import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Returns the N-terminal of the peptide as a String. Returns "NH2" if the
 * terminal is not modified, otherwise returns the name of the modification.
 * /!\ this method will work only if the PTM found in the peptide are in the
 * PTMFactory.
 *
 * @return the N-terminal of the peptide as a String, e.g., "NH2"
 */
public String getNTerminal() {

    String nTerm = "NH2";

    PTMFactory ptmFactory = PTMFactory.getInstance();

    if (modifications != null) {
        for (ModificationMatch modificationMatch : modifications) {
            if (modificationMatch.getModificationSite() == 1) {
                PTM ptm = ptmFactory.getPTM(modificationMatch.getTheoreticPtm());
                if (ptm.getType() != PTM.MODAA && ptm.getType() != PTM.MODMAX) {
                    nTerm = ptm.getShortName();
                }
            }
        }
    }

    nTerm = nTerm.replaceAll("-", " ");
    return nTerm;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Returns an indexed map of all fixed modifications amino acid, (1 is the
 * first) > list of modification names.
 *
 * @return an indexed map of all fixed modifications amino acid
 */
public HashMap<Integer, ArrayList<String>> getIndexedFixedModifications() {

    if (modifications == null) {
        return new HashMap<Integer, ArrayList<String>>(0);
    }

    HashMap<Integer, ArrayList<String>> result = new HashMap<Integer, ArrayList<String>>(modifications.size());
    for (ModificationMatch modificationMatch : modifications) {
        if (!modificationMatch.isVariable()) {
            int aa = modificationMatch.getModificationSite();
            if (!result.containsKey(aa)) {
                result.put(aa, new ArrayList<String>());
            }
            result.get(aa).add(modificationMatch.getTheoreticPtm());
        }
    }
    return result;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Returns a version of the peptide which does not contain the inspected
 * PTMs.
 *
 * @param peptide the original peptide
 * @param ptms list of inspected PTMs
 *
 * @return a not modified version of the peptide
 *
 * @throws IOException exception thrown whenever an error occurred while
 * reading a protein sequence
 * @throws InterruptedException exception thrown whenever an error occurred
 * while reading a protein sequence
 * @throws ClassNotFoundException if a ClassNotFoundException occurs
 * @throws SQLException if an SQLException occurs
 */
public static Peptide getNoModPeptide(Peptide peptide, ArrayList<PTM> ptms) throws IOException, SQLException, ClassNotFoundException, InterruptedException {

    Peptide noModPeptide = new Peptide(peptide.getSequence(), new ArrayList<ModificationMatch>());
    noModPeptide.setParentProteins(peptide.getParentProteinsNoRemapping());

    if (peptide.isModified()) {
        for (ModificationMatch modificationMatch : peptide.getModificationMatches()) {
            boolean found = false;
            for (PTM ptm : ptms) {
                if (modificationMatch.getTheoreticPtm().equals(ptm.getName())) {
                    found = true;
                    break;
                }
            }
            if (!found) {
                noModPeptide.addModificationMatch(modificationMatch);
            }
        }
    }

