Examples with DataEntry cz1.hmm.data.DataEntry used on opensource projects

Example 1 with DataEntry

use of cz1.hmm.data.DataEntry 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 DataEntry

use of cz1.hmm.data.DataEntry 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);
}

Example 3 with DataEntry

use of cz1.hmm.data.DataEntry in project polyGembler by c-zhou.

the class VCFResampling method run.

@Override
public void run() {
    // TODO Auto-generated method stub
    FullSiblings fullSib = new FullSiblings(this.ploidy);
    final List<String> contigs = DataCollection.getContigList(data_in);
    final List<String> samples = DataCollection.getSampleList(data_in);
    int[] founder_index = new int[2];
    Arrays.fill(founder_index, -1);
    for (int i = 0; i != samples.size(); i++) {
        if (samples.get(i).equals(founder_haps[0]))
            founder_index[0] = i;
        else if (samples.get(i).equals(founder_haps[1]))
            founder_index[1] = i;
    }
    for (String contig : contigs) {
        DataEntry data = DataCollection.readDataEntry(data_in, new String[] { contig })[0];
        double[] position = data.getPosition();
        int no = position.length;
        if (no <= min_snp) {
            int[] out = new int[no];
            for (int i = 0; i != no; i++) out[i] = i;
            snp_out.put(contig, out);
            continue;
        }
        double[] segs = fullSib.calcSegs(data, founder_index);
        int l = 0;
        final Map<Integer, List<Integer>> bins = new HashMap<Integer, List<Integer>>();
        for (int i = 0; i != no; i++) {
            while ((l + 1) * window_size < position[i]) l++;
            if (!bins.containsKey(l))
                bins.put(l, new ArrayList<Integer>());
            bins.get(l).add(i);
        }
        List<Integer> selected = new ArrayList<Integer>();
        final Map<Integer, Iterator<Integer>> bins_it = new HashMap<Integer, Iterator<Integer>>();
        for (Map.Entry<Integer, List<Integer>> entry : bins.entrySet()) {
            Collections.sort(entry.getValue(), new Comparator<Integer>() {

                @Override
                public int compare(Integer i0, Integer i1) {
                    // TODO Auto-generated method stub
                    return Double.compare(segs[i0], segs[i1]);
                }
            });
            Iterator<Integer> it = entry.getValue().iterator();
            selected.add(it.next());
            if (it.hasNext())
                bins_it.put(entry.getKey(), it);
        }
        while (selected.size() < min_snp) {
            List<Integer> candidates = new ArrayList<Integer>();
            Set<Integer> key_rm = new HashSet<Integer>();
            for (Map.Entry<Integer, Iterator<Integer>> entry : bins_it.entrySet()) {
                Iterator<Integer> it = entry.getValue();
                candidates.add(it.next());
                if (!it.hasNext())
                    key_rm.add(entry.getKey());
            }
            if (candidates.size() == 0)
                break;
            for (Integer i : key_rm) bins_it.remove(i);
            Collections.sort(candidates, new Comparator<Integer>() {

                @Override
                public int compare(Integer i0, Integer i1) {
                    // TODO Auto-generated method stub
                    return Double.compare(segs[i0], segs[i1]);
                }
            });
            for (Integer i : candidates) {
                if (selected.size() < min_snp)
                    selected.add(i);
                else
                    break;
            }
        }
        Collections.sort(selected);
        snp_out.put(contig, ArrayUtils.toPrimitive(selected.toArray(new Integer[selected.size()])));
    }
    int N = 0;
    for (Map.Entry<String, int[]> entry : snp_out.entrySet()) N += entry.getValue().length;
    System.err.println(N + " SNPs reserved.");
    write();
}