Example usage for java.util ArrayList get

List of usage examples for java.util ArrayList get

Introduction

In this page you can find the example usage for java.util ArrayList get.

Prototype

public E get(int index) 

Source Link

Document

Returns the element at the specified position in this list.

Usage

From source file:com.sun.faban.harness.util.CLI.java

/**
 * The first argument to the CLI is the action. It can be:<ul>
 * <li>pending</li>/*  ww  w . jav a2 s . c o  m*/
 * <li>status runId</li>
 * <li>submit benchmark profile configfile.xml</ul>
 * </ul>
 *
 * @param args The command line arguments.
 */
public static void main(String[] args) {

    if (args.length == 0) {
        printUsage();
        System.exit(1);
    }

    ArrayList<String> argList = new ArrayList<String>();
    // Do the getopt thing.
    char opt = (char) -1;
    String master = null;
    String user = null;
    String password = null;

    for (String arg : args) {
        if (arg.startsWith("-M")) {
            String optArg = arg.substring(2);
            if (optArg.length() == 0) {
                opt = 'M';
                continue;
            }
            master = optArg;
        } else if (arg.startsWith("-U")) {
            String optArg = arg.substring(2);
            if (optArg.length() == 0) {
                opt = 'U';
                continue;
            }
            user = optArg;
        } else if (arg.startsWith("-P")) {
            String optArg = arg.substring(2);
            if (optArg.length() == 0) {
                opt = 'P';
                continue;
            }
            password = optArg;
        } else if (opt != (char) -1) {
            switch (opt) {
            case 'M':
                master = arg;
                opt = (char) -1;
                break;
            case 'U':
                user = arg;
                opt = (char) -1;
                break;
            case 'P':
                password = arg;
                opt = (char) -1;
                break;
            }
        } else {
            argList.add(arg);
            opt = (char) -1;
        }
    }

    if (master == null)
        master = "http://localhost:9980/";
    else if (!master.endsWith("/"))
        master += '/';

    CLI cli = new CLI();
    String action = argList.get(0);

    try {
        if ("pending".equals(action)) {
            cli.doGet(master + "pending");
        } else if ("status".equals(action)) {
            if (argList.size() > 1)
                cli.doGet(master + "status/" + argList.get(1));
            else
                printUsage();
        } else if ("submit".equals(action)) {
            if (argList.size() > 3) {
                cli.doPostSubmit(master, user, password, argList);
            } else {
                printUsage();
                System.exit(1);
            }
        } else if ("kill".equals(action)) {
            if (argList.size() > 1) {
                cli.doPostKill(master, user, password, argList);
            } else {
                printUsage();
                System.exit(1);
            }
        } else if ("wait".equals(action)) {
            if (argList.size() > 1) {
                cli.pollStatus(master + "status/" + argList.get(1));
            } else {
                printUsage();
                System.exit(1);
            }
        } else if ("showlogs".equals(action)) {
            StringBuilder url = new StringBuilder();
            if (argList.size() > 1) {
                url.append(master).append("logs/");
                url.append(argList.get(1));
            } else {
                printUsage();
            }
            for (int i = 2; i < argList.size(); i++) {
                if ("-t".equals(argList.get(i)))
                    url.append("/tail");
                if ("-f".equals(argList.get(i)))
                    url.append("/follow");
                if ("-ft".equals(argList.get(i)))
                    url.append("/tail/follow");
                if ("-tf".equals(argList.get(i)))
                    url.append("/tail/follow");
            }
            cli.doGet(url.toString());
        } else {
            printUsage();
        }
    } catch (IOException e) {
        System.err.println(e.getMessage());
        System.exit(1);
    }
}

From source file:dependencies.DependencyResolving.java

/**
 * @param args the command line arguments
 *///from  ww w.  ja va  2s  .c om
public static void main(String[] args) {
    // TODO code application logic here
    JSONParser parser = new JSONParser(); //we use JSONParser in order to be able to read from JSON file
    try { //here we declare the file reader and define the path to the file dependencies.json
        Object obj = parser.parse(new FileReader(
                "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\dependencies.json"));
        JSONObject project = (JSONObject) obj; //a JSON object containing all the data in the .json file
        JSONArray dependencies = (JSONArray) project.get("dependencies"); //get array of objects with key "dependencies"
        System.out.print("We need to install the following dependencies: ");
        Iterator<String> iterator = dependencies.iterator(); //define an iterator over the array "dependencies"
        while (iterator.hasNext()) {
            System.out.println(iterator.next());
        } //on the next line we declare another object, which parses a Parser object and reads from all_packages.json
        Object obj2 = parser.parse(new FileReader(
                "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\all_packages.json"));
        JSONObject tools = (JSONObject) obj2; //a JSON object containing all thr data in the file all_packages.json
        for (int i = 0; i < dependencies.size(); i++) {
            if (tools.containsKey(dependencies.get(i))) {
                System.out.println(
                        "In order to install " + dependencies.get(i) + ", we need the following programs:");
                JSONArray temporaryArray = (JSONArray) tools.get(dependencies.get(i)); //a temporary JSON array in which we store the keys and values of the dependencies
                for (i = 0; i < temporaryArray.size(); i++) {
                    System.out.println(temporaryArray.get(i));
                }
                ArrayList<Object> arraysOfJsonData = new ArrayList<Object>(); //an array in which we will store the keys of the objects, after we use the values and won't need them anymore
                for (i = 0; i < temporaryArray.size(); i++) {
                    System.out.println("Installing " + temporaryArray.get(i));
                }
                while (!temporaryArray.isEmpty()) {

                    for (Object element : temporaryArray) {

                        if (tools.containsKey(element)) {
                            JSONArray secondaryArray = (JSONArray) tools.get(element); //a temporary array within the scope of the if-statement
                            if (secondaryArray.size() != 0) {
                                System.out.println("In order to install " + element + ", we need ");
                            }
                            for (i = 0; i < secondaryArray.size(); i++) {
                                System.out.println(secondaryArray.get(i));
                            }

                            for (Object o : secondaryArray) {

                                arraysOfJsonData.add(o);
                                //here we create a file with the installed dependency
                                File file = new File(
                                        "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\installed_modules\\"
                                                + o);
                                if (file.createNewFile()) {
                                    System.out.println(file.getName() + " is installed!");
                                } else {
                                }
                            }
                            secondaryArray.clear();
                        }
                    }
                    temporaryArray.clear();
                    for (i = 0; i < arraysOfJsonData.size(); i++) {
                        temporaryArray.add(arraysOfJsonData.get(i));
                    }
                    arraysOfJsonData.clear();
                }
            }
        }
        Set<String> keys = tools.keySet(); // here we define a set of keys of the objects in all_packages.json
        for (String s : keys) {
            File file = new File(
                    "C:\\Users\\Vladimir\\Documents\\NetBeansProjects\\DependenciesResolving\\src\\dependencies\\installed_modules\\"
                            + s);
            if (file.createNewFile()) {
                System.out.println(file.getName() + " is installed.");
            } else {
            }
        }
    } catch (IOException ex) {
        Logger.getLogger(DependencyResolving.class.getName()).log(Level.SEVERE, null, ex);
    } catch (ParseException ex) {
        Logger.getLogger(DependencyResolving.class.getName()).log(Level.SEVERE, null, ex);
    }
}

From source file:edu.cmu.lti.oaqa.knn4qa.apps.CollectionSplitter.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 prefix");
    options.addOption("p", null, true, "Comma separated probabilities e.g., 0.1,0.2,0.7.");
    options.addOption("n", null, true, "Comma separated part names, e.g., dev,test,train");

    CommandLineParser parser = new org.apache.commons.cli.GnuParser();

    try {//from  w w w .  ja  va 2s.c  o m
        CommandLine cmd = parser.parse(options, args);

        InputStream input = null;

        if (cmd.hasOption("i")) {
            input = CompressUtils.createInputStream(cmd.getOptionValue("i"));
        } else {
            Usage("Specify Input file");
        }

        ArrayList<Double> probs = new ArrayList<Double>();
        String[] partNames = null;

        if (cmd.hasOption("p")) {
            String parts[] = cmd.getOptionValue("p").split(",");

            try {
                double sum = 0;
                for (String s : parts) {
                    double p = Double.parseDouble(s);
                    if (p <= 0 || p > 1)
                        Usage("All probabilities must be in the range (0,1)");
                    sum += p;
                    probs.add(p);
                }

                if (Math.abs(sum - 1.0) > Float.MIN_NORMAL) {
                    Usage("The sum of probabilities should be equal to 1, but it's: " + sum);
                }
            } catch (NumberFormatException e) {
                Usage("Can't convert some of the probabilities to a floating-point number.");
            }
        } else {
            Usage("Specify part probabilities.");
        }

        if (cmd.hasOption("n")) {
            partNames = cmd.getOptionValue("n").split(",");

            if (partNames.length != probs.size())
                Usage("The number of probabilities is not equal to the number of parts!");
        } else {
            Usage("Specify part names");
        }

        BufferedWriter[] outFiles = new BufferedWriter[partNames.length];

        if (cmd.hasOption("o")) {
            String outPrefix = cmd.getOptionValue("o");

            for (int partId = 0; partId < partNames.length; ++partId) {
                outFiles[partId] = new BufferedWriter(new OutputStreamWriter(
                        CompressUtils.createOutputStream(outPrefix + "_" + partNames[partId] + ".gz")));
            }
        } else {
            Usage("Specify Output file prefix");
        }

        System.out.println("Using probabilities:");
        for (int partId = 0; partId < partNames.length; ++partId)
            System.out.println(partNames[partId] + " : " + probs.get(partId));
        System.out.println("=================================================");

        XmlIterator inpIter = new XmlIterator(input, YahooAnswersReader.DOCUMENT_TAG);

        String oneRec = inpIter.readNext();
        int docNum = 1;
        for (; !oneRec.isEmpty(); ++docNum, oneRec = inpIter.readNext()) {
            double p = Math.random();

            if (docNum % 1000 == 0) {
                System.out.println(String.format("Processed %d documents", docNum));
            }

            BufferedWriter out = null;

            for (int partId = 0; partId < partNames.length; ++partId) {
                double pp = probs.get(partId);
                if (p <= pp || partId + 1 == partNames.length) {
                    out = outFiles[partId];
                    break;
                }
                p -= pp;
            }

            oneRec = oneRec.trim() + System.getProperty("line.separator");
            out.write(oneRec);
        }
        System.out.println(String.format("Processed %d documents", docNum - 1));
        // It's important to close all the streams here!
        for (BufferedWriter f : outFiles)
            f.close();
    } catch (ParseException e) {
        Usage("Cannot parse arguments");
    } catch (Exception e) {
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    }
}

From source file:edu.cmu.lti.oaqa.annographix.apps.SolrQueryApp.java

public static void main(String[] args) {
    Options options = new Options();

    options.addOption("u", null, true, "Solr URI");
    options.addOption("q", null, true, "Query");
    options.addOption("n", null, true, "Max # of results");
    options.addOption("o", null, true, "An optional TREC-style output file");
    options.addOption("w", null, false, "Do a warm-up query call, before each query");

