/**
* Marshalls the mgf file object to a file. If the file already exists it will be overwritten.
*
* @param file The file to marshall the mgf file to.
*/
public void marshallToFile(File file) throws JMzReaderException {
try {
// create the object to write the file
BufferedWriter writer = new BufferedWriter(new FileWriter(file));
// process all additional parameters
String parameters = marshallAdditionalParameters();
// write the parameters
writer.write(parameters);
// process the pmf spectra
for (PmfQuery q : pmfQueries) writer.write(q.toString() + "\n");
writer.write("\n");
// write the spectra
for (Integer index = 0; index < 1000000; index++) {
if (!ms2Queries.containsKey(index)) continue;
writer.write(ms2Queries.get(index).toString() + "\n");
}
writer.close();
} catch (IOException e) {
throw new JMzReaderException("Failed to write output file", e);
}
}
@Override
public String toString() {
// add the parameters
String string = marshallAdditionalParameters();
// process the pmf spectra
for (PmfQuery q : pmfQueries) string += (q.toString() + "\n");
if (pmfQueries.size() > 0) string += "\n";
// write the spectra
for (Integer index = 0; index < 1000000; index++) {
if (!ms2Queries.containsKey(index)) continue;
string += ms2Queries.get(index).toString() + "\n";
}
return string;
}