Example usage for java.util.logging Level SEVERE

List of usage examples for java.util.logging Level SEVERE

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Prototype

Level SEVERE

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Document

SEVERE is a message level indicating a serious failure.

Usage

From source file:diffhunter.DiffHunter.java

/**
 * @param args the command line arguments
 * @throws org.apache.commons.cli.ParseException
 * @throws java.io.IOException/*from ww w  .ja v  a 2 s .c o m*/
 */
public static void main(String[] args) throws ParseException, IOException {

    //String test_ = Paths.get("J:\\VishalData\\additional\\", "Sasan" + "_BDB").toAbsolutePath().toString();

    // TODO code application logic here
    /*args = new String[]
    {
    "-i", "-b", "J:\\VishalData\\additional\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted.bed", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-o", "J:\\VishalData"
    };*/

    /*args = new String[]
    {
    "-c", "-r", "J:\\VishalData\\additional\\mouse_mm9.txt", "-1", "J:\\VishalData\\Ptbp2_Adult_testis_CLIP_mm9_plus_strand_sorted_BDB", "-2", "J:\\VishalData\\Ptbp2_E18_5_cortex_CLIP_mm9_plus_strand_sorted_BDB", "-w", "200", "-s", "50", "-o", "J:\\VishalData"
    };*/
    Options options = new Options();

    // add t option
    options.addOption("i", "index", false, "Indexing BED files.");
    options.addOption("b", "bed", true, "bed file to be indexed");
    options.addOption("o", "output", true, "Folder that the index/comparison file will be created.");
    options.addOption("r", "reference", true, "Reference annotation file to be used for indexing");
    options.addOption("c", "compare", false, "Finding differences between two conditions");
    options.addOption("1", "first", true, "First sample index location");
    options.addOption("2", "second", true, "Second sample index location");
    options.addOption("w", "window", true, "Length of window for identifying differences");
    options.addOption("s", "sliding", true, "Length of sliding");

    CommandLineParser parser = new BasicParser();
    CommandLine cmd = parser.parse(options, args);

    boolean indexing = false;
    boolean comparing = false;

    //Indexing!
    if (cmd.hasOption("i")) {
        //if(cmd.hasOption("1"))
        //System.err.println("sasan");

        //System.out.println("sasa");
        indexing = true;

    } else if (cmd.hasOption("c")) {
        //System.err.println("");
        comparing = true;

    } else {
        //System.err.println("Option is not deteced.");
        HelpFormatter formatter = new HelpFormatter();
        formatter.printHelp("diffhunter", options);
        return;
    }

    //Indexing is selected
    //
    if (indexing == true) {
        //Since indexing is true.
        //User have to provide file for indexing.
        if (!(cmd.hasOption("o") || cmd.hasOption("r") || cmd.hasOption("b"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String bedfile_ = cmd.getOptionValue("b");
        String reference_file = cmd.getOptionValue("r");
        String folder_loc = cmd.getOptionValue("o");

        String sample_name = FilenameUtils.getBaseName(bedfile_);

        try (Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(
                Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString(), true, sample_name)) {
            Indexer indexing_ = new Indexer(reference_file);
            indexing_.Make_Index(B2, bedfile_,
                    Paths.get(folder_loc, sample_name + "_BDB").toAbsolutePath().toString());
            B2.close();

        }
    } else if (comparing == true) {
        if (!(cmd.hasOption("o") || cmd.hasOption("w") || cmd.hasOption("s") || cmd.hasOption("1")
                || cmd.hasOption("2"))) {
            HelpFormatter formatter = new HelpFormatter();
            formatter.printHelp("diffhunter", options);
            return;
        }
        String folder_loc = cmd.getOptionValue("o");
        int window_ = Integer.parseInt(cmd.getOptionValue("w"));
        //int window_=600;

        int slide_ = Integer.parseInt(cmd.getOptionValue("s"));

        String first = cmd.getOptionValue("1").replace("_BDB", "");
        String second = cmd.getOptionValue("2").replace("_BDB", "");
        String reference_file = cmd.getOptionValue("r");
        //String folder_loc=cmd.getOptionValue("o");

        String sample_name_first = FilenameUtils.getBaseName(first);
        String sample_name_second = FilenameUtils.getBaseName(second);

        Database B1 = BerkeleyDB_Box.Get_BerkeleyDB(first + "_BDB", false, sample_name_first);
        Database B2 = BerkeleyDB_Box.Get_BerkeleyDB(second + "_BDB", false, sample_name_second);