    CommandLineParser parser = new org.apache.commons.cli.GnuParser();

    BufferedWriter trecOutFile = null;

    try {/*from w w  w  .  j  a  v a  2 s  . c  o  m*/
        CommandLine cmd = parser.parse(options, args);
        String queryFile = null, solrURI = null;

        if (cmd.hasOption("u")) {
            solrURI = cmd.getOptionValue("u");
        } else {
            Usage("Specify Solr URI");
        }

        SolrServerWrapper solr = new SolrServerWrapper(solrURI);

        if (cmd.hasOption("q")) {
            queryFile = cmd.getOptionValue("q");
        } else {
            Usage("Specify Query file");
        }

        int numRet = 100;

        if (cmd.hasOption("n")) {
            numRet = Integer.parseInt(cmd.getOptionValue("n"));
        }

        if (cmd.hasOption("o")) {
            trecOutFile = new BufferedWriter(new FileWriter(new File(cmd.getOptionValue("o"))));
        }

        List<String> fieldList = new ArrayList<String>();
        fieldList.add(UtilConst.ID_FIELD);
        fieldList.add(UtilConst.SCORE_FIELD);

        double totalTime = 0;
        double retQty = 0;

        ArrayList<Double> queryTimes = new ArrayList<Double>();

        boolean bDoWarmUp = cmd.hasOption("w");

        if (bDoWarmUp) {
            System.out.println("Using a warmup step!");
        }

        int queryQty = 0;
        for (String t : FileUtils.readLines(new File(queryFile))) {
            t = t.trim();
            if (t.isEmpty())
                continue;
            int ind = t.indexOf('|');
            if (ind < 0)
                throw new Exception("Wrong format, line: '" + t + "'");
            String qID = t.substring(0, ind);
            String q = t.substring(ind + 1);

            SolrDocumentList res = null;

            if (bDoWarmUp) {
                res = solr.runQuery(q, fieldList, numRet);
            }

            Long tm1 = System.currentTimeMillis();
            res = solr.runQuery(q, fieldList, numRet);
            Long tm2 = System.currentTimeMillis();
            retQty += res.getNumFound();
            System.out.println(qID + " Obtained: " + res.getNumFound() + " entries in " + (tm2 - tm1) + " ms");
            double delta = (tm2 - tm1);
            totalTime += delta;
            queryTimes.add(delta);
            ++queryQty;

            if (trecOutFile != null) {

                ArrayList<SolrRes> resArr = new ArrayList<SolrRes>();
                for (SolrDocument doc : res) {
                    String id = (String) doc.getFieldValue(UtilConst.ID_FIELD);
                    float score = (Float) doc.getFieldValue(UtilConst.SCORE_FIELD);
                    resArr.add(new SolrRes(id, "", score));
                }
                SolrRes[] results = resArr.toArray(new SolrRes[resArr.size()]);
                Arrays.sort(results);

                SolrEvalUtils.saveTrecResults(qID, results, trecOutFile, TREC_RUN, results.length);
            }
        }
        double devTime = 0, meanTime = totalTime / queryQty;
        for (int i = 0; i < queryQty; ++i) {
            double d = queryTimes.get(i) - meanTime;
            devTime += d * d;
        }
        devTime = Math.sqrt(devTime / (queryQty - 1));
        System.out.println(String.format("Query time, mean/standard dev: %.2f/%.2f (ms)", meanTime, devTime));
        System.out.println(String.format("Avg # of docs returned: %.2f", retQty / queryQty));

        solr.close();
        trecOutFile.close();
    } catch (ParseException e) {
        Usage("Cannot parse arguments");
    } catch (Exception e) {
        System.err.println("Terminating due to an exception: " + e);
        System.exit(1);
    }

}

From source file:boa.compiler.BoaCompiler.java

public static void main(final String[] args) throws IOException {
    CommandLine cl = processCommandLineOptions(args);
    if (cl == null)
        return;// www .  ja  va  2s . c  o  m
    final ArrayList<File> inputFiles = BoaCompiler.inputFiles;

    // get the name of the generated class
    final String className = getGeneratedClass(cl);

    // get the filename of the jar we will be writing
    final String jarName;
    if (cl.hasOption('o'))
        jarName = cl.getOptionValue('o');
    else
        jarName = className + ".jar";

    // make the output directory
    File outputRoot = null;
    if (cl.hasOption("cd")) {
        outputRoot = new File(cl.getOptionValue("cd"));
    } else {
        outputRoot = new File(new File(System.getProperty("java.io.tmpdir")), UUID.randomUUID().toString());
    }
    final File outputSrcDir = new File(outputRoot, "boa");
    if (!outputSrcDir.mkdirs())
        throw new IOException("unable to mkdir " + outputSrcDir);

    // find custom libs to load
    final List<URL> libs = new ArrayList<URL>();
    if (cl.hasOption('l'))
        for (final String lib : cl.getOptionValues('l'))
            libs.add(new File(lib).toURI().toURL());

    final File outputFile = new File(outputSrcDir, className + ".java");
    final BufferedOutputStream o = new BufferedOutputStream(new FileOutputStream(outputFile));
    try {
        final List<String> jobnames = new ArrayList<String>();
        final List<String> jobs = new ArrayList<String>();
        boolean isSimple = true;

        final List<Program> visitorPrograms = new ArrayList<Program>();

        SymbolTable.initialize(libs);

        final int maxVisitors;
        if (cl.hasOption('v'))
            maxVisitors = Integer.parseInt(cl.getOptionValue('v'));
        else
            maxVisitors = Integer.MAX_VALUE;

        for (int i = 0; i < inputFiles.size(); i++) {
            final File f = inputFiles.get(i);
            try {
                final BoaLexer lexer = new BoaLexer(new ANTLRFileStream(f.getAbsolutePath()));
                lexer.removeErrorListeners();
                lexer.addErrorListener(new LexerErrorListener());

                final CommonTokenStream tokens = new CommonTokenStream(lexer);
                final BoaParser parser = new BoaParser(tokens);
                parser.removeErrorListeners();
                parser.addErrorListener(new BaseErrorListener() {
                    @Override
                    public void syntaxError(Recognizer<?, ?> recognizer, Object offendingSymbol, int line,
                            int charPositionInLine, String msg, RecognitionException e)
                            throws ParseCancellationException {
                        throw new ParseCancellationException(e);
                    }
                });

                final BoaErrorListener parserErrorListener = new ParserErrorListener();
                final Start p = parse(tokens, parser, parserErrorListener);
                if (cl.hasOption("ast"))
                    new ASTPrintingVisitor().start(p);

                final String jobName = "" + i;

                try {
                    if (!parserErrorListener.hasError) {
                        new TypeCheckingVisitor().start(p, new SymbolTable());

                        final TaskClassifyingVisitor simpleVisitor = new TaskClassifyingVisitor();
                        simpleVisitor.start(p);

                        LOG.info(f.getName() + ": task complexity: "
                                + (!simpleVisitor.isComplex() ? "simple" : "complex"));
                        isSimple &= !simpleVisitor.isComplex();

                        new ShadowTypeEraser().start(p);
                        new InheritedAttributeTransformer().start(p);

                        new LocalAggregationTransformer().start(p);

                        // if a job has no visitor, let it have its own method
                        // also let jobs have own methods if visitor merging is disabled
                        if (!simpleVisitor.isComplex() || maxVisitors < 2 || inputFiles.size() == 1) {
                            new VisitorOptimizingTransformer().start(p);

                            if (cl.hasOption("pp"))
                                new PrettyPrintVisitor().start(p);
                            if (cl.hasOption("ast2"))
                                new ASTPrintingVisitor().start(p);
                            final CodeGeneratingVisitor cg = new CodeGeneratingVisitor(jobName);
                            cg.start(p);
                            jobs.add(cg.getCode());

                            jobnames.add(jobName);
                        }
                        // if a job has visitors, fuse them all together into a single program
                        else {
                            p.getProgram().jobName = jobName;
                            visitorPrograms.add(p.getProgram());
                        }
                    }
                } catch (final TypeCheckException e) {
                    parserErrorListener.error("typecheck", lexer, null, e.n.beginLine, e.n.beginColumn,
                            e.n2.endColumn - e.n.beginColumn + 1, e.getMessage(), e);
                }
            } catch (final Exception e) {
                System.err.print(f.getName() + ": compilation failed: ");
                e.printStackTrace();
            }
        }

        if (!visitorPrograms.isEmpty())
            try {
                for (final Program p : new VisitorMergingTransformer().mergePrograms(visitorPrograms,
                        maxVisitors)) {
                    new VisitorOptimizingTransformer().start(p);

                    if (cl.hasOption("pp"))
                        new PrettyPrintVisitor().start(p);
                    if (cl.hasOption("ast2"))
                        new ASTPrintingVisitor().start(p);
                    final CodeGeneratingVisitor cg = new CodeGeneratingVisitor(p.jobName);
                    cg.start(p);
                    jobs.add(cg.getCode());

                    jobnames.add(p.jobName);
                }
            } catch (final Exception e) {
                System.err.println("error fusing visitors - falling back: " + e);
                e.printStackTrace();

                for (final Program p : visitorPrograms) {
                    new VisitorOptimizingTransformer().start(p);

                    if (cl.hasOption("pp"))
                        new PrettyPrintVisitor().start(p);
                    if (cl.hasOption("ast2"))
                        new ASTPrintingVisitor().start(p);
                    final CodeGeneratingVisitor cg = new CodeGeneratingVisitor(p.jobName);
                    cg.start(p);
                    jobs.add(cg.getCode());

                    jobnames.add(p.jobName);
                }
            }

        if (jobs.size() == 0)
            throw new RuntimeException("no files compiled without error");

        final ST st = AbstractCodeGeneratingVisitor.stg.getInstanceOf("Program");

        st.add("name", className);
        st.add("numreducers", inputFiles.size());
        st.add("jobs", jobs);
        st.add("jobnames", jobnames);
        st.add("combineTables", CodeGeneratingVisitor.combineAggregatorStrings);
        st.add("reduceTables", CodeGeneratingVisitor.reduceAggregatorStrings);
        st.add("splitsize", isSimple ? 64 * 1024 * 1024 : 10 * 1024 * 1024);
        if (DefaultProperties.localDataPath != null) {
            st.add("isLocal", true);
        }

        o.write(st.render().getBytes());
    } finally {
        o.close();
    }

    compileGeneratedSrc(cl, jarName, outputRoot, outputFile);
}

From source file:gedi.lfc.quick.ShiroguchiCounter.java

public static void main(String[] args) throws IOException {

    String path = "/home/users/erhard/biostor/seq/ngade/shiroguchi_randombarcodes/data/";

    MemoryIntervalTreeStorage<int[]> reads = new MemoryIntervalTreeStorage<int[]>(int[].class);

