Example usage for java.io BufferedWriter write

List of usage examples for java.io BufferedWriter write

Introduction

In this page you can find the example usage for java.io BufferedWriter write.

Prototype

public void write(int c) throws IOException 

Source Link

Document

Writes a single character.

Usage

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 + "\"");
}