        List<String> first_condition_genes = Files
                .lines(Paths.get(first + "_BDB", sample_name_first + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        List<String> second_condition_genes = Files
                .lines(Paths.get(second + "_BDB", sample_name_second + ".txt").toAbsolutePath())
                .collect(Collectors.toList());
        System.out.println("First and second condition are loaded!!! ");
        List<String> intersection_ = new ArrayList<>(first_condition_genes);
        intersection_.retainAll(second_condition_genes);

        BufferedWriter output = new BufferedWriter(
                new FileWriter(Paths.get(folder_loc, "differences_" + window_ + "_s" + slide_ + "_c" + ".txt")
                        .toAbsolutePath().toString(), false));
        List<Result_Window> final_results = Collections.synchronizedList(new ArrayList<>());
        Worker_New worker_class = new Worker_New();
        worker_class.Read_Reference(reference_file);

        while (!intersection_.isEmpty()) {
            List<String> selected_genes = new ArrayList<>();
            //if (intersection_.size()<=10000){selected_genes.addAll(intersection_.subList(0, intersection_.size()));}
            //else selected_genes.addAll(intersection_.subList(0, 10000));
            if (intersection_.size() <= intersection_.size()) {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            } else {
                selected_genes.addAll(intersection_.subList(0, intersection_.size()));
            }
            intersection_.removeAll(selected_genes);
            //System.out.println("Intersection count is:"+intersection_.size());
            //final List<Result_Window> resultssss_=new ArrayList<>();
            IntStream.range(0, selected_genes.size()).parallel().forEach(i -> {
                System.out.println(selected_genes.get(i) + "\tprocessing......");
                String gene_of_interest = selected_genes.get(i);//"ENSG00000142657|PGD";//intersection_.get(6);////"ENSG00000163395|IGFN1";//"ENSG00000270066|SCARNA2";
                int start = worker_class.dic_genes.get(gene_of_interest).start_loc;
                int end = worker_class.dic_genes.get(gene_of_interest).end_loc;

                Map<Integer, Integer> first_ = Collections.EMPTY_MAP;
                try {
                    first_ = BerkeleyDB_Box.Get_Coord_Read(B1, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }

                Map<Integer, Integer> second_ = Collections.EMPTY_MAP;
                try {
                    second_ = BerkeleyDB_Box.Get_Coord_Read(B2, gene_of_interest);
                } catch (IOException | ClassNotFoundException ex) {
                    Logger.getLogger(DiffHunter.class.getName()).log(Level.SEVERE, null, ex);
                }
                List<Window> top_windows_first = worker_class.Get_Top_Windows(window_, first_, slide_);
                List<Window> top_windows_second = worker_class.Get_Top_Windows(window_, second_, slide_);
                //System.out.println("passed for window peak call for gene \t"+selected_genes.get(i));
                // System.out.println("top_window_first_Count\t"+top_windows_first.size());
                // System.out.println("top_window_second_Count\t"+top_windows_second.size());
                if (top_windows_first.isEmpty() && top_windows_second.isEmpty()) {
                    return;
                }

                List<Result_Window> res_temp = new Worker_New().Get_Significant_Windows(gene_of_interest, start,
                        end, top_windows_first, top_windows_second, second_, first_, sample_name_first,
                        sample_name_second, 0.01);
                if (!res_temp.isEmpty()) {
                    final_results.addAll(res_temp);//final_results.addAll(worker_class.Get_Significant_Windows(gene_of_interest, start, end, top_windows_first, top_windows_second, second_, first_, first_condition, second_condition, 0.01));

                } //System.out.println(selected_genes.get(i)+"\tprocessed.");

            });

            /*selected_genes.parallelStream().forEach(i ->
             {
                    
                    
             });*/
            List<Double> pvals = new ArrayList<>();

            for (int i = 0; i < final_results.size(); i++) {
                pvals.add(final_results.get(i).p_value);
            }
            List<Double> qvals = MultipleTestCorrection.benjaminiHochberg(pvals);

            System.out.println("Writing to file...");
            output.append("Gene_Symbol\tContributing_Sample\tStart\tEnd\tOddsRatio\tp_Value\tFDR");
            output.newLine();

            for (int i = 0; i < final_results.size(); i++) {
                Result_Window item = final_results.get(i);
                output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t"
                        + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value
                        + "\t" + qvals.get(i)); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
                output.newLine();
            }