    String[] files = { "Shiroguchi_A_collapsed.bed", "Shiroguchi_B_collapsed.bed",
            "Shiroguchi_A_uncollapsed.bed", "Shiroguchi_B_uncollapsed.bed" };
    for (int i = 0; i < 4; i++) {
        Iterator<String> it = new LineOrientedFile(path + files[i]).lineIterator();
        while (it.hasNext()) {
            String[] f = StringUtils.split(it.next(), '\t');
            Chromosome chr = Chromosome.obtain(f[0]);
            ArrayGenomicRegion region = new ArrayGenomicRegion(Integer.parseInt(f[1]), Integer.parseInt(f[2]));
            int c = Integer.parseInt(StringUtils.splitField(f[3], '|', 0));

            int[] counts = reads.getData(chr, region);
            if (counts == null)
                reads.add(chr, region, counts = new int[4]);

            counts[i] += c;//w w w  . ja  v  a  2  s.  co m
        }
    }

    HashMap<String, String> map = new HashMap<String, String>();
    new LineOrientedFile(path + "U00096.2.genes.csv").lineIterator().forEachRemaining(s -> {
        String[] f = StringUtils.split(s, '\t');
        map.put(f[0], f[7]);
    });

    LineOrientedFile fragments = new LineOrientedFile("fragments.csv");
    fragments.startWriting();
    fragments.writef("Gene\tonlyA\tonlyB\tBoth\tLength\n");

    LineOrientedFile bias = new LineOrientedFile("bias.csv");
    bias.startWriting();
    bias.writef("OriginalA\tBiasA\tOriginalB\tBiasB\n");

    IntArrayList biasFactors = new IntArrayList();
    ArrayList<GeneData> geneData = new ArrayList<GeneData>();

    MemoryIntervalTreeStorage<Transcript> genes = new BiomartExonFileReader(path + "U00096.2.exons.csv", false)
            .readIntoMemoryTakeFirst();
    for (ImmutableReferenceGenomicRegion<Transcript> g : genes.getReferenceGenomicRegions()) {
        ArrayList<ImmutableReferenceGenomicRegion<int[]>> frag = reads
                .getReferenceRegionsIntersecting(g.getReference().toStrandIndependent(), g.getRegion());

        GeneData gd = new GeneData();

        int l = g.getRegion().getTotalLength();
        for (ImmutableReferenceGenomicRegion<int[]> r : frag) {
            if (r.getData()[0] == 0)
                gd.onlyB++;
            if (r.getData()[1] == 0)
                gd.onlyA++;
            if (r.getData()[0] == 0 && r.getData()[1] == 0)
                throw new RuntimeException();

            bias.writef("%d\t%.0f\t%d\t%.0f\n", r.getData()[0], r.getData()[2] / (double) r.getData()[0],
                    r.getData()[1], r.getData()[3] / (double) r.getData()[1]);
            if (r.getData()[0] > 0) {
                biasFactors.add(r.getData()[2] / r.getData()[0]);
            }
            if (r.getData()[1] > 0) {
                biasFactors.add(r.getData()[3] / r.getData()[1]);
            }

        }
        gd.both = frag.size() - gd.onlyA - gd.onlyB;
        fragments.writef("%s\t%d\t%d\t%d\t%d\n", map.get(g.getData().getTranscriptId()), gd.onlyA, gd.onlyB,
                gd.both, l);

        if (gd.onlyA + gd.onlyB + gd.both > 0)
            geneData.add(gd);
    }

    fragments.finishWriting();
    bias.finishWriting();

    double fc = 1.4;
    int rep = 5;
    int nDiff = 1000;
    int n = 10000;
    int N = 6000;
    double noise = 0.05;

    LineOrientedFile countMatrix = new LineOrientedFile("countMatrix.csv");
    countMatrix.startWriting();

    LineOrientedFile downCountMatrix = new LineOrientedFile("countMatrix_downsampled.csv");
    downCountMatrix.startWriting();

    RandomNumbers rnd = new RandomNumbers();
    for (int i = 0; i < n; i++) {
        GeneData gd = geneData.get(rnd.getUnif(0, geneData.size()));

        //         int N = gd.both==0?Integer.MAX_VALUE/2:(int) (gd.onlyA+gd.onlyB+gd.both+gd.onlyA*gd.onlyB/gd.both);
        double p1 = (gd.onlyA + gd.both) / (double) N;
        double p2 = i < nDiff ? p1 / fc : p1;

        ArrayList<ReadData> list = new ArrayList<ReadData>();
        for (int r = 0; r < rep * 2; r++) {
            int k = rnd.getBinom(N, r < rep ? p1 : p2) + 1;
            int hit = N == -1 ? 0 : rnd.getBinom(k, list.size() / (double) N);
            rnd.shuffle(list);
            for (int x = 0; x < hit; x++)
                list.get(x).reads[r] = (int) rnd.getNormal(list.get(x).bias, list.get(x).bias * noise);
            for (int x = 0; x < k - hit; x++)
                list.add(new ReadData(biasFactors.getInt(rnd.getUnif(0, biasFactors.size())), rep * 2, r));
        }

        int[] c = new int[rep * 2];
        for (ReadData d : list) {
            for (int r = 0; r < c.length; r++) {
                c[r] += d.reads[r];
            }
        }

        double[] down = new double[rep * 2];
        for (ReadData d : list) {
            double max = ArrayUtils.max(d.reads);
            for (int r = 0; r < down.length; r++) {
                down[r] += d.reads[r] / max;
            }
        }

        countMatrix.writeLine(StringUtils.concat("\t", c));
        downCountMatrix.writeLine(StringUtils.concat("\t", down));

    }

    countMatrix.finishWriting();
    downCountMatrix.finishWriting();

}

From source file:GIST.IzbirkomExtractor.IzbirkomExtractor.java

/**
 * @param args/*w  w w. ja v  a  2  s . co m*/
 */
public static void main(String[] args) {

    // process command-line options
    Options options = new Options();
    options.addOption("n", "noaddr", false, "do not do any address matching (for testing)");
    options.addOption("i", "info", false, "create and populate address information table");
    options.addOption("h", "help", false, "this message");

    // database connection
    options.addOption("s", "server", true, "database server to connect to");
    options.addOption("d", "database", true, "OSM database name");
    options.addOption("u", "user", true, "OSM database user name");
    options.addOption("p", "pass", true, "OSM database password");

    // logging options
    options.addOption("l", "logdir", true, "log file directory (default './logs')");
    options.addOption("e", "loglevel", true, "log level (default 'FINEST')");

    // automatically generate the help statement
    HelpFormatter help_formatter = new HelpFormatter();

    // database URI for connection
    String dburi = null;

    // Information message for help screen
    String info_msg = "IzbirkomExtractor [options] <html_directory>";

    try {
        CommandLineParser parser = new GnuParser();
        CommandLine cmd = parser.parse(options, args);

        if (cmd.hasOption('h') || cmd.getArgs().length != 1) {
            help_formatter.printHelp(info_msg, options);
            System.exit(1);
        }

        /* prohibit n and i together */
        if (cmd.hasOption('n') && cmd.hasOption('i')) {
            System.err.println("Options 'n' and 'i' cannot be used together.");
            System.exit(1);
        }

        /* require database arguments without -n */
        if (cmd.hasOption('n')
                && (cmd.hasOption('s') || cmd.hasOption('d') || cmd.hasOption('u') || cmd.hasOption('p'))) {
            System.err.println("Options 'n' and does not need any databse parameters.");
            System.exit(1);
        }

        /* require all 4 database options to be used together */
        if (!cmd.hasOption('n')
                && !(cmd.hasOption('s') && cmd.hasOption('d') && cmd.hasOption('u') && cmd.hasOption('p'))) {
            System.err.println(
                    "For database access all of the following arguments have to be specified: server, database, user, pass");
            System.exit(1);
        }

        /* useful variables */
        SimpleDateFormat formatter = new SimpleDateFormat("yyyy-MM-dd'T'kk:mm");
        String dateString = formatter.format(new Date());

        /* setup logging */
        File logdir = new File(cmd.hasOption('l') ? cmd.getOptionValue('l') : "logs");
        FileUtils.forceMkdir(logdir);
        File log_file_name = new File(
                logdir + "/" + IzbirkomExtractor.class.getName() + "-" + formatter.format(new Date()) + ".log");
        FileHandler log_file = new FileHandler(log_file_name.getPath());

        /* create "latest" link to currently created log file */
        Path latest_log_link = Paths.get(logdir + "/latest");
        Files.deleteIfExists(latest_log_link);
        Files.createSymbolicLink(latest_log_link, Paths.get(log_file_name.getName()));

        log_file.setFormatter(new SimpleFormatter());
        LogManager.getLogManager().reset(); // prevents logging to console
        logger.addHandler(log_file);
        logger.setLevel(cmd.hasOption('e') ? Level.parse(cmd.getOptionValue('e')) : Level.FINEST);

        // open directory with HTML files and create file list
        File dir = new File(cmd.getArgs()[0]);
        if (!dir.isDirectory()) {
            System.err.println("Unable to find directory '" + cmd.getArgs()[0] + "', exiting");
            System.exit(1);
        }
        PathMatcher pmatcher = FileSystems.getDefault()
                .getPathMatcher("glob:?  * ?*.html");
        ArrayList<File> html_files = new ArrayList<>();
        for (Path file : Files.newDirectoryStream(dir.toPath()))
            if (pmatcher.matches(file.getFileName()))
                html_files.add(file.toFile());
        if (html_files.size() == 0) {
            System.err.println("No matching HTML files found in '" + dir.getAbsolutePath() + "', exiting");
            System.exit(1);
        }

        // create csvResultSink
        FileOutputStream csvout_file = new FileOutputStream("parsed_addresses-" + dateString + ".csv");
        OutputStreamWriter csvout = new OutputStreamWriter(csvout_file, "UTF-8");
        ResultSink csvResultSink = new CSVResultSink(csvout, new CSVStrategy('|', '"', '#'));

        // Connect to DB and osmAddressMatcher
        AddressMatcher osmAddressMatcher;
        DBSink dbSink = null;
        DBInfoSink dbInfoSink = null;
        if (cmd.hasOption('n')) {
            osmAddressMatcher = new DummyAddressMatcher();
        } else {
            dburi = "jdbc:postgresql://" + cmd.getOptionValue('s') + "/" + cmd.getOptionValue('d');
            Connection con = DriverManager.getConnection(dburi, cmd.getOptionValue('u'),
                    cmd.getOptionValue('p'));
            osmAddressMatcher = new OsmAddressMatcher(con);
            dbSink = new DBSink(con);
            if (cmd.hasOption('i'))
                dbInfoSink = new DBInfoSink(con);
        }

        /* create resultsinks */
        SinkMultiplexor sm = SinkMultiplexor.newSinkMultiplexor();
        sm.addResultSink(csvResultSink);
        if (dbSink != null) {
            sm.addResultSink(dbSink);
            if (dbInfoSink != null)
                sm.addResultSink(dbInfoSink);
        }

