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

Example 41 with ProbeList

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

the class SubsetNormalisationQuantitation 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("Summation Method"), gbc);
    gbc.gridx = 2;
    summationActions = new JComboBox(new String[] { "Mean", "Sum" });
    optionPanel.add(summationActions, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    optionPanel.add(new JLabel("Target Value"), gbc);
    gbc.gridx = 2;
    targetActions = new JComboBox(new String[] { "Largest", "1" });
    optionPanel.add(targetActions, gbc);
    Vector<DataStore> quantitatedStores = new Vector<DataStore>();
    DataSet[] sets = application.dataCollection().getAllDataSets();
    for (int s = 0; s < sets.length; s++) {
        if (sets[s].isQuantitated()) {
            quantitatedStores.add(sets[s]);
        }
    }
    DataGroup[] groups = application.dataCollection().getAllDataGroups();
    for (int g = 0; g < groups.length; g++) {
        if (groups[g].isQuantitated()) {
            quantitatedStores.add(groups[g]);
        }
    }
    data = quantitatedStores.toArray(new DataStore[0]);
    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 42 with ProbeList

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

the class SubsetNormalisationQuantitation 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[] summedValues = new float[data.length];
    // since we need that whether or not they're taking the mean.
    for (int d = 0; d < data.length; d++) {
        progressUpdated("Calculating correction for " + data[d].name(), d, data.length);
        for (int p = 0; p < calculateProbes.length; p++) {
            try {
                summedValues[d] += data[d].getValueForProbe(calculateProbes[p]);
            } catch (SeqMonkException e) {
                progressExceptionReceived(e);
            }
        }
    }
    if (summationAction == VALUE_MEAN) {
        for (int i = 0; i < summedValues.length; i++) {
            summedValues[i] /= calculateProbes.length;
        }
    }
    float targetValue = 1;
    if (targetAction == TARGET_LARGEST) {
        targetValue = summedValues[0];
        for (int i = 1; i < summedValues.length; i++) {
            if (summedValues[i] > targetValue)
                targetValue = summedValues[i];
        }
    }
    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 correctionFactor = 1;
        if (correctionAction == ADD) {
            correctionFactor = targetValue - summedValues[d];
        } else if (correctionAction == MULTIPLY) {
            correctionFactor = targetValue / summedValues[d];
        }
        System.err.println("For " + data[d].name() + " correction factor is " + correctionFactor);
        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], data[d].getValueForProbe(allProbes[p]) * correctionFactor);
                }
            }
        } catch (SeqMonkException e) {
            progressExceptionReceived(e);
        }
    }
    quantitatonComplete();
}

Example 43 with ProbeList

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

the class EnrichmentNormalisationQuantitation 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[] lowerPercentileValues = new float[data.length];
    float[] upperPercentileValues = new float[data.length];
    // Work out the value at the appropriate percentile
    for (int d = 0; d < data.length; d++) {
        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);
        lowerPercentileValues[d] = getPercentileValue(theseValues, lowerPercentile);
        upperPercentileValues[d] = getPercentileValue(theseValues, upperPercentile);
        System.err.println("Lower percentile for " + data[d].name() + " is " + lowerPercentileValues[d] + " from " + theseValues.length + " values");
    }
    float lowerMedian = SimpleStats.median(Arrays.copyOf(lowerPercentileValues, lowerPercentileValues.length));
    float upperMedian = SimpleStats.median(Arrays.copyOf(upperPercentileValues, upperPercentileValues.length));
    for (int d = 0; d < data.length; d++) {
        System.err.println("Looking at " + data[d].name());
        // See if we need to quit
        if (cancel) {
            progressCancelled();
            return;
        }
        progressUpdated(d, data.length);
        // Now we work out the correction factor we're actually going to use
        float lowerCorrectionFactor = lowerMedian - lowerPercentileValues[d];
        float upperCorrectionFactor = ((upperPercentileValues[d] + lowerCorrectionFactor) - lowerMedian) / (upperMedian - lowerMedian);
        System.err.println("Lower percentile = " + lowerPercentileValues[d]);
        System.err.println("Upper percentile = " + upperPercentileValues[d]);
        System.err.println("Lower median = " + lowerMedian);
        System.err.println("Upper median = " + upperMedian);
        System.err.println("Lower correction = " + lowerCorrectionFactor);
        System.err.println("Upper correction = " + upperCorrectionFactor);
        System.err.println("\n\n");
        // 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;
                }
                float probeValue = data[d].getValueForProbe(allProbes[p]);
                probeValue += lowerCorrectionFactor;
                probeValue -= lowerMedian;
                probeValue /= upperCorrectionFactor;
                probeValue += lowerMedian;
                data[d].setValueForProbe(allProbes[p], probeValue);
            }
        } catch (SeqMonkException e) {
            progressExceptionReceived(e);
        }
    }
    quantitatonComplete();
}

