//提取SWATH 窗口信息
private void buildWindowsRanges()
{
jobInfo.log("Start getting windows", "Getting Windows");
int i = 0;
List <Double> mzList = new List <Double>();
//找到第一张MS1图,如果找不到,则继续往下搜索,如果搜索了500张以上的谱图或者搜索了超过一半的谱图都没有MS1图,则认为数据格式有问题
Spectrum spectrum = spectrumList.spectrum(0);
while (!spectrum.cvParamChild(CVID.MS_ms_level).value.ToString().Equals(MsLevel.MS1))
{
i++;
spectrum = spectrumList.spectrum(i);
if (i > spectrumList.size() / 2 || i > 500)
{
//如果找了一半的spectrum或者找了超过500个spectrum仍然没有找到ms1,那么数据格式有问题,返回空;
jobInfo.logError("Search for more than 500 spectrums and no ms1 was found. File Format Error");
throw new Exception("Search for more than 500 spectrums and no ms1 was found. File Format Error");
}
}
while (true)
{
if (spectrum.cvParamChild(CVID.MS_ms_level).value.ToString().Equals(MsLevel.MS1))
{
ms1Size++;
i++;
spectrum = spectrumList.spectrum(i);
continue;
}
double mz, lowerOffset, upperOffset;
mz = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_target_m_z);
if (mzList.Contains(mz))
{
break;
}
mzList.Add(mz);
lowerOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_lower_offset);
upperOffset = getPrecursorIsolationWindowParams(spectrum, CVID.MS_isolation_window_upper_offset);
WindowRange range = new WindowRange(mz - lowerOffset, mz + upperOffset, mz);
Hashtable features = new Hashtable();
features.Add(Features.original_width, lowerOffset + upperOffset);
features.Add(Features.original_precursor_mz_start, mz - lowerOffset);
features.Add(Features.original_precursor_mz_end, mz + upperOffset);
range.features = FeaturesUtil.toString(features);
ranges.Add(range);
i++;
spectrum = spectrumList.spectrum(i);
}
jobInfo.log("Finished Getting Windows");
}
protected AirdInfo buildBasicInfo()
{
AirdInfo airdInfo = new AirdInfo();
List <DomainsCore.Aird.Software> softwares = new List <DomainsCore.Aird.Software>();
List <ParentFile> parentFiles = new List <ParentFile>();
//Basic Job Info
airdInfo.airdPath = jobInfo.airdFilePath;
airdInfo.fileSize = fileSize;
airdInfo.createDate = new DateTime();
airdInfo.type = jobInfo.type;
airdInfo.totalScanCount = msd.run.spectrumList.size();
airdInfo.creator = jobInfo.jobParams.creator;
airdInfo.activator = activator;
airdInfo.energy = energy;
airdInfo.rtUnit = rtUnit;
airdInfo.msType = msType;
airdInfo.polarity = polarity;
//Scan index and window range info
airdInfo.rangeList = ranges;
//Block index
airdInfo.indexList = indexList;
//Instrument Info
List <Instrument> instruments = new List <Instrument>();
foreach (InstrumentConfiguration ic in msd.instrumentConfigurationList)
{
Instrument instrument = new Instrument();
//仪器设备信息
if (jobInfo.format.Equals("WIFF"))
{
instrument.manufacturer = "SCIEX";
}
if (jobInfo.format.Equals("RAW"))
{
instrument.manufacturer = "THERMO";
}
//设备信息在不同的源文件格式中取法不同,有些是在instrumentConfigurationList中获取,有些是在paramGroups获取,因此出现了以下比较丑陋的写法
if (ic.cvParams.Count != 0)
{
foreach (CVParam cv in ic.cvParams)
{
featuresMap.Add(cv.name, cv.value);
}
instrument.model = ic.cvParams[0].name;
}
else if (msd.paramGroups.Count != 0)
{
foreach (ParamGroup pg in msd.paramGroups)
{
if (pg.cvParams.Count != 0)
