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

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


                for (int aa : aminoAcidPattern.getModificationIndexes()) {
                    for (ModificationMatch modificationMatch : aminoAcidPattern.getModificationsAt(aa)) {
                        if (modificationMatch.isVariable()) {
                            if (advocateId == Advocate.pepnovo.getIndex()) {
                                String pepnovoPtmName = modificationMatch.getTheoreticPtm();
                                PepnovoParameters pepnovoParameters = (PepnovoParameters) searchParameters.getIdentificationAlgorithmParameter(advocateId);
                                String utilitiesPtmName = pepnovoParameters.getUtilitiesPtmName(pepnovoPtmName);
                                if (utilitiesPtmName == null) {
                                    throw new IllegalArgumentException("PepNovo+ PTM " + pepnovoPtmName + " not recognized.");
                                }
                                modificationMatch.setTheoreticPtm(utilitiesPtmName);
                            } else if (advocateId == Advocate.direcTag.getIndex()) {
                                Integer directagIndex = new Integer(modificationMatch.getTheoreticPtm());
                                String utilitiesPtmName = searchParameters.getModificationProfile().getVariableModifications().get(directagIndex);
                                if (utilitiesPtmName == null) {
                                    throw new IllegalArgumentException("DirecTag PTM " + directagIndex + " not recognized.");
                                }
                                modificationMatch.setTheoreticPtm(utilitiesPtmName);
                                PTM ptm = ptmFactory.getPTM(utilitiesPtmName);
                                ArrayList<Character> aaAtTarget = ptm.getPattern().getAminoAcidsAtTarget();
                                if (aaAtTarget.size() > 1) {
                                    throw new IllegalArgumentException("More than one amino acid can be targeted by the modification " + ptm + ", tag duplication required.");
                                }
                                int aaIndex = aa - 1;
                                aminoAcidPattern.setTargeted(aaIndex, aaAtTarget);
                            } else {
                                Advocate notImplemented = Advocate.getAdvocate(advocateId);
                                if (notImplemented == null) {
                                    throw new IllegalArgumentException("Advocate of id " + advocateId + " not recognized.");
                                }
                                throw new IllegalArgumentException("PTM mapping not implemented for " + Advocate.getAdvocate(advocateId).getName() + ".");
                            }
                        }
                    }
                }
            } else if (tagComponent instanceof AminoAcidSequence) {

                AminoAcidSequence aminoAcidSequence = (AminoAcidSequence) tagComponent;

                for (int aa : aminoAcidSequence.getModificationIndexes()) {
                    for (ModificationMatch modificationMatch : aminoAcidSequence.getModificationsAt(aa)) {
                        if (modificationMatch.isVariable()) {
                            if (advocateId == Advocate.pepnovo.getIndex()) {
                                String pepnovoPtmName = modificationMatch.getTheoreticPtm();
                                PepnovoParameters pepnovoParameters = (PepnovoParameters) searchParameters.getIdentificationAlgorithmParameter(advocateId);
                                String utilitiesPtmName = pepnovoParameters.getUtilitiesPtmName(pepnovoPtmName);
                                if (utilitiesPtmName == null) {
                                    throw new IllegalArgumentException("PepNovo+ PTM " + pepnovoPtmName + " not recognized.");
                                }
                                modificationMatch.setTheoreticPtm(utilitiesPtmName);
                            } else if (advocateId == Advocate.direcTag.getIndex()) {
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