Example 44 with ProbeList

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

the class FourCEnrichmentQuantitation method run.

/* (non-Javadoc)
	 * @see java.lang.Runnable#run()
	 */
public void run() {
    // Start off by finding the right HiC data for each 4C dataset
    HiCDataStore[] parentHiC = new HiCDataStore[data.length];
    Probe[] parentProbes = new Probe[data.length];
    ProbeList[] significantLists = new ProbeList[data.length];
    for (int d = 0; d < data.length; d++) {
        String filename = data[d].fileName();
        filename = filename.replaceAll("HiC other end of ", "");
        filename = filename.replaceAll(" for region.*", "");
        System.err.println("Looking for HiC match to " + filename);
        for (int h = 0; h < hiCData.length; h++) {
            if (((DataStore) hiCData[h]).name().equals(filename)) {
                parentHiC[d] = hiCData[h];
            }
        }
        if (parentHiC[d] == null) {
            progressWarningReceived(new SeqMonkException("Failed to find HiC dataset '" + filename + "' for 4C dataset " + data[d].name()));
            continue;
        }
        significantLists[d] = new ProbeList(application.dataCollection().probeSet(), "4C p<0.05 " + data[d].name(), "4C pipeline significance < 0.05", "P-value");
        // Also make up a probe to represent the region from which
        // the dataset was made
        filename = data[d].fileName();
        filename = filename.replaceAll("^.*for region ", "");
        String[] locationSections = filename.split("[-:]");
        if (locationSections.length != 3) {
            progressWarningReceived(new SeqMonkException("Couldn't extract location from " + filename));
            continue;
        }
        try {
            parentProbes[d] = new Probe(application.dataCollection().genome().getChromosome(locationSections[0]).chromosome(), Integer.parseInt(locationSections[1]), Integer.parseInt(locationSections[2]));
        } catch (Exception e) {
            progressExceptionReceived(e);
            return;
        }
    }
    // Make strength calculators for each HiC set
    HiCInteractionStrengthCalculator[] strengthCalculators = new HiCInteractionStrengthCalculator[parentHiC.length];
    for (int i = 0; i < parentHiC.length; i++) {
        strengthCalculators[i] = new HiCInteractionStrengthCalculator(parentHiC[i], true);
    }
    // Get the cis/trans counts for the parent probes
    int[] parentProbeCisCounts = new int[parentHiC.length];
    int[] parentProbeTransCounts = new int[parentHiC.length];
    for (int p = 0; p < parentHiC.length; p++) {
        if (parentHiC[p] == null)
            continue;
        HiCHitCollection hits = parentHiC[p].getHiCReadsForProbe(parentProbes[p]);
        String[] chrNames = hits.getChromosomeNamesWithHits();
        for (int c = 0; c < chrNames.length; c++) {
            if (chrNames[c].equals(hits.getSourceChromosomeName())) {
                parentProbeCisCounts[p] = hits.getSourcePositionsForChromosome(chrNames[c]).length;
            } else {
                parentProbeTransCounts[p] += hits.getSourcePositionsForChromosome(chrNames[c]).length;
            }
        }
    }
    Probe[] probes = application.dataCollection().probeSet().getAllProbes();
    for (int p = 0; p < probes.length; p++) {
        // See if we need to quit
        if (cancel) {
            progressCancelled();
            return;
        }
        progressUpdated(p, probes.length);
        for (int d = 0; d < data.length; d++) {
            if (parentHiC[d] == null)
                continue;
            int thisProbeCisCount = 0;
            int thisProbeTransCount = 0;
            HiCHitCollection hiCHits = parentHiC[d].getHiCReadsForProbe(probes[p]);
            String[] chrNames = hiCHits.getChromosomeNamesWithHits();
            for (int c = 0; c < chrNames.length; c++) {
                if (chrNames[c].equals(hiCHits.getSourceChromosomeName())) {
                    thisProbeCisCount = hiCHits.getSourcePositionsForChromosome(chrNames[c]).length;
                } else {
                    thisProbeTransCount += hiCHits.getSourcePositionsForChromosome(chrNames[c]).length;
                }
            }
            strengthCalculators[d].calculateInteraction(data[d].getReadsForProbe(probes[p]).length, thisProbeCisCount, thisProbeTransCount, parentProbeCisCounts[d], parentProbeTransCounts[d], probes[p], parentProbes[d]);
            float obsExp = (float) strengthCalculators[d].obsExp();
            data[d].setValueForProbe(probes[p], obsExp);
            float pValue = (float) strengthCalculators[d].rawPValue() * probes.length;
            if (pValue < 0.05) {
                significantLists[d].addProbe(probes[p], pValue);
            }
        }
    }
    quantitatonComplete();
}

