/**
* Creates the Andromeda PTM file and saves the PTM indexes in the search parameters.
*
* @param andromedaFolder the Andromeda installation folder
* @param identificationParameters the identification parameters
* @param identificationParametersFile the file where to save the search parameters
* @throws IOException exception thrown whenever an error occurs while writing to the file.
* @throws java.lang.ClassNotFoundException exception thrown whenever an error occurred while
* saving the search parameters
*/
public static void createPtmFile(
File andromedaFolder,
IdentificationParameters identificationParameters,
File identificationParametersFile)
throws IOException, ClassNotFoundException {
File file = new File(andromedaFolder, "conf");
file = new File(file, "modifications.xml");
BufferedWriter bw = new BufferedWriter(new FileWriter(file));
int index = 0;
String date = "0001-01-01T00:00:00";
PTMFactory ptmFactory = PTMFactory.getInstance();
SearchParameters searchParameters = identificationParameters.getSearchParameters();
AndromedaParameters andromedaParameters =
(AndromedaParameters)
searchParameters.getIdentificationAlgorithmParameter(Advocate.andromeda.getIndex());
try {
bw.write("<?xml version=\"1.0\" encoding=\"utf-8\"?>");
bw.newLine();
bw.write(
"<modifications xmlns:xsd=\"http://www.w3.org/2001/XMLSchema\" xmlns:xsi=\"http://www.w3.org/2001/XMLSchema-instance\">");
bw.newLine();
// add the default ptms
for (String ptmName : ptmFactory.getDefaultModifications()) {
PTM ptm = ptmFactory.getPTM(ptmName);
writePtm(bw, date, ptm, index);
andromedaParameters.setPtmIndex(ptmName, index);
index++;
}
// add the user ptms
for (String ptmName : ptmFactory.getUserModifications()) {
PTM ptm = ptmFactory.getPTM(ptmName);
writePtm(bw, date, ptm, index);
andromedaParameters.setPtmIndex(ptmName, index);
index++;
}
bw.write("</modifications>");
bw.newLine();
} finally {
bw.close();
}
IdentificationParameters.saveIdentificationParameters(
identificationParameters, identificationParametersFile);
}
/**
* Get the terminal modifications as a string in the Tide format.
*
* @param modifications the modifications to check
* @param fixed if the modifications are to to be added as fixed or variable
* @param nTerm true if the modifications are n-terminal, false if c-terminal
* @return the terminal modifications as a string in the Tide format
*/
private String getTerminalModifications(
ArrayList<String> modifications, boolean fixed, boolean nTerm) {
String terminalModifications = "";
for (String ptmName : modifications) {
PTM ptm = ptmFactory.getPTM(ptmName);
if ((ptm.isNTerm() && nTerm) || (ptm.isCTerm() && !nTerm)) {
if (!terminalModifications.isEmpty()) {
terminalModifications += ",";
}
// add the number of allowed ptms per peptide
if (!fixed) {
terminalModifications += "1";
}
// add the residues affected
AminoAcidPattern ptmPattern = ptm.getPattern();
String tempPtmPattern = "";
if (ptmPattern != null && ptmPattern.length() > 0) {
for (Character aminoAcid : ptmPattern.getAminoAcidsAtTarget()) {
tempPtmPattern += aminoAcid;
}
}
if (tempPtmPattern.length() == 0) {
tempPtmPattern = "X";
}
terminalModifications += tempPtmPattern;
// add the ptm mass
if (ptm.getRoundedMass() > 0) {
terminalModifications += "+";
}
terminalModifications += ptm.getRoundedMass();
}
}
return terminalModifications;
}
/**
* Get the non-terminal modifications as a string in the Tide format.
*
* @param modifications the modifications to check
* @param fixed if the modifications are to to be added as fixed or variable
* @return the non-terminal modifications as a string in the Tide forma
*/
private String getNonTerminalModifications(ArrayList<String> modifications, boolean fixed) {
// tide ptm pattern: [max_per_peptide]residues[+/-]mass_change
String nonTerminalModifications = "";
for (String ptmName : modifications) {
PTM ptm = ptmFactory.getPTM(ptmName);
if (!ptm.isNTerm() && !ptm.isCTerm()) {
if (!nonTerminalModifications.isEmpty()) {
nonTerminalModifications += ",";
}
// add the number of allowed ptms per peptide
if (!fixed) {
nonTerminalModifications +=
tideParameters
.getMaxVariablePtmsPerTypePerPeptide(); // @TODO: make this modification specific?
