Examples with ProbeList uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList used on opensource projects

Example 6 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class EnrichmentNormalisationQuantitation method getOptionsPanel.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Quantitation.Quantitation#getOptionsPanel(uk.ac.babraham.SeqMonk.SeqMonkApplication)
	 */
public JPanel getOptionsPanel() {
    if (optionPanel != null) {
        // We've done this already
        return optionPanel;
    }
    optionPanel = new JPanel();
    optionPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 1;
    gbc.weightx = 0.5;
    gbc.weighty = 0.1;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionPanel.add(new JLabel("Lower Percentile"), gbc);
    lowerPercentileField = new JTextField("" + lowerPercentile);
    lowerPercentileField.addKeyListener(new NumberKeyListener(true, false));
    gbc.gridx++;
    optionPanel.add(lowerPercentileField, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    optionPanel.add(new JLabel("Upper Percentile"), gbc);
    gbc.gridx = 2;
    upperPercentileField = new JTextField("" + upperPercentile);
    upperPercentileField.addKeyListener(new NumberKeyListener(true, false));
    optionPanel.add(upperPercentileField, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    optionPanel.add(new JLabel("Ignore unquantitated probes"), gbc);
    ignoreUnquantitatedBox = new JCheckBox("", true);
    gbc.gridx++;
    optionPanel.add(ignoreUnquantitatedBox, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    optionPanel.add(new JLabel("Calculate from probe list"), gbc);
    ProbeList[] currentLists = application.dataCollection().probeSet().getAllProbeLists();
    calculateFromProbeList = new JComboBox(currentLists);
    calculateFromProbeList.setPrototypeDisplayValue("No longer than this please");
    for (int i = 0; i < currentLists.length; i++) {
        if (currentLists[i] == application.dataCollection().probeSet().getActiveList()) {
            calculateFromProbeList.setSelectedIndex(i);
        }
    }
    gbc.gridx++;
    optionPanel.add(calculateFromProbeList, gbc);
    return optionPanel;
}

Example 7 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class HiCPCADomainQuantitation method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    // We're going to go through the probes one chromosome at a time so we
    // can reduce the complexity we have to deal with
    Chromosome[] chromosomes = application.dataCollection().genome().getAllChromosomes();
    for (int c = 0; c < chromosomes.length; c++) {
        if (cancel) {
            progressCancelled();
            return;
        }
        currentChromosome = chromosomes[c];
        Probe[] probes = application.dataCollection().probeSet().getProbesForChromosome(chromosomes[c]);
        if (probes.length < 5) {
            progressWarningReceived(new SeqMonkException("Too few probes on chromosome " + currentChromosome.name() + " - assigning zero to everything"));
            // It's not worth trying to find domains
            for (int d = 0; d < data.length; d++) {
                for (int p = 0; p < probes.length; p++) {
                    ((DataStore) data[d]).setValueForProbe(probes[p], 0f);
                }
            }
            continue;
        }
        ProbeList thisChrProbes = new ProbeList(application.dataCollection().probeSet(), chromosomes[c].name(), "", null);
        for (int p = 0; p < probes.length; p++) {
            thisChrProbes.addProbe(probes[p], 0f);
        }
        for (int d = 0; d < data.length; d++) {
            if (cancel) {
                progressCancelled();
                return;
            }
            currentStore = data[d];
            current = (d * chromosomes.length) + c;
            total = chromosomes.length * data.length;
            progressUpdated("Processing chromosome " + chromosomes[c].name() + " for " + data[d].name(), current, total);
            HeatmapMatrix matrix = new HeatmapMatrix(data[d], new ProbeList[] { thisChrProbes }, application.dataCollection().genome(), optionsPanel.minDistance(), optionsPanel.maxDistance(), optionsPanel.minStrength(), optionsPanel.maxSignificance(), optionsPanel.minAbsolute(), optionsPanel.correctLinkage());
            matrix.addProgressListener(this);
            wait = true;
            matrix.startCalculating();
            while (wait) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException e) {
                }
            }
            if (cancel) {
                progressCancelled();
                return;
            }
            if (matrix.filteredInteractions().length < 10) {
                progressWarningReceived(new SeqMonkException("Too few interactions on chromosome " + currentChromosome.name() + " for " + data[d].name() + " - assigning zero to everything"));
                // not going to get a sensible answer anyway.
                for (int p = 0; p < probes.length; p++) {
                    ((DataStore) data[d]).setValueForProbe(probes[p], 0f);
                }
                continue;
            }
            InteractionClusterMatrix clusterMatrix = new InteractionClusterMatrix(matrix.filteredInteractions(), probes.length);
            clusterMatrix.addListener(this);
            wait = true;
            clusterMatrix.startCorrelating();
            while (wait) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException e) {
                }
            }
            float[][] correlationMatrix = clusterMatrix.correlationMatix();
            // Annoyingly the PCA needs a double [][]
            double[][] correlationMatrixDouble = new double[correlationMatrix.length][];
            for (int i = 0; i < correlationMatrix.length; i++) {
                double[] db = new double[correlationMatrix[i].length];
                for (int j = 0; j < db.length; j++) {
                    db[j] = correlationMatrix[i][j];
                }
                correlationMatrixDouble[i] = db;
            }
            // Now we can calculate the PCA values from the correlation matrix
            PCA pca = new PCA(correlationMatrixDouble);
            pca.addProgressListener(this);
            wait = true;
            pca.startCalculating();
            while (wait) {
                try {
                    Thread.sleep(100);
                } catch (InterruptedException e) {
                }
            }
            double[] extractedEigenValues = pca.extractedEigenValues();
            // for these probes
            for (int p = 0; p < probes.length; p++) {
                ((DataStore) data[d]).setValueForProbe(probes[p], (float) extractedEigenValues[p]);
            }
        }
        thisChrProbes.delete();
    }
    quantitatonComplete();
}