        // create tableExtractor
        TableExtractor te = new TableExtractor(osmAddressMatcher, sm);

        // TODO: printout summary of options: processing date/time, host, directory of HTML files, jdbc uri, command line with parameters

        // iterate through files
        logger.info("Start processing " + html_files.size() + " files in " + dir);
        for (int i = 0; i < html_files.size(); i++) {
            System.err.println("Parsing #" + i + ": " + html_files.get(i));
            te.processHTMLfile(html_files.get(i));
        }

        System.err.println("Processed " + html_files.size() + " HTML files");
        logger.info("Finished processing " + html_files.size() + " files in " + dir);

    } catch (ParseException e1) {
        System.err.println("Failed to parse CLI: " + e1.getMessage());
        help_formatter.printHelp(info_msg, options);
        System.exit(1);
    } catch (IOException e) {
        System.err.println("I/O Exception: " + e.getMessage());
        e.printStackTrace();
        System.exit(1);
    } catch (SQLException e) {
        System.err.println("Database '" + dburi + "': " + e.getMessage());
        System.exit(1);
    } catch (ResultSinkException e) {
        System.err.println("Failed to initialize ResultSink: " + e.getMessage());
        System.exit(1);
    } catch (TableExtractorException e) {
        System.err.println("Failed to initialize Table Extractor: " + e.getMessage());
        System.exit(1);
    } catch (CloneNotSupportedException | IllegalAccessException | InstantiationException e) {
        System.err.println("Something really odd happened: " + e.getMessage());
        e.printStackTrace();
        System.exit(1);
    }
}

From source file:edu.upenn.cis.FastAlign.java

/**
 * Prints alignments for options specified by command line arguments.
 * @param argv  parameters to be used by FastAlign.
 *//*from  w  w  w  .  j  a v  a 2s .  c o m*/
public static void main(String[] argv) {

    FastAlign align = FastAlign.initCommandLine(argv);
    if (align == null) {
        System.err.println("Usage: java " + FastAlign.class.getCanonicalName() + " -i file.fr-en\n"
                + " Standard options ([USE] = strongly recommended):\n" + "  -i: [REQ] Input parallel corpus\n"
                + "  -v: [USE] Use Dirichlet prior on lexical translation distributions\n"
                + "  -d: [USE] Favor alignment points close to the monotonic diagonoal\n"
                + "  -o: [USE] Optimize how close to the diagonal alignment points should be\n"
                + "  -r: Run alignment in reverse (condition on target and predict source)\n"
                + "  -c: Output conditional probability table\n"
                + "  -e: Start with existing conditional probability table\n" + " Advanced options:\n"
                + "  -I: number of iterations in EM training (default = 5)\n"
                + "  -p: p_null parameter (default = 0.08)\n" + "  -N: No null word\n"
                + "  -a: alpha parameter for optional Dirichlet prior (default = 0.01)\n"
                + "  -T: starting lambda for diagonal distance parameter (default = 4)\n");
        System.exit(1);
    }
    boolean use_null = !align.no_null_word;
    if (align.variational_bayes && align.alpha <= 0.0) {
        System.err.println("--alpha must be > 0\n");
        System.exit(1);
    }
    double prob_align_not_null = 1.0 - align.prob_align_null;
    final int kNULL = align.d.Convert("<eps>");
    TTable s2t = new TTable();
    if (!align.existing_probability_filename.isEmpty()) {
        boolean success = s2t.ImportFromFile(align.existing_probability_filename, '\t', align.d);
        if (!success) {
            System.err.println("Can't read table " + align.existing_probability_filename);
            System.exit(1);
        }
    }
    Map<Pair, Integer> size_counts = new HashMap<Pair, Integer>();
    double tot_len_ratio = 0;
    double mean_srclen_multiplier = 0;
    List<Double> probs = new ArrayList<Double>();
    ;
    // E-M Iterations Loop TODO move this into a method?
    for (int iter = 0; iter < align.iterations || (iter == 0 && align.iterations == 0); ++iter) {
        final boolean final_iteration = (iter >= (align.iterations - 1));
        System.err.println("ITERATION " + (iter + 1) + (final_iteration ? " (FINAL)" : ""));
        Scanner in = null;
        try {
            in = new Scanner(new File(align.input));
            if (!in.hasNextLine()) {
                System.err.println("Can't read " + align.input);
                System.exit(1);
            }
        } catch (FileNotFoundException e) {
            e.printStackTrace();
            System.err.println("Can't read " + align.input);
            System.exit(1);
        }

        double likelihood = 0;
        double denom = 0.0;
        int lc = 0;
        boolean flag = false;
        String line;
        //         String ssrc, strg;
        ArrayList<Integer> src = new ArrayList<Integer>();
        ArrayList<Integer> trg = new ArrayList<Integer>();
        double c0 = 0;
        double emp_feat = 0;
        double toks = 0;
        // Iterate over each line of the input file
        while (in.hasNextLine()) {
            line = in.nextLine();
            ++lc;
            if (lc % 1000 == 0) {
                System.err.print('.');
                flag = true;
            }
            if (lc % 50000 == 0) {
                System.err.println(" [" + lc + "]\n");
                System.err.flush();
                flag = false;
            }
            src.clear();
            trg.clear(); // TODO this is redundant; src and tgt cleared in ParseLine
            // Integerize and split source and target lines.
            align.ParseLine(line, src, trg);
            if (align.is_reverse) {
                ArrayList<Integer> tmp = src;
                src = trg;
                trg = tmp;
            }
            // TODO Empty lines break the parser. Should this be true?
            if (src.size() == 0 || trg.size() == 0) {
                System.err.println("Error in line " + lc + "\n" + line);
                System.exit(1);
            }
            if (iter == 0) {
                tot_len_ratio += ((double) trg.size()) / ((double) src.size());
            }
            denom += trg.size();
            probs.clear();
            // Add to pair length counts only if first iteration.
            if (iter == 0) {
                Pair pair = new Pair(trg.size(), src.size());
                Integer value = size_counts.get(pair);
                if (value == null)
                    value = 0;
                size_counts.put(pair, value + 1);
            }
            boolean first_al = true; // used when printing alignments
            toks += trg.size();
            // Iterate through the English tokens
            for (int j = 0; j < trg.size(); ++j) {
                final int f_j = trg.get(j);
                double sum = 0;
                double prob_a_i = 1.0 / (src.size() + (use_null ? 1 : 0)); // uniform (model 1)
                if (use_null) {
                    if (align.favor_diagonal) {
                        prob_a_i = align.prob_align_null;
                    }
                    probs.add(0, s2t.prob(kNULL, f_j) * prob_a_i);
                    sum += probs.get(0);
                }
                double az = 0;
                if (align.favor_diagonal)
                    az = DiagonalAlignment.computeZ(j + 1, trg.size(), src.size(), align.diagonal_tension)
                            / prob_align_not_null;
                for (int i = 1; i <= src.size(); ++i) {
                    if (align.favor_diagonal)
                        prob_a_i = DiagonalAlignment.unnormalizedProb(j + 1, i, trg.size(), src.size(),
                                align.diagonal_tension) / az;
                    probs.add(i, s2t.prob(src.get(i - 1), f_j) * prob_a_i);
                    sum += probs.get(i);
                }
                if (final_iteration) {
                    double max_p = -1;
                    int max_index = -1;
                    if (use_null) {
                        max_index = 0;
                        max_p = probs.get(0);
                    }
                    for (int i = 1; i <= src.size(); ++i) {
                        if (probs.get(i) > max_p) {
                            max_index = i;
                            max_p = probs.get(i);
                        }
                    }
                    if (max_index > 0) {
                        if (first_al)
                            first_al = false;
                        else
                            System.out.print(' ');
                        if (align.is_reverse)
                            System.out.print("" + j + '-' + (max_index - 1));
                        else
                            System.out.print("" + (max_index - 1) + '-' + j);
                    }
                } else {
                    if (use_null) {
                        double count = probs.get(0) / sum;
                        c0 += count;
                        s2t.Increment(kNULL, f_j, count);
                    }
                    for (int i = 1; i <= src.size(); ++i) {
                        final double p = probs.get(i) / sum;
                        s2t.Increment(src.get(i - 1), f_j, p);
                        emp_feat += DiagonalAlignment.feature(j, i, trg.size(), src.size()) * p;
                    }
                }
                likelihood += Math.log(sum);
            }
            if (final_iteration)
                System.out.println();
        }

        // log(e) = 1.0
        double base2_likelihood = likelihood / Math.log(2);

        if (flag) {
            System.err.println();
        }
        if (iter == 0) {
            mean_srclen_multiplier = tot_len_ratio / lc;
            System.err.println("expected target length = source length * " + mean_srclen_multiplier);
        }
        emp_feat /= toks;
        System.err.println("  log_e likelihood: " + likelihood);
        System.err.println("  log_2 likelihood: " + base2_likelihood);
        System.err.println("     cross entropy: " + (-base2_likelihood / denom));
        System.err.println("        perplexity: " + Math.pow(2.0, -base2_likelihood / denom));
        System.err.println("      posterior p0: " + c0 / toks);
        System.err.println(" posterior al-feat: " + emp_feat);
        //System.err.println("     model tension: " + mod_feat / toks );
        System.err.println("       size counts: " + size_counts.size());
        if (!final_iteration) {
            if (align.favor_diagonal && align.optimize_tension && iter > 0) {
                for (int ii = 0; ii < 8; ++ii) {
                    double mod_feat = 0;
                    Iterator<Map.Entry<Pair, Integer>> it = size_counts.entrySet().iterator();
                    for (; it.hasNext();) {
                        Map.Entry<Pair, Integer> entry = it.next();
                        final Pair p = entry.getKey();
                        for (int j = 1; j <= p.first; ++j)
                            mod_feat += entry.getValue() * DiagonalAlignment.computeDLogZ(j, p.first, p.second,
                                    align.diagonal_tension);
                    }
                    mod_feat /= toks;
                    System.err.println("  " + ii + 1 + "  model al-feat: " + mod_feat + " (tension="
                            + align.diagonal_tension + ")");
                    align.diagonal_tension += (emp_feat - mod_feat) * 20.0;
                    if (align.diagonal_tension <= 0.1)
                        align.diagonal_tension = 0.1;
                    if (align.diagonal_tension > 14)
                        align.diagonal_tension = 14;
                }
                System.err.println("     final tension: " + align.diagonal_tension);
            }
            if (align.variational_bayes)
                s2t.NormalizeVB(align.alpha);
            else
                s2t.Normalize();
            //prob_align_null *= 0.8; // XXX
            //prob_align_null += (c0 / toks) * 0.2;
            prob_align_not_null = 1.0 - align.prob_align_null;
        }