            /* for (Result_Window item : final_results)
             {
            output.append(item.associated_gene_symbol + "\t" + item.contributing_windows + "\t" + item.start_loc + "\t" + item.end_loc + "\t" + item.oddsratio_ + "\t" + item.p_value); //+ "\t" + item.average_other_readcount_cotributing + "\t" + item.average_other_readcount_cotributing + "\t" + item.average_window_readcount_non + "\t" + item.average_other_readcount_non);
            output.newLine();
             }
               */
            final_results.clear();

        }
        output.close();

    }
    System.out.println("Done.");

}

From source file:org.eclipse.lyo.client.oslc.samples.RQMFormSample.java

/**
 * Login to the RQM server and perform some OSLC actions
 * @param args/*from   www.j a v  a 2  s  . co  m*/
 * @throws ParseException 
 */
public static void main(String[] args) throws ParseException {

    Options options = new Options();

    options.addOption("url", true, "url");
    options.addOption("user", true, "user ID");
    options.addOption("password", true, "password");
    options.addOption("project", true, "project area");

    CommandLineParser cliParser = new GnuParser();

    //Parse the command line
    CommandLine cmd = cliParser.parse(options, args);

    if (!validateOptions(cmd)) {
        logger.severe(
                "Syntax:  java <class_name> -url https://<server>:port/<context>/ -user <user> -password <password> -project \"<project_area>\"");
        logger.severe(
                "Example: java RQMFormSample -url https://exmple.com:9443/ccm -user ADMIN -password ADMIN -project \"JKE Banking (Quality Management)\"");
        return;
    }

    String webContextUrl = cmd.getOptionValue("url");
    String user = cmd.getOptionValue("user");
    String passwd = cmd.getOptionValue("password");
    String projectArea = cmd.getOptionValue("project");

    try {

        //STEP 1: Initialize a Jazz rootservices helper and indicate we're looking for the QualityManagement catalog
        //RQM contains both Quality and Change Management providers, so need to look for QM specifically
        JazzRootServicesHelper helper = new JazzRootServicesHelper(webContextUrl, OSLCConstants.OSLC_QM_V2);

        //STEP 2: Create a new Form Auth client with the supplied user/password
        JazzFormAuthClient client = helper.initFormClient(user, passwd);

        //STEP 3: Login in to Jazz Server
        if (client.formLogin() == HttpStatus.SC_OK) {

            //STEP 4: Get the URL of the OSLC QualityManagement catalog
            String catalogUrl = helper.getCatalogUrl();

            //STEP 5: Find the OSLC Service Provider for the project area we want to work with
            String serviceProviderUrl = client.lookupServiceProviderUrl(catalogUrl, projectArea);

            //STEP 6: Get the Query Capabilities URL so that we can run some OSLC queries
            String queryCapability = client.lookupQueryCapability(serviceProviderUrl, OSLCConstants.OSLC_QM_V2,
                    OSLCConstants.QM_TEST_RESULT_QUERY);

            //SCENARIO A: Run a query for all TestResults with a status of passed with OSLC paging of 10 items per
            //page turned on and list the members of the result
            OslcQueryParameters queryParams = new OslcQueryParameters();
            queryParams.setWhere("oslc_qm:status=\"com.ibm.rqm.execution.common.state.passed\"");
            OslcQuery query = new OslcQuery(client, queryCapability, 10, queryParams);

            OslcQueryResult result = query.submit();

            boolean processAsJavaObjects = true;
            processPagedQueryResults(result, client, processAsJavaObjects);

            System.out.println("\n------------------------------\n");

            //SCENARIO B:  Run a query for a specific TestResult selecting only certain 
            //attributes and then print it as raw XML.  Change the dcterms:title below to match a 
            //real TestResult in your RQM project area
            OslcQueryParameters queryParams2 = new OslcQueryParameters();
            queryParams2
                    .setWhere("dcterms:title=\"Consistent_display_of_currency_Firefox_DB2_WAS_Windows_S1\"");
            queryParams2.setSelect(
                    "dcterms:identifier,dcterms:title,dcterms:creator,dcterms:created,oslc_qm:status");
            OslcQuery query2 = new OslcQuery(client, queryCapability, queryParams2);

            OslcQueryResult result2 = query2.submit();
            ClientResponse rawResponse = result2.getRawResponse();
            processRawResponse(rawResponse);
            rawResponse.consumeContent();

