public void ParallelRun(string path, string outputDir, AveragineType type, ChargerType charger)
{
string file = Path.GetFileNameWithoutExtension(path) + ".mzML";
string output = Path.Combine(outputDir, file);
MZMLProducer mZMLProducer = new MZMLProducer();
var model = mZMLProducer.Produce(path, progressingCounter.Add, type, (mzMLWriter.ChargerType)charger);
var serializer = new XmlSerializer(model.GetType());
var encoding = Encoding.GetEncoding("ISO-8859-1");
XmlWriterSettings xmlWriterSettings = new XmlWriterSettings
{
Indent = true,
OmitXmlDeclaration = false,
Encoding = Encoding.UTF8
};
using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
using (XmlWriter xmlWriter = XmlWriter.Create(writer, xmlWriterSettings))
{
serializer.Serialize(xmlWriter, model);
}
}
}
// update progress
progress.Add();
}
// GetChargerType() -> u32
public static long GetChargerType(ServiceCtx context)
{
ChargerType chargerType = ChargerType.ChargerOrDock;
context.ResponseData.Write((int)chargerType);
Logger.PrintStub(LogClass.ServicePsm, new { chargerType });
return(0);
}
// GetChargerType() -> u32
public static ResultCode GetChargerType(ServiceCtx context)
{
ChargerType chargerType = ChargerType.ChargerOrDock;
context.ResponseData.Write((int)chargerType);
Logger.Stub?.PrintStub(LogClass.ServicePsm, new { chargerType });
return(ResultCode.Success);
}
public static ChargerBase GetCharger(BatteryBase battery, ChargerType type)
{
switch (type)
{
case ChargerType.Theard:
return(new ChargerThread(battery));
case ChargerType.Task:
return(new ChargerTask(battery));
default:
throw new NotImplementedException($"Not implemented logic for {type.ToString()} in {nameof(ChargerType)}");
}
}
public IPowerSource GetPowerSource(ChargerType type, float outputAmperage, float outputVoltage)
{
switch (type)
{
case ChargerType.UsbCharger:
return(new UsbCharger(outputAmperage, outputVoltage));
case ChargerType.WirelessCharger:
return(new WirelessCharger(outputAmperage, outputVoltage));
default:
throw new NotSupportedException();
}
}
private void SelectCharger(object sender, RoutedEventArgs e)
{
if (Patterson.IsChecked == true)
{
charger = ChargerType.Patterson;
}
else if (Fourier.IsChecked == true)
{
charger = ChargerType.Fourier;
}
else if (Combined.IsChecked == true)
{
charger = ChargerType.Combined;
}
}
public void ParallelRun(string path, string outputDir, AveragineType type, ChargerType chargerType)
{
string file = Path.GetFileNameWithoutExtension(path) + ".mgf";
string output = Path.Combine(outputDir, file);
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking(ms1PrcisionPPM);
reader.Init(path);
Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >();
int current = -1;
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
for (int i = start; i < end; i++)
{
if (reader.GetMSnOrder(i) == 1)
{
current = i;
scanGroup[i] = new List <int>();
}
else if (reader.GetMSnOrder(i) == 2)
{
scanGroup[current].Add(i);
}
}
List <MS2Info> ms2Infos = new List <MS2Info>();
Parallel.ForEach(scanGroup, (scanPair) =>
{
if (scanPair.Value.Count > 0)
{
ISpectrum ms1 = reader.GetSpectrum(scanPair.Key);
foreach (int i in scanPair.Value)
{
double mz = reader.GetPrecursorMass(i, reader.GetMSnOrder(i));
List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange);
if (ms1Peaks.Count() == 0)
{
continue;
}
// insert pseudo peaks for large gap
List <IPeak> peaks = new List <IPeak>();
double precision = 0.02;
double last = ms1Peaks.First().GetMZ();
foreach (IPeak peak in ms1Peaks)
{
if (peak.GetMZ() - last > precision)
{
peaks.Add(new GeneralPeak(last + precision / 2, 0));
peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0));
}
peaks.Add(peak);
last = peak.GetMZ();
}
List <IPeak> majorPeaks = picking.Process(peaks);
