peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor());
}
}
if (identification.matchExists(spectrumKey)) {
SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
<BUG>int forwardIon = searchParameters.getIonSearched1();

int rewindIon = searchParameters.getIonSearched2();
</BUG>
PtmSettings modificationProfile = searchParameters.getPtmSettings();

peptideShakerGUI.getUtilitiesUserPreferences().getSpectrumAnnotatedMirroredPeakColor());
}
}
if (identification.matchExists(spectrumKey)) {
SearchParameters searchParameters = peptideShakerGUI.getIdentificationParameters().getSearchParameters();
Integer forwardIon = searchParameters.getForwardIons().get(0);
Integer rewindIon = searchParameters.getRewindIons().get(0);
PtmSettings modificationProfile = searchParameters.getPtmSettings();
