Examples with AminoAcid com.compomics.util.experiment.biology.aminoacids.AminoAcid used on opensource projects

Example 1 with AminoAcid

use of com.compomics.util.experiment.biology.aminoacids.AminoAcid in project peptide-shaker by compomics.

the class PeptideShakerGUI method getCurrentMassDeltas.

/**
 * Get the current delta masses for use when annotating the spectra.
 *
 * @return the current delta masses
 */
public HashMap<Double, String> getCurrentMassDeltas() {
    HashMap<Double, String> knownMassDeltas = new HashMap<>();
    // add the monoisotopic amino acids masses
    knownMassDeltas.put(AminoAcid.A.getMonoisotopicMass(), "A");
    knownMassDeltas.put(AminoAcid.R.getMonoisotopicMass(), "R");
    knownMassDeltas.put(AminoAcid.N.getMonoisotopicMass(), "N");
    knownMassDeltas.put(AminoAcid.D.getMonoisotopicMass(), "D");
    knownMassDeltas.put(AminoAcid.C.getMonoisotopicMass(), "C");
    knownMassDeltas.put(AminoAcid.Q.getMonoisotopicMass(), "Q");
    knownMassDeltas.put(AminoAcid.E.getMonoisotopicMass(), "E");
    knownMassDeltas.put(AminoAcid.G.getMonoisotopicMass(), "G");
    knownMassDeltas.put(AminoAcid.H.getMonoisotopicMass(), "H");
    knownMassDeltas.put(AminoAcid.I.getMonoisotopicMass(), "I/L");
    knownMassDeltas.put(AminoAcid.K.getMonoisotopicMass(), "K");
    knownMassDeltas.put(AminoAcid.M.getMonoisotopicMass(), "M");
    knownMassDeltas.put(AminoAcid.F.getMonoisotopicMass(), "F");
    knownMassDeltas.put(AminoAcid.P.getMonoisotopicMass(), "P");
    knownMassDeltas.put(AminoAcid.S.getMonoisotopicMass(), "S");
    knownMassDeltas.put(AminoAcid.T.getMonoisotopicMass(), "T");
    knownMassDeltas.put(AminoAcid.W.getMonoisotopicMass(), "W");
    knownMassDeltas.put(AminoAcid.Y.getMonoisotopicMass(), "Y");
    knownMassDeltas.put(AminoAcid.V.getMonoisotopicMass(), "V");
    knownMassDeltas.put(AminoAcid.U.getMonoisotopicMass(), "U");
    knownMassDeltas.put(AminoAcid.O.getMonoisotopicMass(), "O");
    // add default neutral losses
    // knownMassDeltas.put(NeutralLoss.H2O.mass, "H2O");
    // knownMassDeltas.put(NeutralLoss.NH3.mass, "NH3");
    // knownMassDeltas.put(NeutralLoss.CH4OS.mass, "CH4OS");
    // knownMassDeltas.put(NeutralLoss.H3PO4.mass, "H3PO4");
    // knownMassDeltas.put(NeutralLoss.HPO3.mass, "HPO3");
    // knownMassDeltas.put(4d, "18O"); // @TODO: should this be added to neutral losses??
    // knownMassDeltas.put(44d, "PEG"); // @TODO: should this be added to neutral losses??
    // add the modifications
    SearchParameters searchParameters = getIdentificationParameters().getSearchParameters();
    ModificationParameters modificationProfile = searchParameters.getModificationParameters();
    ArrayList<String> modificationList = modificationProfile.getAllModifications();
    Collections.sort(modificationList);
    // iterate the modifications list and add the non-terminal modifications
    for (String modName : modificationList) {
        Modification modification = modificationFactory.getModification(modName);
        if (modification.getModificationType() == ModificationType.modaa) {
            for (char aa : modification.getPattern().getAminoAcidsAtTarget()) {
                AminoAcid aminoAcid = AminoAcid.getAminoAcid(aa);
                double massKey = aminoAcid.getMonoisotopicMass() + modification.getMass();
                String annotationValue = String.join("", Character.toString(aa), "<", modification.getShortName(), ">");
                knownMassDeltas.put(massKey, annotationValue);
            }
        }
    }
    return knownMassDeltas;
}

Example 2 with AminoAcid

use of com.compomics.util.experiment.biology.aminoacids.AminoAcid in project peptide-shaker by compomics.

the class PepXmlExport method getModLine.