Example 45 with ProbeList

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

the class ShuffleListProbeGenerator 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;
    }
    ProbeList currentActiveList = null;
    if (collection.probeSet() != null) {
        currentLists = collection.probeSet().getAllProbeLists();
        currentActiveList = collection.probeSet().getActiveList();
    } else {
        currentLists = new ProbeList[0];
    }
    optionPanel = new JPanel();
    optionPanel.setLayout(new GridBagLayout());
    GridBagConstraints gbc = new GridBagConstraints();
    gbc.gridx = 1;
    gbc.gridy = 1;
    gbc.weightx = 0.1;
    gbc.weighty = 0.5;
    gbc.fill = GridBagConstraints.HORIZONTAL;
    optionPanel.add(new JLabel("Select List"), gbc);
    gbc.gridx++;
    gbc.weightx = 0.9;
    selectedListBox = new JComboBox(currentLists);
    selectedListBox.setPrototypeDisplayValue("No longer than this please");
    for (int i = 0; i < currentLists.length; i++) {
        if (currentLists[i] == currentActiveList) {
            selectedListBox.setSelectedIndex(i);
        }
    }
    selectedListBox.addItemListener(new ItemListener() {

        public void itemStateChanged(ItemEvent e) {
            isReady();
        }
    });
    optionPanel.add(selectedListBox, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    gbc.weightx = 0.1;
    optionPanel.add(new JLabel("Maintain Chromosomal Distribution"), gbc);
    gbc.gridx++;
    gbc.weightx = 0.9;
    keepChromosomalDistributionBox = new JCheckBox("", true);
    optionPanel.add(keepChromosomalDistributionBox, gbc);
    gbc.gridx = 1;
    gbc.gridy++;
    gbc.weightx = 0.1;
    optionPanel.add(new JLabel("Constrain within the probeset positions"), gbc);
    gbc.gridx++;
    gbc.weightx = 0.9;
    limitEndsBox = new JCheckBox("", true);
    optionPanel.add(limitEndsBox, gbc);
    return optionPanel;
}