//将最终的数据写入文件中
public void writeToAirdInfoFile()
{
jobInfo.log("Writing Index File", "Writing Index File");
AirdInfo airdInfo = buildBasicInfo();
JsonSerializerSettings jsonSetting = new JsonSerializerSettings {
NullValueHandling = NullValueHandling.Ignore
};
string airdInfoStr = JsonConvert.SerializeObject(airdInfo, jsonSetting);
byte[] airdBytes = Encoding.Default.GetBytes(airdInfoStr);
airdJsonStream.Write(airdBytes, 0, airdBytes.Length);
}
/**
* 使用直接的关键信息进行初始化
*
* @param airdPath Aird文件路径
* @param mzCompressor mz压缩策略
* @param intCompressor intensity压缩策略
* @param mzPrecision mz数字精度
* @param airdType aird类型
* @throws ScanException 扫描异常
*/
public BaseParser(String airdPath, Compressor mzCompressor, Compressor intCompressor, int mzPrecision, String airdType)
{
var indexFile = FileNameUtil.getIndexPathByAirdPath(airdPath);
airdInfo = AirdScanUtil.loadAirdInfo(indexFile);
try
{
airdFile = File.OpenRead(airdPath);
}
catch (FileNotFoundException e)
{
Console.WriteLine(e.ToString());
Console.Write(e.StackTrace);
throw new Exception(ResultCodeEnum.AIRD_FILE_PARSE_ERROR.Message);
}
this.mzCompressor = mzCompressor;
this.intCompressor = intCompressor;
this.mzPrecision = mzPrecision;
this.type = airdType;
}
public BaseParser(string indexPath)
{
airdInfo = AirdScanUtil.loadAirdInfo(indexPath);
if (airdInfo == null)
{
throw new Exception(ResultCodeEnum.AIRD_INDEX_FILE_PARSE_ERROR.Message);
}
try
{
airdFile = File.OpenRead(FileNameUtil.getAirdPathByIndexPath(indexPath));
}
catch (FileNotFoundException e)
{
Console.WriteLine(e.ToString());
Console.Write(e.StackTrace);
throw new Exception(ResultCodeEnum.AIRD_FILE_PARSE_ERROR.Message);
}
mzCompressor = CompressUtil.getMzCompressor(airdInfo.compressors);
intCompressor = CompressUtil.getIntCompressor(airdInfo.compressors);
mzPrecision = mzCompressor.precision;
type = airdInfo.type;
}
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);
}