    return noModPeptide;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Adds a modification to one of the amino acid pattern.
 *
 * @param localization the index of the amino acid retained as target of the
 * modification. 1 is the first amino acid.
 * @param modificationMatch the modification match
 */
public void addModificationMatch(int localization, ModificationMatch modificationMatch) {
    int index = localization - 1;
    if (index < 0) {
        throw new IllegalArgumentException("Wrong modification target index " + localization + ", 1 is the first amino acid for PTM localization.");
    }
    if (targetModifications == null) {
        targetModifications = new HashMap<Integer, ArrayList<ModificationMatch>>();
    }
    ArrayList<ModificationMatch> modificationMatches = targetModifications.get(localization);
    if (modificationMatches == null) {
        modificationMatches = new ArrayList<ModificationMatch>();
        targetModifications.put(localization, modificationMatches);
    }
    modificationMatches.add(modificationMatch);
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Adds a list of modifications to one of the amino acid pattern.
 *
 * @param localization the index of the amino acid retained as target of the
 * modification. 1 is the first amino acid.
 * @param modificationMatches the modification matches
 */
public void addModificationMatches(int localization, ArrayList<ModificationMatch> modificationMatches) {
    int index = localization - 1;
    if (index < 0) {
        throw new IllegalArgumentException("Wrong modification target index " + localization + ", 1 is the first amino acid for PTM localization.");
    }
    if (targetModifications == null) {
        targetModifications = new HashMap<Integer, ArrayList<ModificationMatch>>();
    }
    ArrayList<ModificationMatch> modificationMatchesAtIndex = targetModifications.get(localization);
    if (modificationMatchesAtIndex == null) {
        modificationMatchesAtIndex = new ArrayList<ModificationMatch>();
        targetModifications.put(localization, modificationMatchesAtIndex);
    }
    modificationMatches.addAll(modificationMatches);
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Creates a sequence from another sequence.
 *
 * @param sequence the other sequence
 */
public AminoAcidSequence(AminoAcidSequence sequence) {
    this.sequence = sequence.getSequence();
    HashMap<Integer, ArrayList<ModificationMatch>> modificationMatches = sequence.getModificationMatches();
    if (modificationMatches != null) {
        modifications = new HashMap<Integer, ArrayList<ModificationMatch>>(modificationMatches.size());
        for (int site : modificationMatches.keySet()) {
            ArrayList<ModificationMatch> oldModifications = modificationMatches.get(site);
            ArrayList<ModificationMatch> newModifications = new ArrayList<ModificationMatch>(oldModifications.size());
            for (ModificationMatch modificationMatch : oldModifications) {
                newModifications.add(modificationMatch.clone());
            }
            modifications.put(site, newModifications);
        }
    }
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Appends another sequence at the end of this sequence.
 *
 * @param otherSequence the other sequence to append.
 */
public void appendCTerm(AminoAcidSequence otherSequence) {
    setSequenceStringBuilder(true);
    int previousLength = length();
    sequenceStringBuilder.append(otherSequence.getSequence());
    HashMap<Integer, ArrayList<ModificationMatch>> modificationMatches = otherSequence.getModificationMatches();
    if (modificationMatches != null) {
        for (int otherSite : modificationMatches.keySet()) {
            int newSite = otherSite + previousLength;
            for (ModificationMatch oldModificationMatch : modificationMatches.get(otherSite)) {
                ModificationMatch newModificationMatch = oldModificationMatch.clone();
                oldModificationMatch.setModificationSite(newSite);
                addModificationMatch(newSite, newModificationMatch);
            }
        }
    }
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Adds a modification to one of the amino acid sequence.
 *
 * @param localization the index of the amino acid retained as target of the
 * modification. 1 is the first amino acid.
 * @param modificationMatch the modification match
 */
public void addModificationMatch(int localization, ModificationMatch modificationMatch) {
    int index = localization - 1;
    if (index < 0) {
        throw new IllegalArgumentException("Wrong modification target index " + localization + ", 1 is the first amino acid for PTM localization.");
    }
    if (modifications == null) {
        modifications = new HashMap<Integer, ArrayList<ModificationMatch>>();
    }
    ArrayList<ModificationMatch> modificationMatches = modifications.get(localization);
    if (modificationMatches == null) {
        modificationMatches = new ArrayList<ModificationMatch>();
        modifications.put(localization, modificationMatches);
    }
    modificationMatches.add(modificationMatch);
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Adds a list of modifications to one of the amino acid sequence.
 *
 * @param localization the index of the amino acid retained as target of the
 * modification. 1 is the first amino acid.
 * @param modificationMatches the modification matches
 */
public void addModificationMatches(int localization, ArrayList<ModificationMatch> modificationMatches) {
    int index = localization - 1;
    if (index < 0) {
        throw new IllegalArgumentException("Wrong modification target index " + localization + ", 1 is the first amino acid for PTM localization.");
    }
    if (modifications == null) {
        modifications = new HashMap<Integer, ArrayList<ModificationMatch>>();
    }
    ArrayList<ModificationMatch> modificationMatchesAtIndex = modifications.get(localization);
    if (modificationMatchesAtIndex == null) {
        modificationMatchesAtIndex = new ArrayList<ModificationMatch>();
        modifications.put(localization, modificationMatchesAtIndex);
    }
    modificationMatches.addAll(modificationMatches);
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Returns an amino acid sequence which is a reversed version of the current
 * pattern.
 *
 * @return an amino acid sequence which is a reversed version of the current
 * pattern
 */
public AminoAcidSequence reverse() {
    setSequenceStringBuilder(false);
    AminoAcidSequence newSequence = new AminoAcidSequence((new StringBuilder(sequence)).reverse().toString());
    if (modifications != null) {
        for (int i : modifications.keySet()) {
            int reversed = length() - i + 1;
            for (ModificationMatch modificationMatch : modifications.get(i)) {
                ModificationMatch newMatch = new ModificationMatch(modificationMatch.getTheoreticPtm(), modificationMatch.isVariable(), reversed);
                if (modificationMatch.isConfident()) {
                    newMatch.setConfident(true);
                }
                if (modificationMatch.isInferred()) {
                    newMatch.setInferred(true);
                }
                newSequence.addModificationMatch(reversed, newMatch);
            }
        }
    }
    return newSequence;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
@Override
public Double getMass() {
    setSequenceStringBuilder(false);
    double mass = 0;
    for (int i = 0; i < length(); i++) {
        AminoAcid aminoAcid = AminoAcid.getAminoAcid(sequence.charAt(i));
        mass += aminoAcid.getMonoisotopicMass();
        if (modifications != null) {
            ArrayList<ModificationMatch> modificationAtIndex = modifications.get(i + 1);
            if (modificationAtIndex != null) {
                for (ModificationMatch modificationMatch : modificationAtIndex) {
                    PTM ptm = PTMFactory.getInstance().getPTM(modificationMatch.getTheoreticPtm());
                    mass += ptm.getMass();
                }
            }
        }
    }
    return mass;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Returns a map of the different possible peptides for the different
 * profiles.
 *
 * @param peptide the peptide of interest
 * @param ptms the PTMs to score
 * @param possibleProfiles the different profiles
 *
 * @return a map of the different peptides for the different profiles
 *
 * @throws IOException exception thrown whenever an error occurred while
 * reading a protein sequence
 * @throws InterruptedException exception thrown whenever an error occurred
 * while reading a protein sequence
 * @throws ClassNotFoundException if a ClassNotFoundException occurs
 * @throws SQLException if an SQLException occurs
 */
private static HashMap<String, Peptide> getPossiblePeptidesMap(Peptide peptide, ArrayList<PTM> ptms, ArrayList<ArrayList<Integer>> possibleProfiles) throws IOException, SQLException, ClassNotFoundException, InterruptedException {