            //SCENARIO C:  RQM TestCase creation and update
            TestCase testcase = new TestCase();
            testcase.setTitle("Accessibility verification using a screen reader");
            testcase.setDescription(
                    "This test case uses a screen reader application to ensure that the web browser content fully complies with accessibility standards");
            testcase.addTestsChangeRequest(new Link(new URI("http://cmprovider/changerequest/1"),
                    "Implement accessibility in Pet Store application"));

            //Get the Creation Factory URL for test cases so that we can create a test case
            String testcaseCreation = client.lookupCreationFactory(serviceProviderUrl, OSLCConstants.OSLC_QM_V2,
                    testcase.getRdfTypes()[0].toString());

            //Create the test case
            ClientResponse creationResponse = client.createResource(testcaseCreation, testcase,
                    OslcMediaType.APPLICATION_RDF_XML);
            creationResponse.consumeContent();
            String testcaseLocation = creationResponse.getHeaders().getFirst(HttpHeaders.LOCATION);
            System.out.println("Test Case created a location " + testcaseLocation);

            //Get the test case from the service provider and update its title property 
            testcase = client.getResource(testcaseLocation, OslcMediaType.APPLICATION_RDF_XML)
                    .getEntity(TestCase.class);
            testcase.setTitle(testcase.getTitle() + " (updated)");

            //Create a partial update URL so that only the title will be updated.
            //Assuming (for readability) that the test case URL does not already contain a '?'
            String updateUrl = testcase.getAbout() + "?oslc.properties=dcterms:title";

            //Update the test case at the service provider
            client.updateResource(updateUrl, testcase, OslcMediaType.APPLICATION_RDF_XML).consumeContent();

        }
    } catch (RootServicesException re) {
        logger.log(Level.SEVERE,
                "Unable to access the Jazz rootservices document at: " + webContextUrl + "/rootservices", re);
    } catch (Exception e) {
        logger.log(Level.SEVERE, e.getMessage(), e);
    }

}

From source file:interfaceTisseoWS.ST1.java

/**
 * @param args the command line arguments
 *//*from  w  w  w.  j  a  v a  2s .c  om*/
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(ST1.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(ST1.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(ST1.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(ST1.class.getName()).log(java.util.logging.Level.SEVERE, null, ex);
    }
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        @Override
        public void run() {
            try {
                new ST1().setVisible(true);
            } catch (ParseException ex) {
                Logger.getLogger(ST1.class.getName()).log(Level.SEVERE, null, ex);
            } catch (IOException ex) {
                Logger.getLogger(ST1.class.getName()).log(Level.SEVERE, null, ex);
            } catch (URISyntaxException ex) {
                Logger.getLogger(ST1.class.getName()).log(Level.SEVERE, null, ex);
            }
        }
    });
}

From source file:Visao.grafico.Grafico.java

/**
 * @param args the command line arguments
 *//*from w  w w.  j  ava 2  s  .c  om*/
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(Grafico.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(Grafico.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(Grafico.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(Grafico.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    }
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        public void run() {
            new Grafico().setVisible(true);
        }
    });
}

From source file:gomoku.aneh.MainForm.java

/**
 * @param args the command line arguments
 *///w  w  w  .  ja v a  2 s .  c o m
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(MainForm.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(MainForm.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(MainForm.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(MainForm.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    }
    //</editor-fold>
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        public void run() {
            new MainForm().setVisible(true);
        }
    });
}

From source file:GraphUI.java

/**
 * @param args the command line arguments
 *//*from   w  w  w .  j av a  2 s  . co m*/
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(GraphUI.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(GraphUI.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(GraphUI.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(GraphUI.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    }
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        public void run() {
            new GraphUI().setVisible(true);
        }
    });
}

From source file:com.firmansyah.imam.sewa.kendaraan.FormRegister.java

/**
 * @param args the command line arguments
 *//*from  ww  w  .  j  ava2s  .  c  om*/
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException ex) {
        java.util.logging.Logger.getLogger(FormRegister.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    } catch (InstantiationException ex) {
        java.util.logging.Logger.getLogger(FormRegister.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    } catch (IllegalAccessException ex) {
        java.util.logging.Logger.getLogger(FormRegister.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    } catch (javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(FormRegister.class.getName()).log(java.util.logging.Level.SEVERE,
                null, ex);
    }
    //</editor-fold>

    /* Create and display the form */
    java.awt.EventQueue.invokeLater(new Runnable() {
        public void run() {
            new FormRegister().setVisible(true);
        }
    });
}