ICharger charger = new Patterson();
if (chargerType == ChargerType.Fourier)
{
charger = new Fourier();
}
else if (chargerType == ChargerType.Combined)
{
charger = new PattersonFourierCombine();
}
int charge = charger.Charge(peaks, mz - searchRange, mz + searchRange);
// find evelope cluster
EnvelopeProcess envelope = new EnvelopeProcess();
var cluster = envelope.Cluster(majorPeaks, mz, charge);
if (cluster.Count == 0)
{
continue;
}
// find monopeak
Averagine averagine = new Averagine(type);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
double precursorMZ = result.GetMZ();
// write mgf
ISpectrum ms2 = reader.GetSpectrum(i);
IProcess processer = new WeightedAveraging(new LocalNeighborPicking());
ms2 = processer.Process(ms2);
MS2Info ms2Info = new MS2Info
{
PrecursorMZ = result.GetMZ(),
PrecursorCharge = charge,
Scan = ms2.GetScanNum(),
Retention = ms2.GetRetention(),
Peaks = ms2.GetPeaks()
};
lock (resultLock)
{
ms2Infos.Add(ms2Info);
}
}
}
readingProgress.Add(scanGroup.Count);
});
ms2Infos = ms2Infos.OrderBy(m => m.Scan).ToList();
using (FileStream ostrm = new FileStream(output, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
foreach (MS2Info ms2 in ms2Infos)
{
WriteMGF(writer, path + ",SCANS=" + ms2.Scan.ToString() + ",PRECURSOR=" + ms2.PrecursorMZ, ms2.PrecursorMZ, ms2.PrecursorCharge,
ms2.Scan, ms2.Retention * 60, reader.GetActivation(ms2.Scan), ms2.Peaks);
writer.Flush();
}
}
}
// update progress
progress.Add();
}
public Run Read(string path, AveragineType type, ChargerType charger, string defaultDataProcessingRef,
ProgressUpdate updater)
{
Run data = new Run();
// init reader
ThermoRawSpectrumReader reader = new ThermoRawSpectrumReader();
LocalMaximaPicking picking = new LocalMaximaPicking(ms1PrcisionPPM);
IProcess process = new WeightedAveraging(new LocalNeighborPicking());
reader.Init(path);
data.spectrumList = new SpectrumList();
Dictionary <int, Spectrum> spectrumMap = new Dictionary <int, Spectrum>();
int start = reader.GetFirstScan();
int end = reader.GetLastScan();
Dictionary <int, List <int> > scanGroup = new Dictionary <int, List <int> >();
int current = -1;
for (int i = start; i < end; i++)
{
if (reader.GetMSnOrder(i) == 1)
{
current = i;
scanGroup[i] = new List <int>();
}
else if (reader.GetMSnOrder(i) == 2)
{
scanGroup[current].Add(i);
}
}
Parallel.ForEach(scanGroup, (scanPair) => {
if (scanPair.Value.Count > 0)
{
int parentScan = scanPair.Key;
ISpectrum ms1 = null;
List <IPeak> majorPeaks = new List <IPeak>();
Spectrum ms1Spectrum =
ThermoRawRunFactoryHelper.GetMS1Spectrum(ref reader, parentScan, ref ms1);
if (ms1Spectrum != null)
{
lock (resultLock)
{
spectrumMap[parentScan] = ms1Spectrum;
}
}
foreach (int scan in scanPair.Value)
{
Spectrum ms2Spectrum =
ThermoRawRunFactoryHelper.GetMS2Spectrum(ref reader, scan, type, charger, picking, process, ms1);
if (ms2Spectrum != null)
{
lock (resultLock)
{
spectrumMap[scan] = ms2Spectrum;
}
}
}
}
updater(scanGroup.Count);
});
List <Spectrum> spectrumList =
spectrumMap.OrderBy(s => s.Key).Select(s => s.Value).ToList();
data.spectrumList.spectrum = new Spectrum[spectrumList.Count];
spectrumList = spectrumList.OrderBy(x => int.Parse(x.id.Substring(5))).ToList();
for (int i = 0; i < spectrumList.Count; i++)
{
int scan = int.Parse(spectrumList[i].id.Substring(5));
data.spectrumList.spectrum[i] = spectrumList[i];
data.spectrumList.spectrum[i].index = (scan - 1).ToString();
data.spectrumList.spectrum[i].defaultArrayLength = spectrumList[i].defaultArrayLength;
}
data.spectrumList.count = spectrumList.Count.ToString();
data.spectrumList.defaultDataProcessingRef = defaultDataProcessingRef;
return(data);
}
public List <API.Common.Model.ChargePoint> Process(CoreReferenceData coreRefData)