    String representativePTM = ptms.get(0).getName();
    HashMap<String, Peptide> result = new HashMap<String, Peptide>(possibleProfiles.size());
    int peptideLength = peptide.getSequence().length();
    for (ArrayList<Integer> profile : possibleProfiles) {
        Peptide tempPeptide = Peptide.getNoModPeptide(peptide, ptms);
        for (int pos : profile) {
            int index = pos;
            if (index == 0) {
                index = 1;
            } else if (index == peptideLength + 1) {
                index = peptideLength;
            }
            tempPeptide.addModificationMatch(new ModificationMatch(representativePTM, true, index));
        }
        String profileKey = KeyUtils.getKey(profile);
        result.put(profileKey, tempPeptide);
    }
    return result;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Constructor.
 *
 * @param left left index boundary
 * @param right right index boundary
 * @param character current character stored
 * @param previousContent previous matrix content
 * @param mass current mass
 * @param peptideSequence intermediate peptide sequence
 * @param peptideSequenceSearch intermediate peptide sequence for search
 * @param length current peptide length
 * @param numX number of current X amino acids
 * @param modification index to modification list
 * @param modifications intermediate list of modifications
 * @param modifictationPos index to modification list for ptm
 * @param ambiguousChar ambiguous character
 */
public MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, String peptideSequenceSearch,
        int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int ambiguousChar) {