}
// add the residues affected
AminoAcidPattern ptmPattern = ptm.getPattern();
if (ptmPattern != null && ptmPattern.length() > 0) {
for (Character aminoAcid : ptmPattern.getAminoAcidsAtTarget()) {
nonTerminalModifications += aminoAcid;
}
}
// add the ptm mass
if (ptm.getRoundedMass() > 0) {
nonTerminalModifications += "+";
}
nonTerminalModifications += ptm.getRoundedMass();
}
}
return nonTerminalModifications;
}
/**
* Writes the lines corresponding to the given PTM name.
*
* @param writer the writer used to write
* @param mod the name of the modifications of interest
* @param variable a string (see static fields) indicating whether the modification is fixed or
* variable
* @throws IOException
*/
private static void writePtmLine(BufferedWriter writer, String mod, String variable)
throws IOException {
// Get the PTMFactory
PTMFactory ptmFactory = PTMFactory.getInstance();
PTM ptm = ptmFactory.getPTM(mod);
double ptmMass = ptm.getRoundedMass();
if (ptmMass > maxMassOffsetValue) {
String connector = "";
if (ptmMass > 0) {
connector = "+";
}
// Write a line for each residue
if (ptm.getPattern() == null || ptm.getPattern().getAminoAcidsAtTarget().isEmpty()) {
if (variable.equalsIgnoreCase(FIXED_PTM)) {
variable = VARIABLE_PTM; // PepNovo+ does not support fixed PTMs at the terminals...
}
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
writer.append("N_TERM" + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("N_TERM" + SPACE);
writer.append("^" + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), "^" + connector + Long.toString(Math.round(ptmMass)));
writer.append(ptm.getName().toUpperCase());
writer.newLine();
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
writer.append("C_TERM" + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("C_TERM" + SPACE);
writer.append("$" + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), "$" + connector + Long.toString(Math.round(ptmMass)));
writer.append(ptm.getName().toUpperCase());
writer.newLine();
}
} else {
for (Character residue : ptm.getPattern().getAminoAcidsAtTarget()) {
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
writer.append(residue + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("+1" + SPACE);
writer.append(residue + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
writer.append(residue + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append("-1" + SPACE);
writer.append(residue + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else {
writer.append(residue + SEP);
writer.append(ptmMass + SPACE);
writer.append(variable + SPACE);
writer.append(ALL_LOCATIONS + SPACE);
writer.append(residue + connector + Long.toString(Math.round(ptmMass)) + SPACE);
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
}
writer.append(ptm.getName().toUpperCase());
writer.newLine();
}
}
}
}
/** Fill the modification ID map. */
private static void fillModIdMap() {
// @TODO: is this method really needed anymore?
modIdMap = new HashMap<String, String>();
PTMFactory ptmFactory = PTMFactory.getInstance();
List<String> mods = new ArrayList<String>();
mods.addAll(ptmFactory.getDefaultModifications());
mods.addAll(ptmFactory.getUserModifications());
// Connector string: plus for positive modifications, minus for negative ones
String connector;
// Write the modifications
for (String mod : mods) {
PTM ptm = ptmFactory.getPTM(mod);
double ptmMass = ptm.getRoundedMass();
if (ptmMass > 0) {
connector = "+";
} else {
connector = "";
}
if (ptm.getPattern() == null || ptm.getPattern().getAminoAcidsAtTarget().isEmpty()) {
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
modIdMap.put(ptm.getName(), "^" + connector + Long.toString(Math.round(ptmMass)));
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
modIdMap.put(ptm.getName(), "$" + connector + Long.toString(Math.round(ptmMass)));
}
} else {
for (Character residue : ptmFactory.getPTM(mod).getPattern().getAminoAcidsAtTarget()) {
if (ptmFactory.getPTM(mod).getType() == PTM.MODN
|| ptmFactory.getPTM(mod).getType() == PTM.MODNAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODNP
|| ptmFactory.getPTM(mod).getType() == PTM.MODNPAA) {
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else if (ptmFactory.getPTM(mod).getType() == PTM.MODC
|| ptmFactory.getPTM(mod).getType() == PTM.MODCAA
|| ptmFactory.getPTM(mod).getType() == PTM.MODCP
|| ptmFactory.getPTM(mod).getType() == PTM.MODCPAA) {
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
} else {
modIdMap.put(ptm.getName(), residue + connector + Long.toString(Math.round(ptmMass)));
}
}
}
}
}