{
List <ChargePoint> outputList = new List <ChargePoint>();
string source = InputData;
JObject o = JObject.Parse(source);
var dataList = o["locations"].ToArray();
var submissionStatus = coreRefData.SubmissionStatusTypes.First(s => s.ID == (int)StandardSubmissionStatusTypes.Imported_UnderReview);//imported and under review
var operationalStatus = coreRefData.StatusTypes.First(os => os.ID == 50);
var unknownStatus = coreRefData.StatusTypes.First(os => os.ID == 0);
var usageTypePublic = coreRefData.UsageTypes.First(u => u.ID == 1);
var usageTypePrivate = coreRefData.UsageTypes.First(u => u.ID == 2);
var operatorUnknown = coreRefData.Operators.First(opUnknown => opUnknown.ID == 1);
int itemCount = 0;
foreach (var item in dataList)
{
ChargePoint cp = new ChargePoint();
cp.DataProvider = new DataProvider()
{
ID = this.DataProviderID
}; //carstations.com
cp.DataProvidersReference = item["post_id"].ToString();
cp.DateLastStatusUpdate = DateTime.UtcNow;
cp.AddressInfo = new AddressInfo();
//carstations.com have requested we not use the station names from their data, so we use address
//cp.AddressInfo.Title = item["name"] != null ? item["name"].ToString() : item["address"].ToString();
cp.AddressInfo.Title = item["address"] != null ? item["address"].ToString() : item["post_id"].ToString();
cp.AddressInfo.Title = cp.AddressInfo.Title.Trim().Replace("&", "&");
cp.AddressInfo.RelatedURL = "http://carstations.com/" + cp.DataProvidersReference;
cp.DateLastStatusUpdate = DateTime.UtcNow;
cp.AddressInfo.AddressLine1 = item["address"].ToString().Trim();
cp.AddressInfo.Town = item["city"].ToString().Trim();
cp.AddressInfo.StateOrProvince = item["region"].ToString().Trim();
cp.AddressInfo.Postcode = item["postal_code"].ToString().Trim();
cp.AddressInfo.Latitude = double.Parse(item["latitude"].ToString().Trim());
cp.AddressInfo.Longitude = double.Parse(item["longitude"].ToString().Trim());
cp.AddressInfo.ContactTelephone1 = item["phone"].ToString();
if (!String.IsNullOrEmpty(item["country"].ToString()))
{
string country = item["country"].ToString();
int? countryID = null;
var countryVal = coreRefData.Countries.FirstOrDefault(c => c.Title.ToLower() == country.Trim().ToLower());
if (countryVal == null)
{
country = country.ToUpper();
//match country
if (country == "UNITED STATES" || country == "US" || country == "USA" || country == "U.S." || country == "U.S.A.")
{
countryID = 2;
}
if (country == "UK" || country == "GB" || country == "GREAT BRITAIN" || country == "UNITED KINGDOM")
{
countryID = 1;
}
}
else
{
countryID = countryVal.ID;
}
if (countryID == null)
{
this.Log("Country Not Matched, will require Geolocation:" + item["country"].ToString());
}
else
{
cp.AddressInfo.Country = coreRefData.Countries.FirstOrDefault(cy => cy.ID == countryID);
}
}
else
{
//default to US if no country identified
//cp.AddressInfo.Country = cp.AddressInfo.Country = coreRefData.Countries.FirstOrDefault(cy => cy.ID == 2);
}
//System.Diagnostics.Debug.WriteLine(item.ToString());
string publicCount = item["public"].ToString();
string privateCount = item["private"].ToString();
if (!String.IsNullOrEmpty(publicCount) && publicCount != "0")
{
try
{
cp.NumberOfPoints = int.Parse(publicCount);
}
catch (Exception) { }
cp.UsageType = usageTypePublic;
}
else
{
if (!String.IsNullOrEmpty(privateCount) && privateCount != "0")
{
try
{
cp.NumberOfPoints = int.Parse(privateCount);
}
catch (Exception) { }
cp.UsageType = usageTypePrivate;
}
}
string verifiedFlag = item["verified_flag"].ToString();
if (!string.IsNullOrEmpty(verifiedFlag) && verifiedFlag != "0")
{
cp.StatusType = operationalStatus;
}
else
{
cp.StatusType = unknownStatus;
}
//TODO: allow for multiple operators?