    this.left = left;
    this.right = right;
    this.character = character;
    this.previousContent = previousContent;
    this.mass = mass;
    this.peptideSequence = peptideSequence;
    this.peptideSequenceSearch = peptideSequenceSearch;
    this.length = length;
    this.numX = numX;
    this.modification = modification;
    this.modifications = modifications;
    this.modificationPos = modifictationPos;
    this.numVariants = 0;
    this.numSpecificVariants = new int[]{0, 0, 0};
    this.variant = '\0';
    this.allVariants = null;
    this.ambiguousChar = ambiguousChar;
    this.tagComponent = -1;
    this.allXcomponents = null;
    this.XMassDiff = -1;
    this.allXMassDiffs = null;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Appends an amino acid sequence to the terminus of sequencing.
 *
 * @param aminoAcidSequence an amino acid sequence
 */
public void appendTerminus(AminoAcidSequence aminoAcidSequence) {
    HashMap<Integer, ArrayList<ModificationMatch>> otherModifications = aminoAcidSequence.getModificationMatches();
    if (otherModifications != null) {
        if (modificationMatches == null) {
            modificationMatches = new HashMap<Integer, String>(otherModifications.size());
        }
        for (int index : otherModifications.keySet()) {
            ArrayList<ModificationMatch> modificationMatchesList = otherModifications.get(index);
            if (modificationMatches.size() > 1) {
                throw new IllegalArgumentException("Two PTMs found on the same amino acid when mapping tags. Only one supported.");
            }
            modificationMatches.put(index + length, modificationMatchesList.get(0).getTheoreticPtm());
        }
    }
    length += aminoAcidSequence.length();
    if (nTerminus) {
        terminalIndex -= aminoAcidSequence.length();
    } else {
        terminalIndex += aminoAcidSequence.length();
    }
    mass += aminoAcidSequence.getMass();
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Returns the ms2pip features for the complementary ions of the given
 * peptide at the given charge.
 *
 * @param peptide the peptide
 * @param charge the charge
 * @param ionIndex the ion index
 *
 * @return the ms2pip features for the b ions
 */
public int[] getComplementaryIonsFeatures(Peptide peptide, int charge, int ionIndex) {

    char[] peptideSequence = peptide.getSequence().toCharArray();
    int sequenceLength = peptideSequence.length;
    char[] reversedSequence = new char[sequenceLength];
    for (int i = 0; i < sequenceLength; i++) {
        reversedSequence[i] = peptideSequence[sequenceLength - i - 1];
    }
    ArrayList<ModificationMatch> modificationMatches = peptide.getModificationMatches();
    ArrayList<ModificationMatch> reversedModificationMatches;
    if (modificationMatches != null) {
        reversedModificationMatches = new ArrayList<ModificationMatch>(modificationMatches.size());
        for (ModificationMatch modificationMatch : modificationMatches) {
            ModificationMatch reversedModificationMatch = new ModificationMatch(modificationMatch.getTheoreticPtm(), modificationMatch.isVariable(), sequenceLength - modificationMatch.getModificationSite() + 1);
            reversedModificationMatches.add(reversedModificationMatch);
        }
    } else {
        reversedModificationMatches = null;
    }