Example 8 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class PercentileNormalisationQuantitation method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    if (!isReady()) {
        progressExceptionReceived(new SeqMonkException("Options weren't set correctly"));
    }
    Probe[] allProbes = application.dataCollection().probeSet().getAllProbes();
    Probe[] calculateProbes = ((ProbeList) calculateFromProbeList.getSelectedItem()).getAllProbes();
    float[][] percentileValues = new float[data.length][];
    float[] minValues = new float[data.length];
    // Work out the value at the appropriate percentile
    for (int d = 0; d < data.length; d++) {
        // Otherwise we'll calculate for each percentage (0-100)
        if (autoPercentileBox.isSelected()) {
            percentileValues[d] = new float[101];
        } else {
            percentileValues[d] = new float[1];
        }
        progressUpdated("Calculating correction for " + data[d].name(), d, data.length);
        float[] theseValues = new float[calculateProbes.length];
        for (int p = 0; p < calculateProbes.length; p++) {
            try {
                theseValues[p] = data[d].getValueForProbe(calculateProbes[p]);
            } catch (SeqMonkException e) {
                progressExceptionReceived(e);
            }
        }
        Arrays.sort(theseValues);
        if (autoPercentileBox.isSelected()) {
            for (int i = 0; i <= 100; i++) {
                // percentileValues[d][i] = theseValues[(int)((theseValues.length-1)*i)/100];
                percentileValues[d][i] = getPercentileValue(theseValues, i);
            }
        } else {
            // percentileValues[d][0] = theseValues[(int)((theseValues.length-1)*percentile)/100];
            percentileValues[d][0] = getPercentileValue(theseValues, percentile);
        }
        minValues[d] = theseValues[0];
    }
    float[] maxPercentiles = new float[percentileValues[0].length];
    for (int i = 0; i < percentileValues.length; i++) {
        for (int j = 0; j < maxPercentiles.length; j++) {
            if (i == 0 || percentileValues[i][j] > maxPercentiles[j]) {
                maxPercentiles[j] = percentileValues[i][j];
            }
        }
    }
    for (int d = 0; d < data.length; d++) {
        // See if we need to quit
        if (cancel) {
            progressCancelled();
            return;
        }
        progressUpdated(d, data.length);
        // Get the correction value
        float[] correctionFactors = new float[percentileValues[0].length];
        if (correctionAction == ADD) {
            for (int i = 0; i < correctionFactors.length; i++) {
                correctionFactors[i] = maxPercentiles[i] - percentileValues[d][i];
            }
        } else if (correctionAction == MULTIPLY) {
            for (int i = 0; i < correctionFactors.length; i++) {
                correctionFactors[i] = (maxPercentiles[i] - minValues[d]) / (percentileValues[d][i] - minValues[d]);
            }
        }
        // Now we work out the correction factor we're actually going to use
        float correctionFactor = SimpleStats.median(correctionFactors);
        // Apply the correction to all probes
        try {
            for (int p = 0; p < allProbes.length; p++) {
                // See if we need to quit
                if (cancel) {
                    progressCancelled();
                    return;
                }
                if (correctionAction == ADD) {
                    data[d].setValueForProbe(allProbes[p], data[d].getValueForProbe(allProbes[p]) + correctionFactor);
                } else if (correctionAction == MULTIPLY) {
                    data[d].setValueForProbe(allProbes[p], minValues[d] + ((data[d].getValueForProbe(allProbes[p]) - minValues[d]) * correctionFactor));
                }
            }
        } catch (SeqMonkException e) {
            progressExceptionReceived(e);
        }
    }
    quantitatonComplete();
}