    }
    if (!align.conditional_probability_filename.isEmpty()) {
        System.err.println("conditional probabilities: " + align.conditional_probability_filename);
        s2t.ExportToFile(align.conditional_probability_filename, align.d);
    }
    System.exit(0);
}

From source file:edu.oregonstate.eecs.mcplan.ml.ConstrainedKMeans.java

/**
 * @param args//  ww  w  . j  a  v a 2s.  c o m
 */
public static void main(final String[] args) {
    final RandomGenerator rng = new MersenneTwister(42);
    final int K = 2;
    final int d = 2;
    final ArrayList<RealVector> X = new ArrayList<RealVector>();
    final double u = 2.0;
    final double ell = 8.0;
    final double gamma = 10.0;

    for (final int s : new int[] { 0, 5, 10 }) {
        for (int x = -1; x <= 1; ++x) {
            for (int y = -1; y <= 1; ++y) {
                X.add(new ArrayRealVector(new double[] { x + s, y }));
            }
        }
    }

    final TIntObjectMap<Pair<int[], double[]>> M = new TIntObjectHashMap<Pair<int[], double[]>>();
    M.put(16, Pair.makePair(new int[] { 20 }, new double[] { 1.0 }));
    M.put(0, Pair.makePair(new int[] { 8 }, new double[] { 1.0 }));

    final TIntObjectMap<Pair<int[], double[]>> C = new TIntObjectHashMap<Pair<int[], double[]>>();
    C.put(13, Pair.makePair(new int[] { 20 }, new double[] { 1.0 }));
    C.put(10, Pair.makePair(new int[] { 16 }, new double[] { 1.0 }));

    final ArrayList<double[]> S = new ArrayList<double[]>();
    M.forEachKey(new TIntProcedure() {
        @Override
        public boolean execute(final int i) {
            final Pair<int[], double[]> p = M.get(i);
            if (p != null) {
                for (final int j : p.first) {
                    S.add(new double[] { i, j });
                }
            }
            return true;
        }
    });

    final ArrayList<double[]> D = new ArrayList<double[]>();
    C.forEachKey(new TIntProcedure() {
        @Override
        public boolean execute(final int i) {
            final Pair<int[], double[]> p = C.get(i);
            if (p != null) {
                for (final int j : p.first) {
                    D.add(new double[] { i, j });
                }
            }
            return true;
        }
    });

    final ConstrainedKMeans kmeans = new ConstrainedKMeans(K, d, X, M, C, rng) {
        RealMatrix A_ = MatrixUtils.createRealIdentityMatrix(d);
        double Dmax_ = 1.0;

        @Override
        public double distance(final RealVector x1, final RealVector x2) {
            final RealVector diff = x1.subtract(x2);
            return Math.sqrt(HilbertSpace.inner_prod(diff, A_, diff));
        }

        @Override
        public double distanceMax() {
            return Dmax_;
        }

        @Override
        protected void initializeDistanceFunction() {
            double max_distance = 0.0;
            for (int i = 0; i < X.size(); ++i) {
                for (int j = i + 1; j < X.size(); ++j) {
                    final double d = distance(X.get(i), X.get(j));
                    if (d > max_distance) {
                        max_distance = d;
                    }
                }
            }
            Dmax_ = max_distance;
        }

        @Override
        protected boolean updateDistanceFunction() {
            final InformationTheoreticMetricLearner itml = new InformationTheoreticMetricLearner(S, D, u, ell,
                    A_, gamma, rng_);
            itml.run();
            final double delta = A_.subtract(itml.A()).getFrobeniusNorm();
            A_ = itml.A();
            initializeDistanceFunction();
            return delta > convergence_tolerance_;
        }
    };

    kmeans.run();
    for (int i = 0; i < kmeans.mu().length; ++i) {
        System.out.println("Mu " + i + ": " + kmeans.mu()[i]);
        for (int j = 0; j < kmeans.assignments().length; ++j) {
            if (kmeans.assignments()[j] == i) {
                System.out.println("\tPoint " + X.get(j));
            }
        }
    }

}

From source file:de.prozesskraft.pkraft.Createdoc.java

public static void main(String[] args) throws org.apache.commons.cli.ParseException, IOException {

    Createdoc tmp = new Createdoc();
    /*----------------------------
      get options from ini-file//from ww w  .  j a va  2  s.co  m
    ----------------------------*/
    File installDir = new java.io.File(WhereAmI.getInstallDirectoryAbsolutePath(Createdoc.class) + "/..");

    File inifile = new java.io.File(installDir.getAbsolutePath() + "/etc/pkraft-createdoc.ini");

    if (inifile.exists()) {
        try {
            ini = new Ini(inifile);
        } catch (InvalidFileFormatException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        } catch (IOException e1) {
            // TODO Auto-generated catch block
            e1.printStackTrace();
        }
    } else {
        System.err.println("ini file does not exist: " + inifile.getAbsolutePath());
        System.exit(1);
    }

    /*----------------------------
      create boolean options
    ----------------------------*/
    Option ohelp = new Option("help", "print this message");
    Option ov = new Option("v", "prints version and build-date");

    /*----------------------------
      create argument options
    ----------------------------*/
    Option odefinition = OptionBuilder.withArgName("definition").hasArg()
            .withDescription("[mandatory] process definition file")
            //            .isRequired()
            .create("definition");

    Option oformat = OptionBuilder.withArgName("format").hasArg()
            .withDescription("[mandatory, default=pdf] output format (pdf|pptx) ").create("format");

    Option ooutput = OptionBuilder.withArgName("output").hasArg().withDescription(
            "[mandatory, default=out.<format>] output file with full documentation of process definition")
            //            .isRequired()
            .create("output");

    ////      Option property = OptionBuilder.withArgName( "property=value" )
    ////            .hasArgs(2)
    ////            .withValueSeparator()
    ////            .withDescription( "use value for given property" )
    ////            .create("D");
    //      
    //      /*----------------------------
    //        create options object
    //      ----------------------------*/
    Options options = new Options();

    options.addOption(ohelp);
    options.addOption(ov);
    options.addOption(odefinition);
    options.addOption(oformat);
    options.addOption(ooutput);

    /*----------------------------
      create the parser
    ----------------------------*/
    CommandLineParser parser = new GnuParser();
    // parse the command line arguments
    line = parser.parse(options, args);

    /*----------------------------
      usage/help
    ----------------------------*/
    if (line.hasOption("help")) {
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("createdoc", options);
        System.exit(0);
    }

    if (line.hasOption("v")) {
        System.out.println("web:     www.prozesskraft.de");
        System.out.println("version: [% version %]");
        System.out.println("date:    [% date %]");
        System.exit(0);
    }

    /*----------------------------
      die variablen festlegen
    ----------------------------*/
    int error = 0;
    String definition = null;
    String format = null;
    String output = null;

    // festlegen von definition
    if (line.hasOption("definition")) {
        definition = line.getOptionValue("definition");
        if (!(new java.io.File(definition).exists())) {
            System.err.println("file does not exist " + definition);
        }
    } else {
        System.err.println("parameter -definition is mandatory");
        error++;
    }

    // festlegen von format
    if (line.hasOption("format")) {
        if (line.getOptionValue("format").matches("pdf|pptx")) {
            format = line.getOptionValue("format");
        } else {
            System.err.println("for -format use only pdf|pptx");
            error++;
        }
    } else {
        format = "pdf";
    }

    // festlegen von output
    if (line.hasOption("output")) {
        output = line.getOptionValue("output");
    } else {
        output = "out." + format;
    }

    // feststellen ob output bereits existiert
    if (new java.io.File(output).exists()) {
        System.err.println("output already exists: " + output);
        error++;
    }

    // aussteigen, falls fehler aufgetaucht sind
    if (error > 0) {
        System.err.println("error(s) occured. try -help for help.");
        System.exit(1);
    }

    /*----------------------------
      die lizenz ueberpruefen und ggf abbrechen
    ----------------------------*/

    // check for valid license
    ArrayList<String> allPortAtHost = new ArrayList<String>();
    allPortAtHost.add(ini.get("license-server", "license-server-1"));
    allPortAtHost.add(ini.get("license-server", "license-server-2"));
    allPortAtHost.add(ini.get("license-server", "license-server-3"));

    MyLicense lic = new MyLicense(allPortAtHost, "1", "user-edition", "0.1");

    // lizenz-logging ausgeben
    for (String actLine : (ArrayList<String>) lic.getLog()) {
        System.err.println(actLine);
    }

    // abbruch, wenn lizenz nicht valide
    if (!lic.isValid()) {
        System.exit(1);
    }

    /*----------------------------
      die eigentliche business logic
    ----------------------------*/

    Process process = new Process();
    Reporter report;

    process.setInfilexml(definition);

    System.out.println("info: reading process definition " + definition);

    try {
        process.readXml();
        process.setStepRanks();
    }

    catch (JAXBException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    //festlegen des temporaeren verzeichnisses fuer die Daten und Pfade erzeugen
    long jetztMillis = System.currentTimeMillis();
    String randomPathJasperFilled = "/tmp/" + jetztMillis + "_jasperFilled";
    String randomPathPng = "/tmp/" + jetztMillis + "_png";
    String randomPathPdf = "/tmp/" + jetztMillis + "_pdf";
    String randomPathPptx = "/tmp/" + jetztMillis + "_pptx";

    new File(randomPathJasperFilled).mkdirs();
    new File(randomPathPng).mkdirs();
    new File(randomPathPdf).mkdirs();
    new File(randomPathPptx).mkdirs();

    //////////////////////////////////////////

    // erstellen der Bilder

    // konfigurieren der processing ansicht
    //      PmodelViewPage page = new PmodelViewPage(process);
    PmodelViewPage page = new PmodelViewPage();
    page.einstellungen.getProcess().setStepRanks();
    page.einstellungen.setSize(100);
    page.einstellungen.setZoom(100);
    //      page.einstellungen.setZoom(8 * 100/process.getMaxLevel());
    page.einstellungen.setTextsize(0);
    page.einstellungen.setRanksize(7);
    page.einstellungen.setWidth(2500);
    page.einstellungen.setHeight(750);
    page.einstellungen.setGravx(10);
    page.einstellungen.setGravy(0);
    page.einstellungen.setRootpositionratiox((float) 0.05);
    page.einstellungen.setRootpositionratioy((float) 0.5);
    page.einstellungen.setProcess(process);

    createContents(page);

    // mit open kann die page angezeigt werden
    if (!(produktiv)) {
        open();
    }

    //      // warten
    //      System.out.println("stabilisierung ansicht: 5 sekunden warten gravitation = "+page.einstellungen.getGravx());
    //      long jetzt5 = System.currentTimeMillis();
    //      while (System.currentTimeMillis() < jetzt5 + 5000)
    //      {
    //         
    //      }
    //
    //      page.einstellungen.setGravx(10);
    //
    // warten
    int wartezeitSeconds = 1;
    if (produktiv) {
        wartezeitSeconds = page.einstellungen.getProcess().getStep().size() * 2;
    }
    System.out.println("stabilisierung ansicht: " + wartezeitSeconds + " sekunden warten gravitation = "
            + page.einstellungen.getGravx());
    long jetzt6 = System.currentTimeMillis();
    while (System.currentTimeMillis() < jetzt6 + (wartezeitSeconds * 1000)) {

