Examples with PeptideIdentityDataFile net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.PeptideIdentityDataFile used on opensource projects

Example 1 with PeptideIdentityDataFile

use of net.sf.mzmine.modules.peaklistmethods.identification.mascot.data.PeptideIdentityDataFile in project mzmine2 by mzmine.

the class PeptideUtils method getIonCoverage.

/**
 * Returns the coverage of the ion series.
 *
 * @param dataPoints
 * @param peptide
 * @param ionType
 * @param intensityThreshold
 * @return
 */
public static double getIonCoverage(DataPoint[] dataPoints, Peptide peptide, SerieIonType ionType, double intensityThreshold) {
    PeptideFragmentation fragmentation = peptide.getFragmentation();
    FragmentIon[] fragmentIons = fragmentation.getFragmentIons(ionType);
    PeptideIdentityDataFile peptideDataFile = peptide.getScan().getPeptideDataFile();
    double fragmentIonMassErrorTol = peptideDataFile.getFragmentIonMassErrorTolerance();
    DataPoint[] matchedDataPoints = getMatchedIons(dataPoints, fragmentIons, fragmentIonMassErrorTol, intensityThreshold);
    double ionCoverage = calculateSerieCoverage(matchedDataPoints, fragmentIons);
    return ionCoverage;
}