var operatorsNames = item["brands"].ToArray();
if (operatorsNames.Count() > 0)
{
var operatorName = operatorsNames[0].ToString();
var opDetails = coreRefData.Operators.FirstOrDefault(op => op.Title.ToLower().Contains(operatorName.ToString().ToLower()));
if (opDetails != null)
{
cp.OperatorInfo = opDetails;
}
else
{
Log("Operator not matched:" + operatorName);
}
}
else
{
cp.OperatorInfo = operatorUnknown;
}
var connectorTypes = item["techs"].ToArray();
foreach (var conn in connectorTypes)
{
ConnectionInfo cinfo = new ConnectionInfo()
{
};
ConnectionType cType = new ConnectionType {
ID = 0
};
ChargerType level = null;
cinfo.Reference = conn.ToString();
if (conn.ToString().ToUpper() == "J1772")
{
cType = new ConnectionType();
cType.ID = 1; //J1772
level = new ChargerType {
ID = 2
}; //default to level 2
}
if (conn.ToString().ToUpper() == "CHADEMO")
{
cType = new ConnectionType();
cType.ID = 2; //CHadeMO
level = new ChargerType {
ID = 3
}; //default to level 3
}
if (conn.ToString().ToUpper() == "NEMA5")
{
cType = new ConnectionType();
cType.ID = 9; //NEMA5-20R
level = new ChargerType {
ID = 1
}; //default to level 1
}
if (cType.ID == 0)
{
var conType = coreRefData.ConnectionTypes.FirstOrDefault(ct => ct.Title.ToLower().Contains(conn.ToString().ToLower()));
if (conType != null)
{
cType = conType;
}
}
cinfo.ConnectionType = cType;
cinfo.Level = level;
if (cp.Connections == null)
{
cp.Connections = new List <ConnectionInfo>();
if (!IsConnectionInfoBlank(cinfo))
{
cp.Connections.Add(cinfo);
}
}
}
if (cp.DataQualityLevel == null)
{
cp.DataQualityLevel = 2;
}
cp.SubmissionStatus = submissionStatus;
if (IsPOIValidForImport(cp))
{
outputList.Add(cp);
}
itemCount++;
}
return(outputList);
}
public List <API.Common.Model.ChargePoint> Process(CoreReferenceData coreRefData)
{
List <ChargePoint> outputList = new List <ChargePoint>();
string source = InputData;
JObject o = JObject.Parse(source);
var dataList = o["ChargeDevice"].ToArray();
var submissionStatus = coreRefData.SubmissionStatusTypes.First(s => s.ID == (int)StandardSubmissionStatusTypes.Imported_Published);//imported and published
var operationalStatus = coreRefData.StatusTypes.First(os => os.ID == 50);
var nonoperationalStatus = coreRefData.StatusTypes.First(os => os.ID == 100);
var unknownStatus = coreRefData.StatusTypes.First(os => os.ID == (int)StandardStatusTypes.Unknown);
var usageTypeUnknown = coreRefData.UsageTypes.First(u => u.ID == (int)StandardUsageTypes.Unknown);
var usageTypePublic = coreRefData.UsageTypes.First(u => u.ID == (int)StandardUsageTypes.Public);
var usageTypePublicPayAtLocation = coreRefData.UsageTypes.First(u => u.ID == (int)StandardUsageTypes.Public_PayAtLocation);
var usageTypePrivate = coreRefData.UsageTypes.First(u => u.ID == (int)StandardUsageTypes.PrivateRestricted);
var usageTypePublicMembershipRequired = coreRefData.UsageTypes.First(u => u.ID == (int)StandardUsageTypes.Public_MembershipRequired);
var operatorUnknown = coreRefData.Operators.First(opUnknown => opUnknown.ID == (int)StandardOperators.UnknownOperator);
int itemCount = 0;
foreach (var dataItem in dataList)
{
var item = dataItem;
ChargePoint cp = new ChargePoint();
cp.DataProvider = new DataProvider()
{
ID = 18
}; //UK National Charge Point Registry
cp.DataProvidersReference = item["ChargeDeviceId"].ToString();
cp.DateLastStatusUpdate = DateTime.UtcNow;
cp.AddressInfo = new AddressInfo();
var locationDetails = item["ChargeDeviceLocation"];
var addressDetails = locationDetails["Address"];
cp.AddressInfo.RelatedURL = "";
cp.DateLastStatusUpdate = DateTime.UtcNow;
cp.AddressInfo.AddressLine1 = addressDetails["Street"].ToString().Replace("<br>", ", ");