From source file:javadepchecker.Main.java

/**
 * @param args the command line arguments
 *///from   w  w  w.  j  a  va  2 s. com
public static void main(String[] args) throws IOException {
    int exit = 0;
    try {
        CommandLineParser parser = new PosixParser();
        Options options = new Options();
        options.addOption("h", "help", false, "print help");
        options.addOption("i", "image", true, "image directory");
        options.addOption("v", "verbose", false, "print verbose output");
        CommandLine line = parser.parse(options, args);
        String[] files = line.getArgs();
        if (line.hasOption("h") || files.length == 0) {
            HelpFormatter h = new HelpFormatter();
            h.printHelp("java-dep-check [-i <image>] <package.env>+", options);
        } else {
            image = line.getOptionValue("i", "");

            for (String arg : files) {
                if (line.hasOption('v')) {
                    System.out.println("Checking " + arg);
                }
                if (!checkPkg(new File(arg))) {
                    exit = 1;
                }
            }
        }
    } catch (ParseException ex) {
        Logger.getLogger(Main.class.getName()).log(Level.SEVERE, null, ex);
    }
    System.exit(exit);
}

From source file:jsonbrowse.JsonBrowse.java

/**
 * @param args the command line arguments
 *//*from  ww  w  .  java2s .c o m*/
public static void main(String args[]) {
    /* Set the Nimbus look and feel */
    //<editor-fold defaultstate="collapsed" desc=" Look and feel setting code (optional) ">
    /* If Nimbus (introduced in Java SE 6) is not available, stay with the default look and feel.
     * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
     */
    try {
        for (javax.swing.UIManager.LookAndFeelInfo info : javax.swing.UIManager.getInstalledLookAndFeels()) {
            if ("Nimbus".equals(info.getName())) {
                javax.swing.UIManager.setLookAndFeel(info.getClassName());
                break;
            }
        }
    } catch (ClassNotFoundException | InstantiationException | IllegalAccessException
            | javax.swing.UnsupportedLookAndFeelException ex) {
        java.util.logging.Logger.getLogger(JsonBrowse.class.getName()).log(java.util.logging.Level.SEVERE, null,
                ex);
    }
    //</editor-fold>

    String fileName;

    // Get name of JSON file
    Path jsonFilePath;
    if (args.length < 1) {

        JFileChooser fc = new JFileChooser(System.getProperty("user.dir"));
        fc.setDialogTitle("Select JSON file...");
        fc.setFileFilter(new FileNameExtensionFilter("JSON files (*.json/*.txt)", "json", "txt"));
        if ((fc.showOpenDialog(null) == JFileChooser.APPROVE_OPTION)) {
            jsonFilePath = fc.getSelectedFile().toPath().toAbsolutePath();
        } else {
            return;
        }
    } else {
        Path path = Paths.get(args[0]);
        if (!path.isAbsolute())
            jsonFilePath = Paths.get(System.getProperty("user.dir")).resolve(path);
        else
            jsonFilePath = path;
    }

    // Run app

    try {
        JsonBrowse app = new JsonBrowse(jsonFilePath);
        app.setVisible(true);
    } catch (FileNotFoundException ex) {
        System.out.println("Input file '" + jsonFilePath + "' not found.");
        System.exit(1);
    } catch (IOException ex) {
        System.out.println("Error reading from file '" + jsonFilePath + "'.");
        System.exit(1);
    } catch (InterruptedException ex) {
        Logger.getLogger(JsonBrowse.class.getName()).log(Level.SEVERE, null, ex);
    }

}

From source file:com.pawandubey.griffin.Griffin.java

/**
 * @param args the command line arguments
 * @throws java.io.IOException the exception
 * @throws java.lang.InterruptedException the exception
 *///w w w.  j  a  v a2  s.co  m
public static void main(String[] args) throws IOException, InterruptedException {
    try {
        Griffin griffin = new Griffin();

        CmdLineParser parser = new CmdLineParser(griffin, ParserProperties.defaults().withUsageWidth(120));
        parser.parseArgument(args);

        if (griffin.help || griffin.version || args.length == 0) {
            griffin.printHelpMessage();
            parser.printUsage(System.out);
        } else {
            griffin.commands.execute();
        }
    } catch (CmdLineException ex) {
        Logger.getLogger(Griffin.class.getName()).log(Level.SEVERE, null, ex);
    }
}