    }

    page.einstellungen.setFix(true);

    // VORBEREITUNG) bild speichern
    processTopologyImagePath = randomPathPng + "/processTopology.png";
    page.savePic(processTopologyImagePath);
    // zuerst 1 sekunde warten, dann autocrop
    long jetzt = System.currentTimeMillis();
    while (System.currentTimeMillis() < jetzt + 1000) {

    }
    new AutoCropBorder(processTopologyImagePath);

    // VORBEREITUNG) fuer jeden step ein bild speichern
    for (Step actualStep : process.getStep()) {

        // root ueberspringen
        //         if (actualStep.isRoot());

        String stepImagePath = randomPathPng + "/step_" + actualStep.getName() + "_Topology.png";

        // Farbe des Steps auf finished (gruen) aendern
        page.einstellungen.getProcess().getRootStep().setStatusOverwrite("waiting");
        actualStep.setStatusOverwrite("finished");

        // etwas warten, bis die farbe bezeichnet wurde
        long jetzt4 = System.currentTimeMillis();
        while (System.currentTimeMillis() < jetzt4 + 500) {

        }

        page.savePic(stepImagePath);
        // zuerst 1 sekunde warten, dann autocrop
        long jetzt3 = System.currentTimeMillis();
        while (System.currentTimeMillis() < jetzt3 + 1000) {

        }
        new AutoCropBorder(stepImagePath);

        stepTopologyImagePath.put(actualStep.getName(), stepImagePath);

        // farbe wieder auf grau aendern
        actualStep.setStatusOverwrite(null);

        System.out.println("erstelle bild fuer step: " + actualStep.getName());

        long jetzt2 = System.currentTimeMillis();
        while (System.currentTimeMillis() < jetzt2 + 1000) {

        }
    }

    page.destroy();

    //////////////////////////////////////////
    report = new Reporter();

    // P03) erstellen des p03
    System.out.println("info: generating p03.");

    String pdfPathP03 = null;
    String pptxPathP03 = null;
    String jasperPathP03 = null;
    String jasperFilledPathP03 = null;

    // P03) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
    if (ini.get("pkraft-createdoc", "p03") != null) {
        pdfPathP03 = randomPathPdf + "/p03.pdf";
        pptxPathP03 = randomPathPptx + "/p03.pptx";
        jasperPathP03 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p03");
        jasperFilledPathP03 = (randomPathJasperFilled + "/p03.jasperFilled");

        pdfRankFiles.put("0.0.03", pdfPathP03);
        pptxRankFiles.put("0.0.03", pptxPathP03);
    } else {
        System.err.println("no entry 'p03' found in ini file");
        System.exit(1);
    }

    DateFormat dateFormat = new SimpleDateFormat("dd. MM. yyyy");
    Date date = new Date();

    report.setParameter("processName", process.getName());
    report.setParameter("processVersion", process.getVersion());
    report.setParameter("processDatum", dateFormat.format(date));
    report.setParameter("processArchitectLogoImagePath",
            installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "logo"));
    report.setParameter("processArchitectCompany", process.getArchitectCompany());
    report.setParameter("processArchitectName", process.getArchitectName());
    report.setParameter("processArchitectMail", process.getArchitectMail());
    report.setParameter("processCustomerCompany", process.getCustomerCompany());
    report.setParameter("processCustomerName", process.getCustomerName());
    report.setParameter("processCustomerMail", process.getCustomerMail());

    try {
        report.fillReportFileToFile(jasperPathP03, jasperFilledPathP03);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pdf
    try {
        report.convertFileToPdf(jasperFilledPathP03, pdfPathP03);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pptx
    try {
        report.convertFileToPptx(jasperFilledPathP03, pptxPathP03);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    report = null;

    //System.exit(0);

    //////////////////////////////////////////
    report = new Reporter();

    // P05) erstellen des p05
    System.out.println("info: generating p05.");

    String pdfPathP05 = null;
    String pptxPathP05 = null;
    String jasperPathP05 = null;
    String jasperFilledPathP05 = null;

    // P05) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
    if (ini.get("pkraft-createdoc", "p05") != null) {
        pdfPathP05 = randomPathPdf + "/p05.pdf";
        pptxPathP05 = randomPathPptx + "/p05.pptx";
        jasperPathP05 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p05");
        jasperFilledPathP05 = (randomPathJasperFilled + "/p05.jasperFilled");

        pdfRankFiles.put("0.0.05", pdfPathP05);
        pptxRankFiles.put("0.0.05", pptxPathP05);
    }

    else {
        System.err.println("no entry 'p05' found in ini file");
        System.exit(1);
    }

    report.setParameter("processName", process.getName());
    report.setParameter("processVersion", process.getVersion());
    report.setParameter("processArchitectCompany", process.getArchitectCompany());
    report.setParameter("processArchitectName", process.getArchitectName());
    report.setParameter("processArchitectMail", process.getArchitectMail());
    report.setParameter("processCustomerCompany", process.getCustomerCompany());
    report.setParameter("processCustomerName", process.getCustomerName());
    report.setParameter("processCustomerMail", process.getCustomerMail());

    try {
        report.fillReportFileToFile(jasperPathP05, jasperFilledPathP05);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pdf
    try {
        report.convertFileToPdf(jasperFilledPathP05, pdfPathP05);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pptx
    try {
        report.convertFileToPptx(jasperFilledPathP05, pptxPathP05);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    report = null;

    //System.exit(0);

    //////////////////////////////////////////
    report = new Reporter();

    // P08) erstellen des p08
    System.out.println("info: generating p08.");

    String pdfPathP08 = null;
    String pptxPathP08 = null;
    String jasperPathP08 = null;
    String jasperFilledPathP08 = null;

    // P08) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
    if (ini.get("pkraft-createdoc", "p08") != null) {
        pdfPathP08 = randomPathPdf + "/p08.pdf";
        pptxPathP08 = randomPathPptx + "/p08.pptx";
        jasperPathP08 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p08");
        jasperFilledPathP08 = (randomPathJasperFilled + "/p08.jasperFilled");

        pdfRankFiles.put("0.0.08", pdfPathP08);
        pptxRankFiles.put("0.0.08", pptxPathP08);
    } else {
        System.err.println("no entry 'p08' found in ini file");
        System.exit(1);
    }

    report.setParameter("processName", process.getName());
    report.setParameter("processVersion", process.getVersion());
    report.setParameter("processArchitectCompany", process.getArchitectCompany());
    report.setParameter("processArchitectName", process.getArchitectName());
    report.setParameter("processArchitectMail", process.getArchitectMail());
    report.setParameter("processCustomerCompany", process.getCustomerCompany());
    report.setParameter("processCustomerName", process.getCustomerName());
    report.setParameter("processCustomerMail", process.getCustomerMail());
    report.setParameter("processDescription", process.getDescription());

    try {
        report.fillReportFileToFile(jasperPathP08, jasperFilledPathP08);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pdf
    try {
        report.convertFileToPdf(jasperFilledPathP08, pdfPathP08);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pptx
    try {
        report.convertFileToPptx(jasperFilledPathP08, pptxPathP08);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    report = null;

    //System.exit(0);

    //////////////////////////////////////////

    report = new Reporter();

    // P10) erstellen des p10
    System.out.println("info: generating p10.");

    String pdfPathP10 = null;
    String pptxPathP10 = null;
    String jasperPathP10 = null;
    String jasperFilledPathP10 = null;

    // P10) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
    if (ini.get("pkraft-createdoc", "p10") != null) {
        pdfPathP10 = randomPathPdf + "/p10.pdf";
        pptxPathP10 = randomPathPptx + "/p10.pptx";
        jasperPathP10 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p10");
        jasperFilledPathP10 = (randomPathJasperFilled + "/p10.jasperFilled");

        pdfRankFiles.put("0.0.10", pdfPathP10);
        pptxRankFiles.put("0.0.10", pptxPathP10);
    } else {
        System.err.println("no entry 'p10' found in ini file");
        System.exit(1);
    }

    report.setParameter("processName", process.getName());
    report.setParameter("processVersion", process.getVersion());
    report.setParameter("processArchitectCompany", process.getArchitectCompany());
    report.setParameter("processArchitectName", process.getArchitectName());
    report.setParameter("processArchitectMail", process.getArchitectMail());
    report.setParameter("processCustomerCompany", process.getCustomerCompany());
    report.setParameter("processCustomerName", process.getCustomerName());
    report.setParameter("processCustomerMail", process.getCustomerMail());

    // rootstep holen
    Step rootStep = process.getStep(process.getRootstepname());

    // ueber alle commit iterieren
    for (Commit actualCommit : rootStep.getCommit()) {

        // ueber alle files iterieren
        for (de.prozesskraft.pkraft.File actualFile : actualCommit.getFile()) {
            HashMap<String, Object> row = new HashMap<String, Object>();

            // Spalte 'origin'
            row.put("origin", "user/cb2");

            // Spalte 'objectType'
            row.put("objectType", "file");

            // Spalte 'minOccur'
            row.put("minOccur", "" + actualFile.getMinoccur());

            // Spalte 'maxOccur'
            row.put("maxOccur", "" + actualFile.getMaxoccur());

            // Spalte 'objectKey'
            row.put("objectKey", actualFile.getKey());

            // die steps herausfinden, die dieses file benoetigen
            ArrayList<Step> allStepsThatNeedThisFileFromRoot = process.getStepWhichNeedFromRoot("file",
                    actualFile.getKey());
            String stepnameListe = "";
            for (Step actStep : allStepsThatNeedThisFileFromRoot) {
                stepnameListe += "\n=> " + actStep.getName();
            }

            // Spalte 'objectDescription'
            row.put("objectDescription", actualFile.getDescription() + stepnameListe);

            // Datensatz dem report hinzufuegen
            report.addField(row);
        }

        // ueber alle variablen iterieren
        for (de.prozesskraft.pkraft.Variable actualVariable : actualCommit.getVariable()) {
            HashMap<String, Object> row = new HashMap<String, Object>();

            // Spalte 'origin'
            row.put("origin", "user/cb2");

            // Spalte 'objectType'
            row.put("objectType", "variable");

            // Spalte 'minOccur'
            row.put("minOccur", "" + actualVariable.getMinoccur());

            // Spalte 'maxOccur'
            row.put("maxOccur", "" + actualVariable.getMaxoccur());

            // Spalte 'objectKey'
            row.put("objectKey", actualVariable.getKey());

            // die steps herausfinden, die dieses file benoetigen
            ArrayList<Step> allStepsThatNeedThisObjectFromRoot = process.getStepWhichNeedFromRoot("variable",
                    actualVariable.getKey());
            String stepnameListe = "";
            for (Step actStep : allStepsThatNeedThisObjectFromRoot) {
                stepnameListe += "\n=> " + actStep.getName();
            }