    return getIonsFeatures(reversedSequence, reversedModificationMatches, charge, ionIndex);
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Parses modification matches from a modification string.
 *
 * @param modificationsString the modification string
 *
 * @return a list of modificaiton matches
 *
 * @throws UnsupportedEncodingException exception thrown whenever an error
 * occurred while decoding the string
 */
private ArrayList<ModificationMatch> getModificationMatches(String modificationsString) throws UnsupportedEncodingException {
    if (modificationsString.length() == 0) {
        return new ArrayList<ModificationMatch>(0);
    }
    String decodedString = URLDecoder.decode(modificationsString, "utf-8");
    String[] modifications = decodedString.split(Peptide.MODIFICATION_SEPARATOR);
    ArrayList<ModificationMatch> modificationMatches = new ArrayList<ModificationMatch>(modifications.length);
    for (String modification : modifications) {
        String[] modificationSplit = modification.split(Peptide.MODIFICATION_LOCALIZATION_SEPARATOR);
        String modificationName = modificationSplit[0];
        Integer site = new Integer(modificationSplit[1]);
        ModificationMatch modificationMatch = new ModificationMatch(modificationName, true, site);
        modificationMatches.add(modificationMatch);
    }
    return modificationMatches;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * Returns a Peptide Assumption from an Andromeda line.
 *
 * @param line the line to parse
 * @param rank the rank of the assumption
 *
 * @return the corresponding assumption
 */
private PeptideAssumption getAssumptionFromLine(String line, int rank) {

    String[] temp = line.trim().split("\t");

    String[] temp1 = temp[4].split(",");
    ArrayList<ModificationMatch> modMatches = new ArrayList<ModificationMatch>();

    for (int aa = 0; aa < temp1.length; aa++) {
        String mod = temp1[aa];
        if (!mod.equals("A")) {
            modMatches.add(new ModificationMatch(mod, true, aa));
        }
    }

    String sequence = temp[0];
    Peptide peptide = new Peptide(sequence, modMatches, true);

    Charge charge = new Charge(Charge.PLUS, new Integer(temp[6]));
    Double score = new Double(temp[1]);
    Double p = FastMath.pow(10, -(score / 10));
    PeptideAssumption peptideAssumption = new PeptideAssumption(peptide, rank, Advocate.andromeda.getIndex(), charge, p, fileName);
    peptideAssumption.setRawScore(score);
    return peptideAssumption;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
/**
 * This method load all sequences in a memory
 *
 * @param databaseName
 * @return
 */
private static HashSet<DBEntry> getDBEntries(String databaseName) throws IOException {
    HashSet<DBEntry> dbEntries = new HashSet<DBEntry>();
    DBLoader loader = DBLoaderLoader.loadDB(new File(databaseName));
    Protein protein = null;
    // get a crossLinkerName object        
    while ((protein = loader.nextProtein()) != null) {
        String sequence = protein.getSequence().getSequence();
        String descrp = protein.getHeader().getDescription(),
                acc = protein.getHeader().getAccession();
        Peptide tmpPep = new Peptide(sequence, new ArrayList<ModificationMatch>());
        double tmpPepMass = tmpPep.getMass();
        DBEntry dbEntry = new DBEntry(tmpPep, descrp, acc, tmpPepMass);
        dbEntries.add(dbEntry);
    }
    return dbEntries;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
public PepIonID ClonePepIonID() {
    PepIonID newpeptide = new PepIonID();
    newpeptide.Sequence = Sequence;
    newpeptide.Charge = Charge;
    newpeptide.Is_NonDegenerate = Is_NonDegenerate;
    newpeptide.ModSequence = ModSequence;
    newpeptide.Modifications = (ArrayList<ModificationMatch>) Modifications.clone();
    if (PeakArea != null) {
        newpeptide.PeakArea = new float[PeakArea.length];
        newpeptide.PeakHeight = new float[PeakHeight.length];
    }
    return newpeptide;
}
 

import com.compomics.util.experiment.identification.matches.ModificationMatch; //导入依赖的package包/类
public String GetModificationString() {
    String ModificationString = "";
    for (ModificationMatch mod : Modifications) {
        ModificationString += mod.getTheoreticPtm() + "(" + mod.getModificationSite() + ");";
    }
    return ModificationString;
}