// Added by Fawaz Ghali 13/05/2014 exportProteoAnnotator
private String proteoAnnotatorLineToString(ProteinAmbiguityGroup pag) {
String line = "";
List<UserParam> userParams = pag.getUserParam();
String countNonA = "";
String scoreNonA = "";
String nonAPeptide = "";
String aGenes = "";
String qValue = "";
for (int i = 0; i < userParams.size(); i++) {
UserParam userParam = userParams.get(i);
if (userParam.getName().equals("nonAPeptide")) {
nonAPeptide = userParam.getValue();
}
}
List<CvParam> cvParamList = pag.getCvParam();
for (int i = 0; i < cvParamList.size(); i++) {
CvParam cvParam = cvParamList.get(i);
if (cvParam.getAccession().equals("MS:1002474")) {
scoreNonA = cvParam.getValue();
}
if (cvParam.getAccession().equals("MS:1002475")) {
countNonA = cvParam.getValue();
}
if (cvParam.getAccession().equals("MS:1002373")) {
qValue = cvParam.getValue();
}
}
List<ProteinDetectionHypothesis> proteinDetectionHypothesisList =
pag.getProteinDetectionHypothesis();
for (int i = 0; i < proteinDetectionHypothesisList.size(); i++) {
ProteinDetectionHypothesis proteinDetectionHypothesis = proteinDetectionHypothesisList.get(i);
if (proteinDetectionHypothesis.getDBSequenceRef().startsWith("dbseq_generic|A_"))
aGenes = aGenes + proteinDetectionHypothesis.getDBSequenceRef() + ";";
}
line = countNonA + sep + scoreNonA + sep + nonAPeptide + sep + aGenes + sep + qValue;
return line;
}
