/** 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)));
}
}
}
}
}
/**
* 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);
}
