public Params(Params other) {
// copy values from other
debug = other.debug;
verbose = other.verbose;
ignoreVParams = other.ignoreVParams;
stopLevel = other.stopLevel;
Species = other.Species;
WoodType = other.WoodType;
Seed = other.Seed;
Smooth = other.Smooth;
// create paramDB
paramDB = new Hashtable();
levelParams = new LevelParams[4];
for (int l = 0; l < 4; l++) {
levelParams[l] = new LevelParams(l, paramDB);
}
registerParams();
// copy param values
for (Enumeration e = paramDB.elements(); e.hasMoreElements(); ) {
AbstractParam p = ((AbstractParam) e.nextElement());
try {
AbstractParam otherParam = other.getParam(p.name);
if (!otherParam.empty()) {
p.setValue(otherParam.getValue());
} // else use default value
} catch (ParamError err) {
System.err.println("Error copying params: " + err.getMessage());
}
}
}
public TreeMap getParamGroup(int level, String group) {
TreeMap result = new TreeMap();
for (Enumeration e = paramDB.elements(); e.hasMoreElements(); ) {
AbstractParam p = (AbstractParam) e.nextElement();
if (p.getLevel() == level && p.getGroup().equals(group)) {
result.put(new Integer(p.getOrder()), p);
}
}
return result;
}
public void setParam(String name, String value) throws ParamError {
AbstractParam p = (AbstractParam) paramDB.get(name);
if (p != null) {
p.setValue(value);
if (debug) {
System.err.println("Params.setParam(): set " + name + " to " + value);
}
} else {
throw new ParamError("Unknown parameter " + name + "!");
}
}
private String siiToString(SpectrumIdentificationItem sii) {
String siiString = "";
siiString =
"\""
+ sii.getId()
+ "\""
+ sep
+ sii.getRank()
+ sep
+ sii.isPassThreshold()
+ sep
+ sii.getCalculatedMassToCharge()
+ sep
+ sii.getExperimentalMassToCharge()
+ sep
+ sii.getChargeState();
Peptide pep =
peptideIdHashMap.get(sii.getPeptideRef()); // get Peptide via the hash for this object
siiString += sep + "\"" + pep.getPeptideSequence() + "\"";
// Handle Mods
siiString += sep;
String modString = "";
if (pep.getModification() != null) {
int i = 0;
for (Modification mod : pep.getModification()) {
if (i > 0) {
modString += ";"; // Add an extra separator between mods
}
modString += modToString(mod);
i++;
}
}
if (pep.getSubstitutionModification() != null) {
int i = 0;
for (SubstitutionModification subMod : pep.getSubstitutionModification()) {
if (i > 0 || !modString.equals("")) {
modString += ";"; // Add an extra separator between mods
}
modString += subModToString(subMod);
i++;
}
}
siiString += modString;
Map<String, String> mapNameToValue = new HashMap<>();
for (AbstractParam param : sii.getParamGroup()) {
mapNameToValue.put(param.getName(), param.getValue());
// System.out.println("test1" + param.getName() + "-> " + param.getValue());
}
// Handle scores
for (int i = 0; i < columnToScoreMap.size(); i++) {
String score = columnToScoreMap.get(i);
// System.out.println("test2" + score);
if (mapNameToValue.containsKey(score)) {
String scoreValue = mapNameToValue.get(score);
// System.out.println("test3" + scoreValue);
siiString += sep + scoreValue;
} else {
siiString += sep;
}
}
// Handle all protein maps
siiString += sep + "\"";
List<PeptideEvidenceRef> peptideEvidenceRefList = sii.getPeptideEvidenceRef();
Boolean isDecoy = false;
for (int i = 0; i < peptideEvidenceRefList.size(); i++) {
PeptideEvidenceRef peptideEvidenceRef = peptideEvidenceRefList.get(i);
PeptideEvidence peptideEvidence =
peptideEvidenceIdHashMap.get(peptideEvidenceRef.getPeptideEvidenceRef());
DBSequence dbSeq = dbSequenceIdHashMap.get(peptideEvidence.getDBSequenceRef());
if (i > 0) {
siiString += ";"; // Add an extra separator between mods
}
siiString +=
dbSeq.getAccession()
+ "_"
+ peptideEvidence.getStart()
+ "_"
+ peptideEvidence.getEnd()
+ "_"
+ peptideEvidence.getPre()
+ "_"
+ peptideEvidence.getPost();
if (peptideEvidence.isIsDecoy()) {
isDecoy = true;
}
}
siiString += "\"";
siiString += sep + isDecoy;
return siiString;
}
