Package com.compomics.util.experiment.identification.identification_parameters

Examples of com.compomics.util.experiment.identification.identification_parameters.XtandemParameters


    private synchronized void verifyXTandemPtms() {
        if (!xTandemPtmsCheck) {
            ModificationProfile modificationProfile = searchParameters.getModificationProfile();
            IdentificationAlgorithmParameter algorithmParameter = searchParameters.getIdentificationAlgorithmParameter(Advocate.xtandem.getIndex());
            if (algorithmParameter != null) {
                XtandemParameters xtandemParameters = (XtandemParameters) algorithmParameter;
                if (xtandemParameters.isProteinQuickAcetyl() && !modificationProfile.contains("acetylation of protein n-term")) {
                    PTM ptm = PTMFactory.getInstance().getPTM("acetylation of protein n-term");
                    modificationProfile.addVariableModification(ptm);
                }
                String[] pyroMods = {"pyro-cmc", "pyro-glu from n-term e", "pyro-glu from n-term q"};
                if (xtandemParameters.isQuickPyrolidone()) {
                    for (String ptmName : pyroMods) {
                        if (!modificationProfile.getVariableModifications().contains(ptmName)) {
                            PTM ptm = PTMFactory.getInstance().getPTM(ptmName);
                            modificationProfile.addVariableModification(ptm);
                        }
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