{
foreach (CVParam cv in pg.cvParams)
{
if (!featuresMap.ContainsKey(cv.name))
{
featuresMap.Add(cv.name, cv.value.ToString());
}
}
instrument.model = pg.cvParams[0].name;
}
}
}
foreach (Component component in ic.componentList)
{
switch (component.type)
{
case ComponentType.ComponentType_Analyzer:
foreach (CVParam cv in component.cvParams)
{
instrument.analyzer.Add(cv.name);
}
break;
case ComponentType.ComponentType_Source:
foreach (CVParam cv in component.cvParams)
{
instrument.source.Add(cv.name);
}
break;
case ComponentType.ComponentType_Detector:
foreach (CVParam cv in component.cvParams)
{
instrument.detector.Add(cv.name);
}
break;
}
}
instruments.Add(instrument);
}
airdInfo.instruments = instruments;
//Software Info
foreach (Software soft in msd.softwareList)
{
DomainsCore.Aird.Software software = new DomainsCore.Aird.Software();
software.name = soft.id;
software.version = soft.version;
softwares.Add(software);
}
DomainsCore.Aird.Software airdPro = new DomainsCore.Aird.Software();
airdPro.name = SoftwareInfo.NAME;
airdPro.version = SoftwareInfo.VERSION;
airdPro.type = "DataFormatConversion";
softwares.Add(airdPro);
airdInfo.softwares = softwares;
//Parent Files Info
foreach (SourceFile sf in msd.fileDescription.sourceFiles)
{
ParentFile file = new ParentFile();
file.name = sf.name;
file.location = sf.location;
file.formatType = sf.id;
parentFiles.Add(file);
}
airdInfo.parentFiles = parentFiles;
//Compressor Info
List <Compressor> coms = new List <Compressor>();
//mz compressor
Compressor mzCompressor = new Compressor();
if (jobInfo.jobParams.useStackZDPD())
{
mzCompressor.addMethod(Compressor.METHOD_STACK);
mzCompressor.digit = jobInfo.jobParams.digit;
}
mzCompressor.addMethod(Compressor.METHOD_PFOR);
mzCompressor.addMethod(Compressor.METHOD_ZLIB);
mzCompressor.target = Compressor.TARGET_MZ;
mzCompressor.precision = (int)(Math.Ceiling(1 / jobInfo.jobParams.mzPrecision));
coms.Add(mzCompressor);
//intensity compressor
Compressor intCompressor = new Compressor();
if (jobInfo.jobParams.useStackZDPD())
{
intCompressor.addMethod(Compressor.METHOD_STACK);
intCompressor.digit = jobInfo.jobParams.digit;
}
if (jobInfo.jobParams.log2)
{
intCompressor.addMethod(Compressor.METHOD_LOG10);
intCompressor.addMethod(Compressor.METHOD_ZLIB);
}
else
{
intCompressor.addMethod(Compressor.METHOD_ZLIB);
}
intCompressor.target = Compressor.TARGET_INTENSITY;
intCompressor.precision = 10; //intensity默认精确到小数点后1位
coms.Add(intCompressor);
airdInfo.compressors = coms;
airdInfo.ignoreZeroIntensityPoint = jobInfo.jobParams.ignoreZeroIntensity;
//Features Info
featuresMap.Add(Features.raw_id, msd.id);
featuresMap.Add(Features.ignore_zero_intensity, jobInfo.jobParams.ignoreZeroIntensity);
featuresMap.Add(Features.source_file_format, jobInfo.format);
featuresMap.Add(Features.byte_order, ByteOrder.LITTLE_ENDIAN);
featuresMap.Add(Features.aird_algorithm, jobInfo.jobParams.getAirdAlgorithmStr());
airdInfo.features = FeaturesUtil.toString(featuresMap);
airdInfo.version = SoftwareInfo.VERSION;
airdInfo.versionCode = SoftwareInfo.VERSION_CODE;
return(airdInfo);
}