cp.AddressInfo.Title = String.IsNullOrEmpty(locationDetails["LocationShortDescription"].ToString()) ? cp.AddressInfo.AddressLine1 : locationDetails["LocationShortDescription"].ToString();
cp.AddressInfo.Title = cp.AddressInfo.Title.Replace("&", "&");
cp.AddressInfo.Title = cp.AddressInfo.Title.Replace("<br>", ", ");
cp.AddressInfo.Town = addressDetails["PostTown"].ToString();
cp.AddressInfo.StateOrProvince = addressDetails["DependantLocality"].ToString();
cp.AddressInfo.Postcode = addressDetails["PostCode"].ToString();
cp.AddressInfo.Latitude = double.Parse(locationDetails["Latitude"].ToString());
cp.AddressInfo.Longitude = double.Parse(locationDetails["Longitude"].ToString());
cp.AddressInfo.AccessComments = locationDetails["LocationLongDescription"].ToString().Replace("<br>", ", ").Replace("\r\n", ", ").Replace("\n", ", ");
//TODO: if address wasn't provide in address details try to parse from "LocationLongDescription":
/*if (String.IsNullOrEmpty(cp.AddressInfo.AddressLine1) && string.IsNullOrEmpty(cp.AddressInfo.AddressLine2) && string.IsNullOrEmpty(cp.AddressInfo.Town) && string.IsNullOrEmpty(cp.AddressInfo.Postcode))
* {
*
* }*/
//if title is empty, attempt to add a suitable replacement
if (String.IsNullOrEmpty(cp.AddressInfo.Title))
{
if (!String.IsNullOrEmpty(cp.AddressInfo.AddressLine1))
{
cp.AddressInfo.Title = cp.AddressInfo.AddressLine1;
}
else
{
cp.AddressInfo.Title = cp.AddressInfo.Postcode;
}
}
//cp.AddressInfo.ContactTelephone1 = item["phone"].ToString();
if (!String.IsNullOrEmpty(addressDetails["Country"].ToString()))
{
string country = addressDetails["Country"].ToString();
int? countryID = null;
var countryVal = coreRefData.Countries.FirstOrDefault(c => c.Title.ToLower() == country.Trim().ToLower());
if (countryVal == null)
{
country = country.ToUpper();
//match country
if (country == "gb" || country == "US" || country == "USA" || country == "U.S." || country == "U.S.A.")
{
countryID = 2;
}
if (country == "UK" || country == "GB" || country == "GREAT BRITAIN" || country == "UNITED KINGDOM")
{
countryID = 1;
}
}
else
{
countryID = countryVal.ID;
}
if (countryID == null)
{
this.Log("Country Not Matched, will require Geolocation:" + item["country"].ToString());
}
else
{
cp.AddressInfo.Country = coreRefData.Countries.FirstOrDefault(cy => cy.ID == countryID);
}
}
else
{
//default to US if no country identified
//cp.AddressInfo.Country = cp.AddressInfo.Country = coreRefData.Countries.FirstOrDefault(cy => cy.ID == 2);
}
//operator from DeviceController
var deviceController = item["DeviceController"];
cp.AddressInfo.RelatedURL = deviceController["Website"].ToString();
var deviceOperator = coreRefData.Operators.FirstOrDefault(devOp => devOp.Title.Contains(deviceController["OrganisationName"].ToString()));
if (deviceOperator != null)
{
cp.OperatorInfo = deviceOperator;
}
else
{
//operator from device owner
var devOwner = item["DeviceOwner"];
deviceOperator = coreRefData.Operators.FirstOrDefault(devOp => devOp.Title.Contains(devOwner["OrganisationName"].ToString()));
if (deviceOperator != null)
{
cp.OperatorInfo = deviceOperator;
}
}
//determine most likely usage type
cp.UsageType = usageTypeUnknown;
if (item["SubscriptionRequiredFlag"].ToString().ToUpper() == "TRUE")
{
//membership required
cp.UsageType = usageTypePublicMembershipRequired;
}
else
{
if (item["PaymentRequiredFlag"].ToString().ToUpper() == "TRUE")
{
//payment required
cp.UsageType = usageTypePublicPayAtLocation;
}
else
{
//accessible 24 hours, payment not required and membership not required, assume public
if (item["Accessible24Hours"].ToString().ToUpper() == "TRUE")
{
cp.UsageType = usageTypePublic;
}
}
}
//add connections
var connectorList = item["Connector"].ToArray();
foreach (var conn in connectorList)
{
string connectorType = conn["ConnectorType"].ToString();
if (!String.IsNullOrEmpty(connectorType))
