private static PScan GetPScan(ScanStatistics scanStats, CentroidStream centroidStream, int msOrder,
string fileName, double?precursorMz = null, int?precursorCharge = null)
{
var scan = new PScan
{
FileName = fileName,
BasePeakMass = scanStats.BasePeakMass,
ScanType = scanStats.ScanType,
BasePeakIntensity = scanStats.BasePeakIntensity,
PacketType = scanStats.PacketType,
ScanNumber = scanStats.ScanNumber,
RetentionTime = scanStats.StartTime,
Masses = centroidStream.Masses.ToArray(),
Intensities = centroidStream.Intensities.ToArray(),
LowMass = scanStats.LowMass,
HighMass = scanStats.HighMass,
TIC = scanStats.TIC,
FileId = fileName + ".raw",
PrecursorMz = precursorMz,
PrecursorCharge = precursorCharge,
MsOrder = msOrder
};
return(scan);
}
public ScanStatistics getScansStatistics(long scanId, resultClass token)
{
ScanStatistics scanStatistics = new ScanStatistics();
string path = String.Empty;
try
{
get httpGet = new get();
secure token_secure = new secure(token);
token_secure.findToken(token);
path = token_secure.get_rest_Uri(String.Format(CxConstant.CxScanStatistics, scanId));
if (token.debug && token.verbosity > 1)
{
Console.WriteLine("API: {0}", path);
}
httpGet.get_Http(token, path);
if (token.status == 0)
{
scanStatistics = JsonConvert.DeserializeObject <ScanStatistics>(token.op_result);
}
}
catch (Exception ex)
{
if (token.debug && token.verbosity > 0)
{
Console.Error.WriteLine("getScansStatistics: {0}, Message: {1} Trace: {2}", path, ex.Message, ex.StackTrace);
}
}
return(scanStatistics);
}
/// <summary>
/// Get and set data from the mass spectrum
/// </summary>
/// <param name="inputRawFile"></param>
private void GetSpectrumData(IRawDataPlus inputRawFile)
{
// Get the first and last scan from the RAW file
int firstScanNumber = inputRawFile.RunHeaderEx.FirstSpectrum;
int lastScanNumber = inputRawFile.RunHeaderEx.LastSpectrum;
string itHeaderParam = "Ion Injection Time (ms)";
// Set up empty variables to populate with mass spectrum data
TICList = new double[lastScanNumber];
ITList = new double[lastScanNumber];
RetentionTimeList = new double[lastScanNumber];
try
{
//get out information from mass spectra for each scan
for (int scan = 0; scan <= (ScanNumList.Length - 1); scan++)
{
int thisScan = ScanNumList[scan];
// get the scan statistics for this scan number
ScanStatistics scanStatistic = inputRawFile.GetScanStatsForScanNumber(thisScan);
//get the TIC
TICList[scan] = scanStatistic.TIC;
//get retention time
RetentionTimeList[scan] = inputRawFile.RetentionTimeFromScanNumber(thisScan);
ITList[scan] = GetScanExtraDouble(inputRawFile, thisScan, itHeaderParam);
//TODO: get out noise for peaks
}
}
catch (Exception ex)
{
Console.Write("Error in accessing spectrum data: " + ex);
}
}
/*
* public List<ScanObject> projectId_in_scan(List<ScanObject> scans, string project_name)
* {
* if (String.IsNullOrEmpty(project_name))
* {
* return scans;
* }
* List<ScanObject> pclass = new List<ScanObject>();
* foreach (ScanObject scan in scans)
* {
* if (scan.Project.Name.Contains(project_name))
* {
* pclass.Add(scan);
* }
* }
* return pclass;
* }
*
*/
public bool get_result_statistics(resultClass token, long scanId)
{
getScans scans = new getScans();
if (!CxSettings.ContainsKey(scanId))
{
ScanStatistics scanStatistics = scans.getScansStatistics(scanId, token);
CxResultStatistics.Add(scanId, scanStatistics);
}
return(true);
}
private string getLanguages(List <ScanObject> scans, Dictionary <long, ScanStatistics> scannedStatistics, long scanId)
{
ScanStatistics scanStatistics = scannedStatistics[scanId];
List <string> lang = new List <string>();
LanguageStateCollection[] lstates = getScanObject(scans, scanId).ScanState.LanguageStateCollection;
foreach (LanguageStateCollection state in lstates)
{
lang.Add(state.LanguageName);
}
return(String.Join(",", lang.ToArray()));
}
private bool findFirstorLastScan(long projectId, ScanObject scan, Dictionary <string, Teams> teams, Dictionary <long, ReportStaging> keyValuePairs, bool operation)
{
getScans scans = new getScans();
string fullName = teams[scan.OwningTeamId].fullName;
if (keyValuePairs.ContainsKey(scan.Project.Id))
{
bool start = false;
ReportStaging reportStaging = keyValuePairs[scan.Project.Id];
long diff = DateTimeOffset.Compare(reportStaging.dateTime, (DateTimeOffset)scan.DateAndTime.StartedOn);
if (operation)
{
start = (diff > 0) ? true : false;
}
else
{
start = (diff < 0) ? true : false;
}
if (start)
{
ScanStatistics scanStatistics = scans.getScansStatistics(scan.Id, token);
ReportStaging staging = new ReportStaging()
{
ProjectId = scan.Project.Id,
ProjectName = scan.Project.Name,
TeamName = fullName,
dateTime = (DateTimeOffset)scan.DateAndTime.StartedOn,
