Examples with HiddenMarkovModel cz1.hmm.model.HiddenMarkovModel used on opensource projects

Example 1 with HiddenMarkovModel

use of cz1.hmm.model.HiddenMarkovModel in project polyGembler by c-zhou.

the class Haplotyper method run.

@Override
public void run() {
    // TODO Auto-generated method stub
    myLogger.info("Random seed - " + Constants.seed);
    DataEntry[] de = start_pos == null ? DataCollection.readDataEntry(in_zip, scaff) : DataCollection.readDataEntry(in_zip, scaff, start_pos, end_pos);
    // DataEntry[] de = DataCollection.readDataEntry(in_zip, Constants._ploidy_H);
    final HiddenMarkovModel hmm = vbt ? new HiddenMarkovModelVBT(de, seperation, reverse, trainExp, field, founder_hap_coeff) : // new HiddenMarkovModelRST(de, seperation, reverse, trainExp, field, resampling):
    (hmm_file == null ? new HiddenMarkovModelBWT(de, seperation, reverse, trainExp, field, founder_hap_coeff) : new HiddenMarkovModelBWT(de, seperation, reverse, trainExp, field, founder_hap_coeff, hmm_file));
    if (Constants.plot()) {
        Runnable run = new Runnable() {

            public void run() {
                try {
                    hmmf = new HMMFrame();
                    hmmf.clearTabs();
                    if (Constants.showHMM)
                        hmmp = hmmf.addHMMTab(hmm, hmm.de(), new File(out_prefix));
                } catch (Exception e) {
                    Thread t = Thread.currentThread();
                    t.getUncaughtExceptionHandler().uncaughtException(t, e);
                    e.printStackTrace();
                }
            }
        };
        Thread th = new Thread(run);
        th.run();
    }
    if (Constants.plot()) {
        hmmf.pack();
        hmmf.setVisible(true);
    }
    double ll, ll0 = hmm.loglik();
    for (int i = 0; i < max_iter; i++) {
        hmm.train();
        if (Constants.plot())
            hmmp.update();
        ll = hmm.loglik();
        myLogger.info("----------loglik " + ll);
        if (ll < ll0) {
            // throw new RuntimeException("Fatal error!!!");
            myLogger.info("LOGLIK DECREASED!!!");
            // break;
            ll0 = ll;
            continue;
        }
        if (ll0 != Double.NEGATIVE_INFINITY && Math.abs((ll - ll0) / ll0) < Constants.minImprov)
            break;
        ll0 = ll;
    }
    if (Constants.printPlots()) {
        try {
            float width = hmmf.jframe.getSize().width, height = hmmf.jframe.getSize().height;
            Document document = new Document(new Rectangle(width, height));
            PdfWriter writer = PdfWriter.getInstance(document, new FileOutputStream(plot_pdf));
            document.open();
            PdfContentByte canvas = writer.getDirectContent();
            PdfTemplate template = canvas.createTemplate(width, height);
            Graphics2D g2d = new PdfGraphics2D(template, width, height);
            hmmf.jframe.paint(g2d);
            g2d.dispose();
            canvas.addTemplate(template, 0, 0);
            document.close();
        } catch (FileNotFoundException | DocumentException e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    String scaff_str = scaff[0] + (start_pos == null || start_pos[0] == Integer.MIN_VALUE ? "" : "_" + start_pos[0]) + (end_pos == null || end_pos[0] == Integer.MAX_VALUE ? "" : "_" + end_pos[0]);
    for (int i = 1; i < scaff.length; i++) {
        if (scaff_str.length() + scaff[i].length() + 32 <= Constants.MAX_FILE_ID_LENGTH)
            scaff_str += Constants.scaff_collapsed_str + scaff[i] + (start_pos == null || start_pos[i] == Integer.MIN_VALUE ? "" : "_" + start_pos[i]) + (end_pos == null || end_pos[i] == Integer.MAX_VALUE ? "" : "_" + end_pos[i]);
        else {
            scaff_str += Constants.scaff_collapsed_str + "etc" + scaff.length;
            break;
        }
    }
    hmm.write(out_prefix, expr_id, scaff_str, resampling);
}

Example 2 with HiddenMarkovModel

use of cz1.hmm.model.HiddenMarkovModel in project polyGembler by c-zhou.

the class Resampler method run.

@Override
public void run() {
    // TODO Auto-generated method stub
    myLogger.info("Random seed - " + Constants.seed);
    DataEntry[] de = start_pos == null ? DataCollection.readDataEntry(in_zip, scaff) : DataCollection.readDataEntry(in_zip, scaff, start_pos, end_pos);
    // DataEntry[] de = DataCollection.readDataEntry(in_zip, Constants._ploidy_H);
    final HiddenMarkovModel hmm = vbt ? new HiddenMarkovModelVBT(de, seperation, reverse, trainExp, field) : (hmm_file == null ? new HiddenMarkovModelBWT(de, seperation, reverse, trainExp, field) : new HiddenMarkovModelBWT(de, seperation, reverse, trainExp, field, hmm_file));
    double ll, ll0 = hmm.loglik();
    String scaff_str = scaff[0] + (start_pos == null || start_pos[0] == Integer.MIN_VALUE ? "" : "_" + start_pos[0]) + (end_pos == null || end_pos[0] == Integer.MAX_VALUE ? "" : "_" + end_pos[0]);
    for (int i = 1; i < scaff.length; i++) {
        if (scaff_str.length() + scaff[i].length() + 32 <= Constants.MAX_FILE_ID_LENGTH)
            scaff_str += Constants.scaff_collapsed_str + scaff[i] + (start_pos == null || start_pos[i] == Integer.MIN_VALUE ? "" : "_" + start_pos[i]) + (end_pos == null || end_pos[i] == Integer.MAX_VALUE ? "" : "_" + end_pos[i]);
        else {
            scaff_str += Constants.scaff_collapsed_str + "etc" + scaff.length;
            break;
        }
    }
    hmm.write(out_prefix, expr_id, scaff_str, resampling);
}