{
ConnectionInfo cinfo = new ConnectionInfo()
{
};
ConnectionType cType = new ConnectionType {
ID = 0
};
ChargerType level = null;
cinfo.Reference = conn["ConnectorId"].ToString();
if (connectorType.ToUpper().Contains("BS 1363"))
{
cType = new ConnectionType();
cType.ID = 3; //UK 13 amp plug
level = new ChargerType {
ID = 2
}; //default to level 2
}
if (connectorType.ToUpper() == "IEC 62196-2 TYPE 1 (SAE J1772)")
{
cType = new ConnectionType();
cType.ID = 2; //J1772
level = new ChargerType {
ID = 2
}; //default to level 2
}
if (connectorType.ToUpper() == "IEC 62196-2 TYPE 2")
{
cType = new ConnectionType();
cType.ID = 25; //Mennkes Type 2
level = new ChargerType {
ID = 2
}; //default to level 2
}
if (connectorType.ToUpper() == "JEVS G 105 (CHADEMO)")
{
cType = new ConnectionType();
cType.ID = 2; //CHadeMO
level = new ChargerType {
ID = 3
}; //default to level 3
}
if (connectorType.ToUpper() == "IEC 62196-2 TYPE 3")
{
cType = new ConnectionType();
cType.ID = 26; //IEC 62196-2 type 3
level = new ChargerType {
ID = 2
}; //default to level 2
}
if (cType.ID == 0)
{
var conType = coreRefData.ConnectionTypes.FirstOrDefault(ct => ct.Title.ToLower().Contains(conn.ToString().ToLower()));
if (conType != null)
{
cType = conType;
}
}
if (!String.IsNullOrEmpty(conn["RatedOutputVoltage"].ToString()))
{
cinfo.Voltage = int.Parse(conn["RatedOutputVoltage"].ToString());
}
if (!String.IsNullOrEmpty(conn["RatedOutputCurrent"].ToString()))
{
cinfo.Amps = int.Parse(conn["RatedOutputCurrent"].ToString());
}
//TODO: use AC/DC/3 Phase data
if (conn["ChargePointStatus"] != null)
{
cinfo.StatusType = operationalStatus;
if (conn["ChargePointStatus"].ToString() == "Out of service")
{
cinfo.StatusType = nonoperationalStatus;
}
}
if (conn["RatedOutputkW"] != null)
{
double tmpKw = 0;
if (double.TryParse(conn["RatedOutputkW"].ToString(), out tmpKw))
{
cinfo.PowerKW = tmpKw;
}
}
if (conn["RatedOutputVoltage"] != null)
{
int tmpV = 0;
if (int.TryParse(conn["RatedOutputVoltage"].ToString(), out tmpV))
{
cinfo.Voltage = tmpV;
}
}
if (conn["RatedOutputCurrent"] != null)
{
int tmpA = 0;
if (int.TryParse(conn["RatedOutputCurrent"].ToString(), out tmpA))
{
cinfo.Amps = tmpA;
}
}
if (conn["ChargeMethod"] != null && !String.IsNullOrEmpty(conn["ChargeMethod"].ToString()))
{
string method = conn["ChargeMethod"].ToString();
//Single Phase AC, Three Phase AC, DC
if (method == "Single Phase AC")
{
cinfo.CurrentTypeID = (int)StandardCurrentTypes.SinglePhaseAC;
}
if (method == "Three Phase AC")
{
cinfo.CurrentTypeID = (int)StandardCurrentTypes.ThreePhaseAC;
}
if (method == "DC")
{
cinfo.CurrentTypeID = (int)StandardCurrentTypes.DC;
}
}
cinfo.ConnectionType = cType;
cinfo.Level = level;
if (cp.Connections == null)
{
cp.Connections = new List <ConnectionInfo>();
if (!IsConnectionInfoBlank(cinfo))
{
//TODO: skip items with blank address info
cp.Connections.Add(cinfo);
}
}
}
}
//apply data attribution metadata
if (cp.MetadataValues == null)
{
cp.MetadataValues = new List <MetadataValue>();
}
cp.MetadataValues.Add(new MetadataValue {
MetadataFieldID = (int)StandardMetadataFields.Attribution, ItemValue = DataAttribution
});
if (cp.DataQualityLevel == null)
{
cp.DataQualityLevel = 3;
}
cp.SubmissionStatus = submissionStatus;
outputList.Add(cp);
itemCount++;
}
return(outputList);
}
public MSmzML Produce(string path, ProgressUpdate updater, AveragineType type, ChargerType charger)
{
var model = new MSmzML();
// cvList
model.cvList = new CVList();
CV[] cvArray = new CV[2];
cvArray[0] = new CV()
{
id = "MS",
fullName = "Proteomics Standards Initiative Mass Spectrometry Ontology",
version = "2.26.0",
URI = "http://psidev.cvs.sourceforge.net/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo"
};
cvArray[1] = new CV