/**
 * Gets the line for a modification.
 *
 * @param modification the modification
 * @param variable a boolean indicating whether the modification is variable
 *
 * @return the line for a modification
 */
private String getModLine(Modification modification, boolean variable) {
    StringBuilder modificationLine = new StringBuilder();
    ModificationType modificationType = modification.getModificationType();
    if (modificationType == ModificationType.modaa || modificationType == ModificationType.modnaa_peptide || modificationType == ModificationType.modnaa_protein || modificationType == ModificationType.modcaa_peptide || modificationType == ModificationType.modcaa_protein) {
        modificationLine.append("<aminoacid_modification ");
        AminoAcidPattern aminoAcidPattern = modification.getPattern();
        modificationLine.append("aminoacid=\"").append(aminoAcidPattern.toString()).append("\" ");
        modificationLine.append("massdiff=\"").append(modification.getMass()).append("\" ");
        if (aminoAcidPattern.getAminoAcidsAtTarget().size() == 1) {
            Character aa = aminoAcidPattern.getAminoAcidsAtTarget().get(0);
            AminoAcid aminoAcid = AminoAcid.getAminoAcid(aa);
            if (!aminoAcid.iscombination()) {
                Double mass = aminoAcid.getMonoisotopicMass() + modification.getMass();
                modificationLine.append("mass=\"").append(mass).append("\" ");
            }
        }
        if (modificationType.isCTerm()) {
            modificationLine.append("peptide_terminus=\"c\" ");
        }
        if (modificationType.isNTerm()) {
            modificationLine.append("peptide_terminus=\"n\" ");
        }
    } else {
        modificationLine.append("<terminal_modification ");
        if (modificationType.isCTerm()) {
            modificationLine.append("terminus=\"c\" ");
        }
        if (modificationType.isNTerm()) {
            modificationLine.append("terminus=\"n\" ");
        }
        modificationLine.append("massdiff=\"").append(modification.getMass()).append("\" ");
        if (modificationType == ModificationType.modc_protein) {
            modificationLine.append("protein_terminus=\"c\" ");
        }
        if (modificationType == ModificationType.modn_protein) {
            modificationLine.append("protein_terminus=\"n\" ");
        }
        if (modificationType.isNTerm()) {
            double mass = Atom.H.getMonoisotopicMass() + modification.getMass();
            modificationLine.append("mass=\"").append(mass).append("\" ");
        }
        if (modificationType.isCTerm()) {
            double mass = Atom.H.getMonoisotopicMass() + Atom.O.getMonoisotopicMass() + modification.getMass();
            modificationLine.append("mass=\"").append(mass).append("\" ");
        }
    }
    if (variable) {
        modificationLine.append("variable=\"Y\" ");
    } else {
        modificationLine.append("variable=\"N\" ");
    }
    modificationLine.append("symbol=\"").append(modification.getName()).append("\" ");
    CvTerm cvTerm = modification.getUnimodCvTerm();
    if (cvTerm != null) {
        modificationLine.append("description=\"").append(cvTerm.getAccession()).append("\"");
    } else {
        // try PSI-MOD instead
        cvTerm = modification.getPsiModCvTerm();
        if (cvTerm != null) {
            modificationLine.append("description=\"").append(cvTerm.getAccession()).append("\"");
        }
    }
    modificationLine.append("/>");
    return modificationLine.toString();
}