High = scanStatistics.HighSeverity,
Medium = scanStatistics.MediumSeverity,
Low = scanStatistics.LowSeverity,
ScanId = scan.Id
};
keyValuePairs[scan.Project.Id] = staging;
}
}
else
{
ScanStatistics scanStatistics = scans.getScansStatistics(scan.Id, token);
keyValuePairs.Add(scan.Project.Id, new ReportStaging()
{
ProjectId = scan.Project.Id,
ProjectName = scan.Project.Name,
TeamName = fullName,
dateTime = (DateTimeOffset)scan.DateAndTime.StartedOn,
High = scanStatistics.HighSeverity,
Medium = scanStatistics.MediumSeverity,
Low = scanStatistics.LowSeverity,
ScanId = scan.Id
});
}
return(true);
}
public ScanStatistics getScansStatistics(long scanId, resultClass token)
{
get httpGet = new get();
ScanStatistics scanStatistics = new ScanStatistics();
secure token_secure = new secure(token);
token_secure.findToken(token);
string path = token_secure.get_rest_Uri(String.Format(CxConstant.CxScanStatistics, scanId));
httpGet.get_Http(token, path);
if (token.status == 0)
{
scanStatistics = JsonConvert.DeserializeObject <ScanStatistics>(token.op_result);
}
return(scanStatistics);
}
public List <ReportLastScan> reportLastScan(resultClass token, List <ScanObject> scans, Dictionary <string, Teams> allTeams, Dictionary <long, ScanStatistics> scannedStatistics, Dictionary <long, ScanSettings> settings, Dictionary <long, Presets> presets)
{
List <ReportLastScan> reportScan = new List <ReportLastScan>();
foreach (ScanObject scan in scans)
{
ScanStatistics scanStatistics = scannedStatistics[scan.Id];
List <string> lang = new List <string>();
LanguageStateCollection[] lstates = scan.ScanState.LanguageStateCollection;
foreach (LanguageStateCollection state in lstates)
{
lang.Add(state.LanguageName);
}
ReportLastScan oneScan = new ReportLastScan()
{
Comment = scan.Comment,
ScanId = scan.Id,
Preset = presets[settings[scan.Project.Id].preset.id].name,
ProjectId = scan.Project.Id,
ProjectName = scan.Project.Name,
ScanFinishDate = scan.DateAndTime.FinishedOn.ToString(),
ScanStartDate = scan.DateAndTime.StartedOn.ToString(),
EngineStartDate = scan.DateAndTime.EngineStartedOn.ToString(),
TeamName = allTeams[scan.OwningTeamId].fullName,
ScanType = scan.ScanType.Value,
Owner = scan.Owner,
LOC = scan.ScanState.LinesOfCode,
FailedLOC = scan.ScanState.FailedLinesOfCode,
FileCount = scan.ScanState.FilesCount,
Origin = scan.Origin,
Languages = String.Join(",", lang.ToArray()),
isIncremental = scan.IsIncremental ? "true" : "false",
High = scanStatistics.HighSeverity,
Medium = scanStatistics.MediumSeverity,
Low = scanStatistics.LowSeverity,
Info = scanStatistics.InfoSeverity
};
reportScan.Add(oneScan);
}
return(reportScan);
}
private bool findFirstandLastScan(long projectId, ScanObject scan, ScanStatistics scanStatistics, Dictionary <long, ReportStaging> keyStartPairs, Dictionary <long, ReportStaging> keyLastPairs)
{
getScans scans = new getScans();
if (keyStartPairs.ContainsKey(scan.Project.Id))
{
ReportStaging reportStaging = keyStartPairs[scan.Project.Id];
long diff = DateTimeOffset.Compare(reportStaging.dateTime, (DateTimeOffset)scan.DateAndTime.StartedOn);
if (diff > 0)
{
ReportStaging staging = new ReportStaging()
{
ProjectId = scan.Project.Id,
ProjectName = scan.Project.Name,
dateTime = (DateTimeOffset)scan.DateAndTime.StartedOn,
High = scanStatistics.HighSeverity,
Medium = scanStatistics.MediumSeverity,
Low = scanStatistics.LowSeverity,
ScanId = scan.Id
};
keyStartPairs[scan.Project.Id] = staging;
}
}
else
{
keyStartPairs.Add(scan.Project.Id, new ReportStaging()
{
ProjectId = scan.Project.Id,
ProjectName = scan.Project.Name,
dateTime = (DateTimeOffset)scan.DateAndTime.StartedOn,
High = scanStatistics.HighSeverity,
Medium = scanStatistics.MediumSeverity,
Low = scanStatistics.LowSeverity,
ScanId = scan.Id
});
}
if (keyLastPairs.ContainsKey(scan.Project.Id))
{
ReportStaging reportStaging = keyLastPairs[scan.Project.Id];
long diff = DateTimeOffset.Compare(reportStaging.dateTime, (DateTimeOffset)scan.DateAndTime.StartedOn);
if (diff < 0)
{
ReportStaging staging = new ReportStaging()
{
ProjectId = scan.Project.Id,
ProjectName = scan.Project.Name,
dateTime = (DateTimeOffset)scan.DateAndTime.StartedOn,
High = scanStatistics.HighSeverity,
Medium = scanStatistics.MediumSeverity,
Low = scanStatistics.LowSeverity,
ScanId = scan.Id
};
keyLastPairs[scan.Project.Id] = staging;
}
}
else
{
keyLastPairs.Add(scan.Project.Id, new ReportStaging()
{
ProjectId = scan.Project.Id,
ProjectName = scan.Project.Name,
dateTime = (DateTimeOffset)scan.DateAndTime.StartedOn,
High = scanStatistics.HighSeverity,
Medium = scanStatistics.MediumSeverity,
Low = scanStatistics.LowSeverity,
ScanId = scan.Id
});
}
return(true);
}