Example 9 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class PercentileNormalisationQuantitation method getOptionsPanel.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.Quantitation.Quantitation#getOptionsPanel(uk.ac.babraham.SeqMonk.SeqMonkApplication)
	 */
public JPanel getOptionsPanel() {
    if (optionPanel != null) {
        // We've done this already
        return optionPanel;
    }
    optionPanel = new JPanel();
    optionPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 1;
    gbc.weightx = 0.5;
    gbc.weighty = 0.1;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionPanel.add(new JLabel("Method of correction"), gbc);
    gbc.gridx = 2;
    correctionActions = new JComboBox(new String[] { "Add", "Multiply" });
    optionPanel.add(correctionActions, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    optionPanel.add(new JLabel("Percentile"), gbc);
    JPanel percentilePanel = new JPanel();
    percentilePanel.setLayout(new BorderLayout());
    autoPercentileBox = new JCheckBox("Auto", false);
    percentilePanel.add(autoPercentileBox, BorderLayout.WEST);
    percentileField = new JTextField("" + percentile);
    percentileField.addKeyListener(new NumberKeyListener(true, false));
    percentilePanel.add(percentileField, BorderLayout.CENTER);
    autoPercentileBox.addActionListener(new ActionListener() {

        public void actionPerformed(ActionEvent e) {
            percentileField.setEnabled(!autoPercentileBox.isSelected());
        }
    });
    gbc.gridx++;
    optionPanel.add(percentilePanel, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    optionPanel.add(new JLabel("Ignore unquantitated probes"), gbc);
    ignoreUnquantitatedBox = new JCheckBox("", true);
    gbc.gridx++;
    optionPanel.add(ignoreUnquantitatedBox, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    optionPanel.add(new JLabel("Calculate from probe list"), gbc);
    ProbeList[] currentLists = application.dataCollection().probeSet().getAllProbeLists();
    calculateFromProbeList = new JComboBox(currentLists);
    calculateFromProbeList.setPrototypeDisplayValue("No longer than this please");
    for (int i = 0; i < currentLists.length; i++) {
        if (currentLists[i] == application.dataCollection().probeSet().getActiveList()) {
            calculateFromProbeList.setSelectedIndex(i);
        }
    }
    gbc.gridx++;
    optionPanel.add(calculateFromProbeList, gbc);
    return optionPanel;
}

Example 10 with ProbeList

use of uk.ac.babraham.SeqMonk.DataTypes.Probes.ProbeList in project SeqMonk by s-andrews.

the class DeduplicationProbeGenerator method getOptionsPanel.

/* (non-Javadoc)
	 * @see uk.ac.babraham.SeqMonk.ProbeGenerators.ProbeGenerator#getOptionsPanel(uk.ac.babraham.SeqMonk.SeqMonkApplication)
	 */
public JPanel getOptionsPanel() {
    if (optionPanel != null) {
        // We've done this already
        return optionPanel;
    }
    optionPanel = new JPanel();
    optionPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 1;
    gbc.weightx = 0.5;
    gbc.weighty = 0.5;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionPanel.add(new JLabel("Starting Probe List"), gbc);
    gbc.gridx = 2;
    if (collection.probeSet() == null) {
        probeListBox = new JComboBox(new ProbeList[0]);
    } else {
        probeListBox = new JComboBox(collection.probeSet().getAllProbeLists());
    }
    probeListBox.setPrototypeDisplayValue("No longer than this please");
    probeListBox.addItemListener(this);
    optionPanel.add(probeListBox, gbc);
    gbc.gridy++;
    gbc.gridx = 1;
    optionPanel.add(new JLabel("Merge probes separated by less than (bp)"), gbc);
    gbc.gridx = 2;
    maxDistanceField = new JTextField("0");
    maxDistanceField.addKeyListener(new NumberKeyListener(false, false));
    optionPanel.add(maxDistanceField, gbc);
    gbc.gridy++;
    gbc.gridx = 1;
    optionPanel.add(new JLabel("Merge strands separately"), gbc);
    gbc.gridx = 2;
    separateStrandsBox = new JCheckBox("", true);
    optionPanel.add(separateStrandsBox, gbc);
    return optionPanel;
}