            // Spalte 'objectDescription'
            row.put("objectDescription", actualVariable.getDescription() + stepnameListe);

            // Datensatz dem report hinzufuegen
            report.addField(row);
        }

    }

    try {
        report.fillReportFileToFile(jasperPathP10, jasperFilledPathP10);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pdf
    try {
        report.convertFileToPdf(jasperFilledPathP10, pdfPathP10);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pptx
    try {
        report.convertFileToPptx(jasperFilledPathP10, pptxPathP10);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    report = null;

    //////////////////////////////////////////

    report = new Reporter();

    // P20) erstellen des p20
    System.out.println("info: generating p20.");

    String pdfPathP20 = null;
    String pptxPathP20 = null;
    String jasperPathP20 = null;
    String jasperFilledPathP20 = null;

    // P20) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
    if (ini.get("pkraft-createdoc", "p20") != null) {
        pdfPathP20 = randomPathPdf + "/p20.pdf";
        pptxPathP20 = randomPathPptx + "/p20.pptx";
        jasperPathP20 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p20");
        jasperFilledPathP20 = (randomPathJasperFilled + "/p20.jasperFilled");

        pdfRankFiles.put("0.0.20", pdfPathP20);
        pptxRankFiles.put("0.0.20", pptxPathP20);
    } else {
        System.err.println("no entry 'p20' found in ini file");
        System.exit(1);
    }

    report.setParameter("processName", process.getName());
    report.setParameter("processVersion", process.getVersion());
    report.setParameter("processArchitectCompany", process.getArchitectCompany());
    report.setParameter("processArchitectName", process.getArchitectName());
    report.setParameter("processArchitectMail", process.getArchitectMail());
    report.setParameter("processCustomerCompany", process.getCustomerCompany());
    report.setParameter("processCustomerName", process.getCustomerName());
    report.setParameter("processCustomerMail", process.getCustomerMail());

    // ueber alle steps iterieren (ausser root)
    for (Step actualStep : (ArrayList<Step>) process.getStep()) {

        // ueberspringen wenn es sich um root handelt
        if (!(actualStep.getName().equals(process.getRootstepname()))) {
            // ueber alle commit iterieren
            for (Commit actualCommit : actualStep.getCommit()) {

                // nur die, die toroot=true ( und spaeter auch tosdm=true)
                if (actualCommit.isTorootPresent()) {
                    // ueber alle files iterieren
                    for (de.prozesskraft.pkraft.File actualFile : actualCommit.getFile()) {

                        HashMap<String, Object> row = new HashMap<String, Object>();

                        // Spalte 'destination'
                        row.put("destination", "user/cb2");

                        // Spalte 'objectType'
                        row.put("objectType", "file");

                        // Spalte 'minOccur'
                        row.put("minOccur", "" + actualFile.getMinoccur());

                        // Spalte 'maxOccur'
                        row.put("maxOccur", "" + actualFile.getMaxoccur());

                        // Spalte 'objectKey'
                        row.put("objectKey", actualFile.getKey());

                        // Spalte 'objectDescription'
                        row.put("objectDescription",
                                actualFile.getDescription() + "\n<= " + actualStep.getName());

                        // Datensatz dem report hinzufuegen
                        report.addField(row);
                    }

                    // ueber alle variablen iterieren
                    for (de.prozesskraft.pkraft.Variable actualVariable : actualCommit.getVariable()) {
                        HashMap<String, Object> row = new HashMap<String, Object>();

                        // Spalte 'objectType'
                        row.put("destination", "user/cb2");

                        // Spalte 'objectType'
                        row.put("objectType", "variable");

                        // Spalte 'minOccur'
                        row.put("minOccur", "" + actualVariable.getMinoccur());

                        // Spalte 'maxOccur'
                        row.put("maxOccur", "" + actualVariable.getMaxoccur());

                        // Spalte 'objectKey'
                        row.put("objectKey", actualVariable.getKey());

                        // Spalte 'objectDescription'
                        row.put("objectDescription",
                                actualVariable.getDescription() + "\n<= " + actualStep.getName());

                        // Datensatz dem report hinzufuegen
                        report.addField(row);
                    }
                }
            }
        }

    }

    try {
        report.fillReportFileToFile(jasperPathP20, jasperFilledPathP20);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pdf
    try {
        report.convertFileToPdf(jasperFilledPathP20, pdfPathP20);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pptx
    try {
        report.convertFileToPptx(jasperFilledPathP20, pptxPathP20);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    report = null;

    //////////////////////////////////////////

    report = new Reporter();

    // P30) erstellen des p30
    System.out.println("info: generating p30.");

    String pdfPathP30 = null;
    String pptxPathP30 = null;
    String jasperPathP30 = null;
    String jasperFilledPathP30 = null;

    // P30) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
    if (ini.get("pkraft-createdoc", "p30") != null) {
        pdfPathP30 = randomPathPdf + "/p30.pdf";
        pptxPathP30 = randomPathPptx + "/p30.pptx";
        jasperPathP30 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p30");
        jasperFilledPathP30 = (randomPathJasperFilled + "/p30.jasperFilled");

        pdfRankFiles.put("0.0.30", pdfPathP30);
        pptxRankFiles.put("0.0.30", pptxPathP30);
    } else {
        System.err.println("no entry 'p30' found in ini file");
        System.exit(1);
    }

    report.setParameter("processName", process.getName());
    report.setParameter("processVersion", process.getVersion());
    report.setParameter("processArchitectCompany", process.getArchitectCompany());
    report.setParameter("processArchitectName", process.getArchitectName());
    report.setParameter("processArchitectMail", process.getArchitectMail());
    report.setParameter("processCustomerCompany", process.getCustomerCompany());
    report.setParameter("processCustomerName", process.getCustomerName());
    report.setParameter("processCustomerMail", process.getCustomerMail());

    // P1) bild an report melden
    report.setParameter("processTopologyImagePath", processTopologyImagePath);

    try {
        report.fillReportFileToFile(jasperPathP30, jasperFilledPathP30);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pdf
    try {
        report.convertFileToPdf(jasperFilledPathP30, pdfPathP30);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pptx
    try {
        report.convertFileToPptx(jasperFilledPathP30, pptxPathP30);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    report = null;

    //      System.exit(0);
    //////////////////////////////////////////

    report = new Reporter();

    // P40) erstellen des p40
    System.out.println("info: generating p40.");

    String pdfPathP40 = null;
    String pptxPathP40 = null;
    String jasperPathP40 = null;
    String jasperFilledPathP40 = null;

    // P40) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
    if (ini.get("pkraft-createdoc", "p40") != null) {
        pdfPathP40 = randomPathPdf + "/p40.pdf";
        pptxPathP40 = randomPathPptx + "/p40.pptx";
        jasperPathP40 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p40");
        jasperFilledPathP40 = (randomPathJasperFilled + "/p40.jasperFilled");

        pdfRankFiles.put("0.0.40", pdfPathP40);
        pptxRankFiles.put("0.0.40", pptxPathP40);
    } else {
        System.err.println("no entry 'p40' found in ini file");
        System.exit(1);
    }

    report.setParameter("processName", process.getName());
    report.setParameter("processVersion", process.getVersion());
    report.setParameter("processArchitectCompany", process.getArchitectCompany());
    report.setParameter("processArchitectName", process.getArchitectName());
    report.setParameter("processArchitectMail", process.getArchitectMail());
    report.setParameter("processCustomerCompany", process.getCustomerCompany());
    report.setParameter("processCustomerName", process.getCustomerName());
    report.setParameter("processCustomerMail", process.getCustomerMail());

    // P40) bild an report melden
    report.setParameter("processTopologyImagePath", processTopologyImagePath);

    // Tabelle erzeugen

    ArrayList<Step> steps = process.getStep();
    for (int x = 0; x < steps.size(); x++) {
        HashMap<String, Object> row = new HashMap<String, Object>();
        Step actualStep = steps.get(x);

        // erste Spalte ist 'rank'
        // um die korrekte sortierung zu erhalten soll der rank-string auf jeweils 2 Stellen erweitert werden
        String[] rankArray = actualStep.getRank().split("\\.");
        Integer[] rankArrayInt = new Integer[rankArray.length];
        for (int y = 0; y < rankArray.length; y++) {
            rankArrayInt[y] = Integer.parseInt(rankArray[y]);
        }
        String rankFormated = String.format("%02d.%02d", rankArrayInt);
        row.put("stepRank", rankFormated);

        // zweite Spalte ist 'stepname'
        row.put("stepName", actualStep.getName());
        //            System.out.println("stepName: "+actualStep.getName());

        // dritte Spalte ist 'Beschreibung'
        row.put("stepDescription", actualStep.getDescription());
        //            System.out.println("stepRank: "+actualStep.getDescription());

        // wenn nicht der root-step, dann row eintragen
        if (!(actualStep.getName().equals(process.getRootstepname()))) {
            report.addField(row);
        }
    }

    try {
        report.fillReportFileToFile(jasperPathP40, jasperFilledPathP40);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pdf
    try {
        report.convertFileToPdf(jasperFilledPathP40, pdfPathP40);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    // export to pptx
    try {
        report.convertFileToPptx(jasperFilledPathP40, pptxPathP40);
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (JRException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }

    report = null;

    //////////////////////////////////////////

    // fuer jeden Step einen eigenen Input Report erzeugen

    for (Step actualStep : process.getStep()) {
        // root-step ueberspringen
        if (actualStep.getName().equals(process.getRootstepname())) {
            System.out.println("skipping step root");
        }

        // alle anderen auswerten
        else {

            report = new Reporter();

            // P51x) erstellen des p51
            System.out.println(
                    "info: generating p51 for step " + actualStep.getRank() + " => " + actualStep.getName());

            String stepRank = actualStep.getRank();

            String pdfPathP51 = null;
            String pptxPathP51 = null;
            String jasperPathP51 = null;
            String jasperFilledPathP51 = null;

            // P51x) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
            if (ini.get("pkraft-createdoc", "p51") != null) {
                pdfPathP51 = randomPathPdf + "/p5." + stepRank + ".1.pdf";
                pptxPathP51 = randomPathPptx + "/p5." + stepRank + ".1.pptx";
                jasperPathP51 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p51");
                jasperFilledPathP51 = randomPathJasperFilled + "/p5." + stepRank + ".1.jasperFilled";