{
id = "UO",
fullName = "Unit Ontology",
version = "14:07:2009",
URI = "http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo"
};
model.cvList.cv = cvArray;
model.cvList.count = "2";
// fileDescription
model.fileDescription = new FileDescription();
model.fileDescription.fileContent = new FileContent();
model.fileDescription.fileContent.cvParam = new CVParam[2];
model.fileDescription.fileContent.cvParam[0] = new CVParam
{
cvRef = "MS",
accession = "MS:1000580",
name = "MSn spectrum",
value = ""
};
model.fileDescription.fileContent.cvParam[1] = new CVParam
{
cvRef = "MS",
accession = "MS:1000127",
name = "centroid spectrum",
value = ""
};
model.fileDescription.sourceFileList = new SourceFileList();
model.fileDescription.sourceFileList.sourceFile = new SourceFile[1];
string fileName = Path.GetFileName(path);
model.fileDescription.sourceFileList.sourceFile[0] = new SourceFile
{
id = fileName,
name = fileName,
location = path
};
model.fileDescription.sourceFileList.count = "1";
model.fileDescription.contact = new Contact();
model.fileDescription.contact.cvParam = new CVParam[2];
model.fileDescription.contact.cvParam[0] = new CVParam
{
cvRef = "MS",
accession = "MS:1000586",
name = "contact name",
value = contactPerson
};
model.fileDescription.contact.cvParam[1] = new CVParam
{
cvRef = "MS",
accession = "MS:1000589",
name = "contact email",
value = contactEmail
};
// softwareList
model.softwareList = new SoftwareList();
model.softwareList.software = new Software[1];
model.softwareList.software[0] = new Software
{
id = software,
version = softwareVersion
};
model.softwareList.count = "1";
// instrumentConfiguration
string instrumentConfigurationID = "UNKNOWN";
model.instrumentConfigurationList = new InstrumentConfigurationList();
model.instrumentConfigurationList.instrumentConfiguration = new InstrumentConfiguration[1];
model.instrumentConfigurationList.instrumentConfiguration[0] = new InstrumentConfiguration()
{
id = instrumentConfigurationID
};
model.instrumentConfigurationList.count = "1";
// data processing
model.dataProcessingList = new DataProcessingList();
model.dataProcessingList.dataProcessing = new DataProcessing[1];
model.dataProcessingList.dataProcessing[0] = new DataProcessing();
model.dataProcessingList.dataProcessing[0].id = dataProcessingID;
model.dataProcessingList.dataProcessing[0].processingMethod = new ProcessingMethod[1];
model.dataProcessingList.dataProcessing[0].processingMethod[0] = new ProcessingMethod()
{
order = "1",
softwareRef = software
};
model.dataProcessingList.dataProcessing[0].processingMethod[0].cvParam = new CVParam[2];
model.dataProcessingList.dataProcessing[0].processingMethod[0].cvParam[0] = new CVParam()
{
cvRef = "MS",
accession = "MS:1000035",
name = "peak picking",
value = ""
};
model.dataProcessingList.dataProcessing[0].processingMethod[0].cvParam[1] = new CVParam()
{
cvRef = "MS",
accession = "MS:1000544",
name = "Conversion to mzML",
value = ""
};
model.dataProcessingList.count = "1";
// spectrum data
ThermoRawRunFactory factory = new ThermoRawRunFactory();
model.run = factory.Read(path, type, charger,
model.dataProcessingList.dataProcessing[0].id, updater);
model.run.id = Guid.NewGuid().ToString();
model.run.defaultInstrumentConfigurationRef = instrumentConfigurationID;
return(model);
}
public static Spectrum GetMS2Spectrum(ref ThermoRawSpectrumReader reader,
int scan, AveragineType type, ChargerType chargerType, LocalMaximaPicking picking, IProcess process,
ISpectrum ms1)
{
// scan header
Spectrum spectrum = new Spectrum
{
id = "scan=" + scan.ToString()
};
double dLowMass = 0;
double dHighMass = 0;
double dTIC = 0;
double dBasePeakMass = 0;
double dBasePeakIntensity = 0;
reader.GetScanHeaderInfoForScanNum(scan, ref dLowMass, ref dHighMass,
