// 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;
}
private String pdhToString(ProteinDetectionHypothesis pdh) {
String pdhString =
"\""
+ dbSequenceIdHashMap.get(pdh.getDBSequenceRef()).getAccession()
+ "\""
+ sep
+ pdh.isPassThreshold()
+ sep;
DBSequence dbSeq = dbSequenceIdHashMap.get(pdh.getDBSequenceRef());
String protDesc = "";
String protGroupMembership = "";
if (dbSeq != null) {
for (CvParam cvParam : dbSeq.getCvParam()) {
if (cvParam.getAccession().equals("MS:1001088")) { // Protein description
String description = cvParam.getValue().replaceAll("\"", ""); // remove internal "
protDesc = "\"" + description + "\"";
}
}
}
Map<String, String> mapNameToValue = new HashMap<>();
for (CvParam cvParam : pdh.getCvParam()) {
if (cvParam.getAccession().equals("MS:1001591")
|| cvParam.getAccession().equals("MS:1001592")
|| cvParam.getAccession().equals("MS:1001593")
|| cvParam.getAccession().equals("MS:1001594")
|| cvParam.getAccession().equals("MS:1001595")
|| cvParam.getAccession().equals("MS:1001596")
|| cvParam.getAccession().equals("MS:1001597")
|| cvParam.getAccession().equals("MS:1001598")
|| cvParam.getAccession().equals("MS:1001599")) { // Protein description
protGroupMembership = "\"" + cvParam.getName();
if (cvParam.getValue() != null) {
protGroupMembership += ":" + cvParam.getValue();
}
protGroupMembership += "\"";
} else {
mapNameToValue.put(cvParam.getName(), cvParam.getValue());
}
}
for (UserParam userParam : pdh.getUserParam()) {
mapNameToValue.put(userParam.getName(), userParam.getValue());
}
pdhString += protDesc + sep + protGroupMembership + sep;
// Handle scores
for (int i = 0; i < columnToProtScoreMap.size(); i++) {
String score = columnToProtScoreMap.get(i);
// System.out.println("test2" + score);
if (mapNameToValue.containsKey(score)) {
String scoreValue = mapNameToValue.get(score);
// System.out.println("test3" + scoreValue);
pdhString += scoreValue + sep;
} else {
pdhString += sep;
}
}
return pdhString;
}