                String[] rankArray = stepRank.split("\\.");
                Integer[] rankArrayInt = new Integer[rankArray.length];
                for (int x = 0; x < rankArray.length; x++) {
                    rankArrayInt[x] = Integer.parseInt(rankArray[x]);
                }
                String rankFormated = String.format("%03d.%03d", rankArrayInt);

                pdfRankFiles.put(rankFormated + ".1", pdfPathP51);
                pptxRankFiles.put(rankFormated + ".1", pptxPathP51);
            } else {
                System.err.println("no entry 'p51' found in ini file");
                System.exit(1);
            }

            report.setParameter("processName", process.getName());
            report.setParameter("processVersion", process.getVersion());
            report.setParameter("processArchitectCompany", process.getArchitectCompany());
            report.setParameter("processArchitectName", process.getArchitectName());
            report.setParameter("processArchitectMail", process.getArchitectMail());
            report.setParameter("processCustomerCompany", process.getCustomerCompany());
            report.setParameter("processCustomerName", process.getCustomerName());
            report.setParameter("processCustomerMail", process.getCustomerMail());

            report.setParameter("stepName", actualStep.getName());
            report.setParameter("stepRank", stepRank);
            report.setParameter("stepDescription", actualStep.getDescription());

            String aufruf = "";
            if (actualStep.getWork() != null) {
                // zusammensetzen des scriptaufrufs
                String interpreter = "";

                if (actualStep.getWork().getInterpreter() != null) {
                    interpreter = actualStep.getWork().getInterpreter();
                }

                aufruf = interpreter + " " + actualStep.getWork().getCommand();
                for (Callitem actualCallitem : actualStep.getWork().getCallitem()) {
                    aufruf += " " + actualCallitem.getPar();
                    if (!(actualCallitem.getDel() == null)) {
                        aufruf += actualCallitem.getDel();
                    }
                    if (!(actualCallitem.getVal() == null)) {
                        aufruf += actualCallitem.getVal();
                    }
                }
            } else if (actualStep.getSubprocess() != null) {
                aufruf = ini.get("apps", "pkraft-startinstance");
                aufruf += " --pdomain " + actualStep.getSubprocess().getDomain();
                aufruf += " --pname " + actualStep.getSubprocess().getName();
                aufruf += " --pversion " + actualStep.getSubprocess().getVersion();

                for (Commit actCommit : actualStep.getSubprocess().getStep().getCommit()) {
                    for (de.prozesskraft.pkraft.File actFile : actCommit.getFile()) {
                        aufruf += " --commitfile " + actFile.getGlob();
                    }
                    for (Variable actVariable : actCommit.getVariable()) {
                        aufruf += " --commitvariable " + actVariable.getKey() + "=" + actVariable.getValue();
                    }
                }
            }
            report.setParameter("stepWorkCall", aufruf);

            // P51x) bild an report melden
            report.setParameter("stepTopologyImagePath", stepTopologyImagePath.get(actualStep.getName()));

            // ueber alle lists iterieren
            for (List actualList : actualStep.getList()) {
                HashMap<String, Object> row = new HashMap<String, Object>();

                // Spalte 'Woher?'
                row.put("origin", "-");

                // Spalte 'typ'
                row.put("objectType", "wert");

                // Spalte 'minOccur'
                row.put("minOccur", "-");

                // Spalte 'maxOccur'
                row.put("maxOccur", "-");

                // Spalte 'Label'
                row.put("objectKey", actualList.getName());

                // Spalte 'Label'
                String listString = actualList.getItem().toString();
                row.put("objectDescription", listString.substring(1, listString.length() - 1));

                report.addField(row);
            }

            // ueber alle inits iterieren
            for (Init actualInit : actualStep.getInit()) {
                HashMap<String, Object> row = new HashMap<String, Object>();

                // Spalte 'Woher?'
                if (actualInit.getFromstep().equals(process.getRootstepname())) {
                    row.put("origin", "user/cb2");
                } else {
                    row.put("origin", actualInit.getFromstep());
                }

                // Spalte 'typ'
                row.put("objectType", actualInit.getFromobjecttype());

                // Spalte 'minOccur'
                row.put("minOccur", "" + actualInit.getMinoccur());

                // Spalte 'maxOccur'
                row.put("maxOccur", "" + actualInit.getMaxoccur());

                // Spalte 'Label'
                row.put("objectKey", actualInit.getListname());

                // Spalte 'Label'
                row.put("objectDescription", "-");

                report.addField(row);
            }

            try {
                report.fillReportFileToFile(jasperPathP51, jasperFilledPathP51);
            } catch (FileNotFoundException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            } catch (JRException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }

            // export to pdf
            try {
                report.convertFileToPdf(jasperFilledPathP51, pdfPathP51);
            } catch (FileNotFoundException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            } catch (JRException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }

            // export to pptx
            try {
                report.convertFileToPptx(jasperFilledPathP51, pptxPathP51);
            } catch (FileNotFoundException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            } catch (JRException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }

            report = null;
        }
    }

    //////////////////////////////////////////

    // fuer jeden Step einen eigenen Output Report erzeugen

    for (Step actualStep : process.getStep()) {
        // root-step ueberspringen
        if (actualStep.getName().equals(process.getRootstepname())) {
            System.out.println("skipping step root");
        }

        // alle anderen auswerten
        else {

            report = new Reporter();

            // P52x) erstellen des p52
            System.out.println(
                    "info: generating p52 for step " + actualStep.getRank() + " => " + actualStep.getName());

            String stepRank = actualStep.getRank();

            String pdfPathP52 = null;
            String pptxPathP52 = null;
            String jasperPathP52 = null;
            String jasperFilledPathP52 = null;

            // P52x) feststellen, welches jasperreports-template fuer den angeforderten typ verwendet werden soll
            if (ini.get("pkraft-createdoc", "p52") != null) {
                pdfPathP52 = randomPathPdf + "/p5." + stepRank + ".2.pdf";
                pptxPathP52 = randomPathPptx + "/p5." + stepRank + ".2.pptx";
                jasperPathP52 = installDir.getAbsolutePath() + "/" + ini.get("pkraft-createdoc", "p52");
                jasperFilledPathP52 = randomPathJasperFilled + "/p5." + stepRank + ".1.jasperFilled";

                String[] rankArray = stepRank.split("\\.");
                Integer[] rankArrayInt = new Integer[rankArray.length];
                for (int x = 0; x < rankArray.length; x++) {
                    rankArrayInt[x] = Integer.parseInt(rankArray[x]);
                }
                String rankFormated = String.format("%03d.%03d", rankArrayInt);

                pdfRankFiles.put(rankFormated + ".2", pdfPathP52);
                pptxRankFiles.put(rankFormated + ".2", pptxPathP52);
            } else {
                System.err.println("no entry 'p52' found in ini file");
                System.exit(1);
            }

            report.setParameter("processName", process.getName());
            report.setParameter("processVersion", process.getVersion());
            report.setParameter("processArchitectCompany", process.getArchitectCompany());
            report.setParameter("processArchitectName", process.getArchitectName());
            report.setParameter("processArchitectMail", process.getArchitectMail());
            report.setParameter("processCustomerCompany", process.getCustomerCompany());
            report.setParameter("processCustomerName", process.getCustomerName());
            report.setParameter("processCustomerMail", process.getCustomerMail());

            report.setParameter("stepName", actualStep.getName());
            report.setParameter("stepRank", stepRank);

            // logfile ermitteln
            String logfile = "-";
            if (actualStep.getWork() != null) {
                if (actualStep.getWork().getLogfile() == null || actualStep.getWork().getLogfile().equals("")) {
                    report.setParameter("stepWorkLogfile", actualStep.getWork().getLogfile());
                }
            } else if (actualStep.getSubprocess() != null) {
                logfile = ".log";
            }
            report.setParameter("stepWorkLogfile", logfile);

            // zusammensetzen der return/exitcode informationen
            String exitInfo = "exit 0 = kein fehler aufgetreten";
            exitInfo += "\nexit >0 = ein fehler ist aufgetreten.";
            if (actualStep.getWork() != null) {
                for (Exit actualExit : actualStep.getWork().getExit()) {
                    exitInfo += "\nexit " + actualExit.getValue() + " = " + actualExit.getMsg();
                }
            }
            report.setParameter("stepWorkExit", exitInfo);

            // P52x) bild an report melden
            report.setParameter("stepTopologyImagePath", stepTopologyImagePath.get(actualStep.getName()));

            // ueber alle inits iterieren
            for (Commit actualCommit : actualStep.getCommit()) {

                // ueber alle files iterieren
                for (de.prozesskraft.pkraft.File actualFile : actualCommit.getFile()) {

                    HashMap<String, Object> row = new HashMap<String, Object>();

                    // Spalte 'destination'
                    if (actualCommit.isTorootPresent()) {
                        row.put("destination", "user/cb2");
                    } else {
                        row.put("destination", "prozessintern");
                    }

                    // Spalte 'objectType'
                    row.put("objectType", "file");

                    // Spalte 'minOccur'
                    row.put("minOccur", "" + actualFile.getMinoccur());

                    // Spalte 'maxOccur'
                    row.put("maxOccur", "" + actualFile.getMaxoccur());

                    // Spalte 'objectKey'
                    row.put("objectKey", actualFile.getKey());

                    // Spalte 'objectDescription'
                    row.put("objectDescription", actualFile.getDescription());

                    // Datensatz dem report hinzufuegen
                    report.addField(row);
                }

                // ueber alle variablen iterieren
                for (de.prozesskraft.pkraft.Variable actualVariable : actualCommit.getVariable()) {
                    HashMap<String, Object> row = new HashMap<String, Object>();

                    // Spalte 'destination'
                    if (actualCommit.isTorootPresent()) {
                        row.put("destination", "user/cb2");
                    } else {
                        row.put("destination", "prozessintern");
                    }

                    // Spalte 'objectType'
                    row.put("objectType", "variable");

                    // Spalte 'minOccur'
                    row.put("minOccur", "" + actualVariable.getMinoccur());

                    // Spalte 'maxOccur'
                    row.put("maxOccur", "" + actualVariable.getMaxoccur());

                    // Spalte 'objectKey'
                    row.put("objectKey", actualVariable.getKey());

                    // Spalte 'objectDescription'
                    row.put("objectDescription", actualVariable.getDescription());

                    // Datensatz dem report hinzufuegen
                    report.addField(row);
                }

            }
            try {
                report.fillReportFileToFile(jasperPathP52, jasperFilledPathP52);
            } catch (FileNotFoundException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            } catch (JRException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }

            // export to pdf
            try {
                report.convertFileToPdf(jasperFilledPathP52, pdfPathP52);
            } catch (FileNotFoundException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            } catch (JRException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }

            // export to pptx
            try {
                report.convertFileToPptx(jasperFilledPathP52, pptxPathP52);
            } catch (FileNotFoundException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            } catch (JRException e) {
                // TODO Auto-generated catch block
                e.printStackTrace();
            }

            report = null;
        }
    }

    // warten bis alles auf platte geschrieben ist
    try {
        Thread.sleep(1000);
    } catch (InterruptedException ex) {
        Thread.currentThread().interrupt();
    }

    // merge and output
    if (format.equals("pdf")) {
        mergePdf(pdfRankFiles, output);
    } else if (format.equals("pptx")) {
        mergePptx(pptxRankFiles, output);
    }

    System.out.println("info: generating process documentation ready.");
    System.exit(0);
}