + " <Group name=\"SystemInfo\">\n" + " <Key name=\"NAME_FULL\">???</Key>\n" + " <Key name=\"ClientId\">5300001976914</Key>\n" + " <Key name=\"CertNo\">df630b</Key>\n" + " <Key name=\"SaicSysNo\">766350979</Key>\n" + " <Key name=\"DEP_IN_CODE\">5300</Key>\n" + " <Key name=\"REG_CO_CGAC\">4403180237</Key>\n" + " <Key name=\"ENT_SEQ_NO\">000000000000315537</Key>\n" + " <Key name=\"ENT_TYPE\">3</Key>\n" + " <Key name=\"IcCode\">8930000011040</Key>\n" + " <Key name=\"OperatorName\">?</Key>\n" + " <Key name=\"DEP_CODE_CHG\">5305</Key>\n" + " <Key name=\"SessionId\">AE2533938D521A9972186B07BBBEB244</Key>\n" + " </Group>\n" + " <Group name=\"DataPresentation\">\n" + " <Key name=\"SignatureAlgorithm\"/>\n" + " <Key name=\"EncryptAlgorithm\"/>\n" + " <Key name=\"CompressAlgorithm\"/>\n" + " </Group>\n" + " <Group name=\"Default\">\n" + " <Key name=\"clientSystemId\">0400620001</Key>\n" + " <Key name=\"needWebInvoke\">True</Key>\n" + " </Group>\n" + "</RequestContext>").getBytes(); byte[] requestData = ("<?xml version=\"1.0\"?>\n" + "<DecQueryListRequest xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\" xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\">\n" + " <OperType>0</OperType>\n" + " <DecType>\n" + " <TrnType>0</TrnType>\n" + " <IEFlag>" + value_3 + "</IEFlag>\n" + " <DecSubType />\n" + " </DecType>\n" + " <CopeCode>766350979</CopeCode>\n" + " <AgentCode>4403180237</AgentCode>\n" + " <SeqNo>" + value_1 + "</SeqNo>\n" + " <UserType>0</UserType>\n" + "</DecQueryListRequest>").getBytes(); Holder<byte[]> responseData = new Holder<>(); // <?xml version="1.0" encoding="UTF-8" standalone="no"?><ResponseContext><ResponseCode>0</ResponseCode><ResponseMessage>success</ResponseMessage><ServiceResponseCode>0</ServiceResponseCode><ServiceResponseMessage>?</ServiceResponseMessage><ExceptionDetail/><Group name="DataPresentation"><Key name="CompressAlgorithm"/><Key name="SignatureAlgorithm"/><Key name="EncryptAlgorithm"/></Group></ResponseContext> // <?xml version="1.0" encoding="UTF-8" standalone="yes"?><DecQueryListResponse><QueryResponseData><EntryId>531820161181010544</EntryId><SeqNo>000000001139524197</SeqNo><BillNo>2016051920160523</BillNo><IEDate>20160621</IEDate><TradeMode>0615</TradeMode><ItemsNum>19</ItemsNum><TrafName></TrafName><Status>O</Status><AgentName>???</AgentName><IEFlag>I</IEFlag><CustomsCode>5318</CustomsCode><DeclTrnRel>0</DeclTrnRel><RetExplain>;?</RetExplain><NoticeDate>2016-06-29</NoticeDate><TradeName>()??</TradeName><ExtendField><DecDeclareSysType>2</DecDeclareSysType><TrnSysType>1</TrnSysType><AssureExamRet>0</AssureExamRet><RelatedDocumentType> </RelatedDocumentType><DeclareSeqNo> </DeclareSeqNo><ExtendField53>P</ExtendField53><ExtendField>21 P</ExtendField></ExtendField><EntryType>M</EntryType></QueryResponseData></DecQueryListResponse> // String responseContext = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\"?><ResponseContext><ResponseCode>0</ResponseCode><ResponseMessage>success</ResponseMessage><ServiceResponseCode>0</ServiceResponseCode><ServiceResponseMessage>?</ServiceResponseMessage><ExceptionDetail/><Group name=\"DataPresentation\"><Key name=\"CompressAlgorithm\"/><Key name=\"SignatureAlgorithm\"/><Key name=\"EncryptAlgorithm\"/></Group></ResponseContext>"; // String queryListResponse = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?><DecQueryListResponse><QueryResponseData><EntryId>531820161181010544</EntryId><SeqNo>000000001139524197</SeqNo><BillNo>2016051920160523</BillNo><IEDate>20160621</IEDate><TradeMode>0615</TradeMode><ItemsNum>19</ItemsNum><TrafName></TrafName><Status>O</Status><AgentName>???</AgentName><IEFlag>I</IEFlag><CustomsCode>5318</CustomsCode><DeclTrnRel>0</DeclTrnRel><RetExplain>;?</RetExplain><NoticeDate>2016-06-29</NoticeDate><TradeName>()??</TradeName><ExtendField><DecDeclareSysType>2</DecDeclareSysType><TrnSysType>1</TrnSysType><AssureExamRet>0</AssureExamRet><RelatedDocumentType> </RelatedDocumentType><DeclareSeqNo> </DeclareSeqNo><ExtendField53>P</ExtendField53><ExtendField>21 P</ExtendField></ExtendField><EntryType>M</EntryType></QueryResponseData></DecQueryListResponse>"; String responseContext = new String( superPass.service(serviceName, requestContext, requestData, responseData)); String queryListResponse = new String(responseData.value); System.out.println("RESPONSE_CONTEXT:" + responseContext); System.out.println("QUERY_LIST_RESPONSE:" + queryListResponse); String serviceResponseCode = parsingReceiptStatus(responseContext); System.out.println("SERVICE_RESPONSE_CODE:" + serviceResponseCode); if (serviceResponseCode.equals("0")) { String data = parsingReceiptData(queryListResponse); System.out.println("DATA:" + data); succeededWriter.write(data); succeededWriter.flush(); } else { failedWriter.write(param + "\n"); failedWriter.flush(); } Thread.sleep(6 * 1000); } catch (Exception e) { failedWriter.write(param + "\n"); failedWriter.flush(); } } succeededWriter.close(); failedWriter.close(); }
From source file:FileUtils.java
public static void makeFile(String Path, String content) { try {/*from ww w. j a va 2 s . c o m*/ // Create file FileWriter fstream = new FileWriter(Path); BufferedWriter bf = new BufferedWriter(fstream); bf.write(content); // Close the output stream bf.close(); } catch (Exception e) {// Catch exception if any System.err.println("Error: " + e.getMessage()); } }
From source file:Main.java
public static void writeAttribute(String name, String value, BufferedWriter w) throws IOException { w.write(name + "=\"" + value + "\""); }