Examples with ExtendedIsotopePattern net.sf.mzmine.datamodel.impl.ExtendedIsotopePattern used on opensource projects

Example 6 with ExtendedIsotopePattern

use of net.sf.mzmine.datamodel.impl.ExtendedIsotopePattern in project mzmine2 by mzmine.

the class IsotopePeakScannerSetupDialog method calculateIsotopePattern.

private ExtendedIsotopePattern calculateIsotopePattern() {
    if (!checkParameters())
        return null;
    String strPattern = "";
    int currentCarbonPattern = Integer.parseInt(txtCurrentPatternIndex.getText());
    if (autoCarbon)
        strPattern = "C" + String.valueOf(currentCarbonPattern) + element;
    else
        strPattern = element;
    if (strPattern.equals(""))
        return null;
    logger.info("Calculating isotope pattern: " + strPattern);
    ExtendedIsotopePattern pattern;
    PolarityType pol = (charge > 0) ? PolarityType.POSITIVE : PolarityType.NEGATIVE;
    charge = (charge > 0) ? charge : charge * -1;
    try {
        // *0.2 so the user can see the peaks below the threshold
        pattern = (ExtendedIsotopePattern) IsotopePatternCalculator.calculateIsotopePattern(strPattern, minIntensity * 0.1, mergeWidth, charge, pol, true);
    } catch (Exception e) {
        logger.warning("The entered Sum formula is invalid.");
        return null;
    }
    return pattern;
}

Example 7 with ExtendedIsotopePattern

use of net.sf.mzmine.datamodel.impl.ExtendedIsotopePattern in project mzmine2 by mzmine.

the class DynamicParameterUtils method buildFormulaRangeOnIsotopePatternResults.

/**
 * Creates an ElementParameter based on the previous processing results. If no results were
 * detected, the default value is returned. Upper and lower boundaries are chosen according to
 * lowerElementBoundaryPercentage and upperElementBoundaryPercentage values of this utility class.
 * These values can be set via {@link #setLowerElementBoundaryPercentage} and
 * {@link #setUpperElementBoundaryPercentage}. The elements contained in
 *
 * @param dp The data point to build a parameter for.
 * @param def The default set of parameters.
 * @return The built ElementsParameter
 */
public static MolecularFormulaRange buildFormulaRangeOnIsotopePatternResults(ProcessedDataPoint dp, MolecularFormulaRange def) {
    DPPIsotopePatternResult result = (DPPIsotopePatternResult) dp.getFirstResultByType(ResultType.ISOTOPEPATTERN);
    if (result == null)
        return def;
    if (!(result.getValue() instanceof ExtendedIsotopePattern))
        return def;
    ExtendedIsotopePattern pattern = (ExtendedIsotopePattern) result.getValue();
    String form = IsotopePatternUtils.makePatternSuggestion(pattern.getIsotopeCompositions());
    MolecularFormulaRange range = new MolecularFormulaRange();
    IMolecularFormula formula = FormulaUtils.createMajorIsotopeMolFormula(form);
    if (formula == null) {
        logger.finest("could not generate formula for m/z " + dp.getMZ() + " " + form);
        return def;
    }
    for (IIsotope isotope : def.isotopes()) range.addIsotope(isotope, def.getIsotopeCountMin(isotope), def.getIsotopeCountMax(isotope));
    for (IIsotope isotope : formula.isotopes()) {
        if (range.contains(isotope))
            continue;
        int count = formula.getIsotopeCount(isotope);
        range.addIsotope(isotope, (int) (count * lowerElementBoundaryPercentage), (int) (count * upperElementBoundaryPercentage));
    }
    for (IIsotope isotope : range.isotopes()) {
        int min = range.getIsotopeCountMin(isotope);
        int max = range.getIsotopeCountMax(isotope);
    // logger.info("m/z = " + dp.getMZ() + " " + isotope.getSymbol() + " " + min + " - " + max);
    }
    return range;
}

Example 8 with ExtendedIsotopePattern

use of net.sf.mzmine.datamodel.impl.ExtendedIsotopePattern in project mzmine2 by mzmine.

the class IsotopePatternUtils method convertIsotopicPeakResultsToPattern.

/**
 * Takes all DPPIsotopicPeakResults of one charge and puts them into one isotope pattern (per
 * charge).
 *
 * @param dp A ProcessedDataPoint
 * @param keepResults if false, all DPPIsotopicPeakResults will be removed from this data point.
 */
public static void convertIsotopicPeakResultsToPattern(ProcessedDataPoint dp, boolean keepResults) {
    sortAndRemoveDuplicateIsotopicPeakResult(dp);
    List<DPPIsotopicPeakResult> iprs = getIsotopicPeakResults(dp);
    if (iprs.isEmpty())
        return;
    List<Integer> charges = getChargeStates(iprs);
    List<ProcessedDataPoint> peaks = new ArrayList<>();
    List<String> isotopes = new ArrayList<>();
    peaks.add(dp);
    isotopes.add("");
    for (int charge : charges) {
        for (DPPIsotopicPeakResult ipr : iprs) {
            if (ipr.getCharge() == charge) {
                peaks.add(ipr.getValue());
                isotopes.add(mergeIsotopicPeakDescription(ipr.getIsotope()));
            }
        }
        ProcessedDataPoint[] dps = peaks.toArray(new ProcessedDataPoint[0]);
        String[] isos = isotopes.toArray(new String[0]);
        ExtendedIsotopePattern pattern = new ExtendedIsotopePattern(dps, IsotopePatternStatus.DETECTED, format.format(dp.getMZ()), /*+ Arrays.toString(isos)*/
        isos);
        dp.addResult(new DPPIsotopePatternResult(pattern, (ProcessedDataPoint[]) pattern.getDataPoints(), charge));
        peaks.clear();
        isotopes.clear();
    }
    if (!keepResults)
        dp.removeAllResultsByType(ResultType.ISOTOPICPEAK);
}