ref dTIC, ref dBasePeakMass, ref dBasePeakIntensity);
SetScanHeader(spectrum, dLowMass, dHighMass, dTIC,
dBasePeakMass, dBasePeakIntensity);
// binary data
spectrum.binaryDataArrayList = new BinaryDataArrayList();
SetBinaryDataArrayHeader(spectrum.binaryDataArrayList);
spectrum.cvParam[0] = new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000511",
name = "ms level",
value = "2",
};
double mz = reader.GetPrecursorMass(scan, reader.GetMSnOrder(scan));
List <IPeak> ms1Peaks = FilterPeaks(ms1.GetPeaks(), mz, searchRange);
if (ms1Peaks.Count() == 0)
{
return(null);
}
// insert pseudo peaks for large gaps
List <IPeak> peaks = new List <IPeak>();
double precision = 0.02;
double last = ms1Peaks.First().GetMZ();
foreach (IPeak peak in ms1Peaks)
{
if (peak.GetMZ() - last > precision)
{
peaks.Add(new GeneralPeak(last + precision / 2, 0));
peaks.Add(new GeneralPeak(peak.GetMZ() - precision / 2, 0));
}
peaks.Add(peak);
last = peak.GetMZ();
}
List <IPeak> majorPeaks = picking.Process(peaks);
ICharger charger = new Patterson();
if (chargerType == ChargerType.Fourier)
{
charger = new Fourier();
}
else if (chargerType == ChargerType.Combined)
{
charger = new PattersonFourierCombine();
}
int charge = charger.Charge(peaks, mz - searchRange, mz + searchRange);
// find evelope cluster
EnvelopeProcess envelope = new EnvelopeProcess();
var cluster = envelope.Cluster(majorPeaks, mz, charge);
if (cluster.Count == 0)
{
return(null);
}
// find monopeak
Averagine averagine = new Averagine(type);
BrainCSharp braincs = new BrainCSharp();
MonoisotopicSearcher searcher = new MonoisotopicSearcher(averagine, braincs);
MonoisotopicScore result = searcher.Search(mz, charge, cluster);
// process spectrum
ISpectrum ms2 = reader.GetSpectrum(scan);
List <IPeak> ms2Peaks = process.Process(ms2).GetPeaks();
spectrum.binaryDataArrayList.binaryDataArray[0].binary =
ms2Peaks.SelectMany(p => BitConverter.GetBytes(p.GetMZ())).ToArray();
spectrum.binaryDataArrayList.binaryDataArray[1].binary =
ms2Peaks.SelectMany(p => BitConverter.GetBytes(p.GetIntensity())).ToArray();
spectrum.defaultArrayLength = ms2Peaks.Count.ToString();
spectrum.precursorList = new PrecursorList
{
count = "1",
precursor = new Precursor[1]
};
for (int i = 0; i < spectrum.precursorList.precursor.Length; i++)
{
spectrum.precursorList.precursor[i] = new Precursor();
}
spectrum.precursorList.precursor[0].selectedIonList = new SelectedIonList
{
count = "1",
selectedIon = new SelectedIon[1]
};
for (int i = 0; i < spectrum.precursorList.precursor[0].selectedIonList.selectedIon.Length; i++)
{
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[i] = new SelectedIon();
}
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam = new Component.CVParam[2];
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[0] = new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000744",
name = "selected ion m/z",
value = result.GetMZ().ToString(),
unitCvRef = "MS",
unitAccession = "MS:1000040",
unitName = "m/z"
};
spectrum.precursorList.precursor[0].selectedIonList.selectedIon[0].cvParam[1] = new Component.CVParam()
{
cvRef = "MS",
accession = "MS:1000041",
name = "charge state",
value = charge.ToString()
};
spectrum.precursorList.precursor[0].activation = new Activation
{
cvParam = new Component.CVParam[1]
};
spectrum.precursorList.precursor[0].activation.cvParam[0] =
ActivationCVParam(reader.GetActivation(scan));
spectrum.binaryDataArrayList.binaryDataArray[0].encodedLength =
Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[0].binary).Length.ToString();
spectrum.binaryDataArrayList.binaryDataArray[1].encodedLength =
Convert.ToBase64String(spectrum.binaryDataArrayList.binaryDataArray[1].binary).Length.ToString();
return(spectrum);
}