Example 9 with ExtendedIsotopePattern

use of net.sf.mzmine.datamodel.impl.ExtendedIsotopePattern in project mzmine2 by mzmine.

the class IsotopePatternCalculator method removeDataPointsBelowIntensity.

public static IsotopePattern removeDataPointsBelowIntensity(IsotopePattern pattern, double minIntensity) {
    DataPoint[] dp = pattern.getDataPoints();
    for (int i = 0; i < pattern.getNumberOfDataPoints(); i++) {
        if (dp[i].getIntensity() < minIntensity) {
            dp[i] = null;
        }
    }
    ArrayList<DataPoint> newDP = new ArrayList<DataPoint>();
    ArrayList<String> newComp = new ArrayList<String>();
    for (int i = 0; i < dp.length; i++) {
        DataPoint p = dp[i];
        if (dp[i] != null) {
            newDP.add(p);
            if (pattern instanceof ExtendedIsotopePattern) {
                newComp.add(((ExtendedIsotopePattern) pattern).getIsotopeComposition(i));
            }
        }
    }
    if (pattern instanceof ExtendedIsotopePattern)
        return new ExtendedIsotopePattern(newDP.toArray(new DataPoint[0]), pattern.getStatus(), pattern.getDescription(), newComp.toArray(new String[0]));
    else
        return new SimpleIsotopePattern(newDP.toArray(new DataPoint[0]), pattern.getStatus(), pattern.getDescription());
}

Example 10 with ExtendedIsotopePattern

use of net.sf.mzmine.datamodel.impl.ExtendedIsotopePattern in project mzmine2 by mzmine.

the class DPPAnyElementIsotopeGrouperTask method run.

@Override
public void run() {
    if (!checkParameterSet() || !checkValues()) {
        setStatus(TaskStatus.ERROR);
        return;
    }
    // check formula
    if (elements == null || elements.equals("") || !FormulaUtils.checkMolecularFormula(elements)) {
        setErrorMessage("Invalid element parameter in " + getTaskDescription());
        setStatus(TaskStatus.ERROR);
        logger.warning("Invalid element parameter in " + getTaskDescription());
        return;
    }
    if (!FormulaUtils.checkMolecularFormula(elements)) {
        setStatus(TaskStatus.ERROR);
        logger.warning("Data point/Spectra processing: Invalid element parameter in " + getTaskDescription());
    }
    if (getDataPoints().length == 0) {
        logger.info("Data point/Spectra processing: 0 data points were passed to " + getTaskDescription() + " Please check the parameters.");
        setStatus(TaskStatus.CANCELED);
        return;
    }
    if (!(getDataPoints() instanceof ProcessedDataPoint[])) {
        logger.warning("Data point/Spectra processing: The data points passed to Isotope Grouper were not an instance of processed data points." + " Make sure to run mass detection first.");
        setStatus(TaskStatus.CANCELED);
        return;
    }
    setStatus(TaskStatus.PROCESSING);
    ExtendedIsotopePattern[] elementPattern = getIsotopePatterns(elements, mergeWidth, minAbundance);
    ProcessedDataPoint[] originalDataPoints = (ProcessedDataPoint[]) getDataPoints();
    totalSteps = originalDataPoints.length * 2 + 1;
    // one loop for every element
    for (ExtendedIsotopePattern pattern : elementPattern) {
        // we search by ascending mz
        for (int i_dp = 0; i_dp < originalDataPoints.length; i_dp++) {
            // dp is the peak we are currently searching an isotope pattern for
            ProcessedDataPoint dp = originalDataPoints[i_dp];
            if (!mzrange.contains(dp.getMZ()))
                continue;
            IsotopePatternUtils.findIsotopicPeaks(dp, originalDataPoints, mzTolerance, pattern, mzrange, maxCharge);
            processedSteps++;
        }
        if (isCanceled())
            return;
    }
    for (int x = 0; x < originalDataPoints.length; x++) {
        ProcessedDataPoint dp = originalDataPoints[x];
        if (!mzrange.contains(dp.getMZ()))
            continue;
        if (isCanceled())
            return;
        IsotopePatternUtils.mergeIsotopicPeakResults(dp);
    }
    for (int x = 0; x < originalDataPoints.length; x++) {
        ProcessedDataPoint dp = originalDataPoints[x];
        if (!mzrange.contains(dp.getMZ()))
            continue;
        if (isCanceled())
            return;
        IsotopePatternUtils.convertIsotopicPeakResultsToPattern(dp, false);
    }
    List<ProcessedDataPoint> results = new ArrayList<>();
    for (ProcessedDataPoint dp : originalDataPoints) {
        if (autoRemove) {
            if (dp.resultTypeExists(ResultType.ISOTOPEPATTERN))
                results.add(dp);
        } else
            results.add(dp);
    }
    setResults(results.toArray(new ProcessedDataPoint[0]));
    setStatus(TaskStatus.FINISHED);
}