public void WriteHeader(StreamWriter writer, Param para)
{
string localtime = DateTime.Now.ToString() + DateTime.Now.Millisecond.ToString();
writer.WriteLine("{0} {1}", "H\tCreationDate\t", localtime);
writer.WriteLine("{0} {1}", "H\tExtractor\t", "wiff");
writer.WriteLine("{0} {1}", "H\tExtractorVersion\t", "1.0.0.1");
writer.WriteLine("{0} {1}", "H\tComments\t", "Owned by pFind Studio, 2016");
writer.WriteLine("{0} {1}", "H\tDataType\t", (para.cent == true) ? "Centroid" : "Profile");
}
public static void extract(string wiffpath, Param para)
{
WiffFile wifffile = WiffFile.Create(wiffpath);
int pos = wiffpath.LastIndexOf(".");
if (para.outputPath == "")
{
para.outputPath = wiffpath.Substring(0, pos);
}
else
{
para.outputPath = para.outputPath + "\\" + wifffile.name;
}
Console.WriteLine("{0} {1}", "[wiff] Begin to extract ", wiffpath);
Spectrum spec = new Spectrum();
string mgffile = para.outputPath + ".mgf";
string ms1file = para.outputPath + ".ms1";
string ms2file = para.outputPath + ".ms2";
for (int sample = 1; sample <= wifffile.m_batch.GetSampleNames().Length; ++sample)
{
wifffile.GetSample(sample);
//Experiment数目
int experimentCount = wifffile.m_sample.MassSpectrometerSample.ExperimentCount;
spec.array = new TotalIonChromatogram[experimentCount];
spec.scan = 0;
for (int i = 0; i < experimentCount; i++)
{
spec.m_msExperiment = wifffile.m_sample.MassSpectrometerSample.GetMSExperiment(i);
spec.wiffExperiments.Add(spec.m_msExperiment);
spec.array[i] = spec.m_msExperiment.GetTotalIonChromatogram();
}
int numDataPoints = spec.array[0].NumDataPoints;
//Cycle数目
Parse(spec,wifffile,numDataPoints,experimentCount,ms1file,ms2file,mgffile,para);
}
Console.WriteLine("[wiff] Output Files Completed!");
//到此结束
}
public static void Parse(Spectrum spec, WiffFile wifffile, int cycleCount,
int experimentCount, string ms1file, string ms2file,
string mgffile, Param para)
{
StreamWriter writerms1 = null;
StreamWriter writerms2 = null;
StreamWriter writermgf = null;
// 输出Locus2Scan的哈希表
StreamWriter writerLocus2Scan = null;
string locus2scanName = ms1file.Substring(0, ms1file.LastIndexOf('.')) + ".Locus2Scan";
writerLocus2Scan = new StreamWriter(new FileStream(locus2scanName, FileMode.Create, FileAccess.Write));
// 输出 .xtract FLAG 文件
string flagMsFileName = ms1file.Substring(0, ms1file.LastIndexOf('.')) + ".xtract";
if (para.ms1 == 1){
writerms1 = new StreamWriter(new FileStream(ms1file, FileMode.Create, FileAccess.Write));
spec.WriteHeader(writerms1,para); // 写表头
}
if (para.ms2 == 1){
writerms2 = new StreamWriter(new FileStream(ms2file, FileMode.Create, FileAccess.Write));
spec.WriteHeader(writerms2, para); // 写表头
}
if (para.mgf == 1){
writermgf = new StreamWriter(new FileStream(mgffile, FileMode.Create, FileAccess.Write));
}
for (int j = 0; j < cycleCount; j++){
string header = "[wiff] <Output files>: ";
Console.Write("\r" + header + String.Format("{0:F3}", (double)(j + 1) / (double)cycleCount * 100) + "%");
for (int i = 0; i < experimentCount; i++){
TotalIonChromatogram totalIonChromatogram = spec.array[i];
float num = (float)totalIonChromatogram.GetYValue(j);
if (i == 0 || num > 0f){
bool doCentroid = false;
spec.cycle = j + 1;
spec.experiment = i + 1;
spec.m_msExperiment = spec.wiffExperiments[i];
//spec.m_spectrum = spec.m_msExperiment.GetMassSpectrum(j);
try{ // AB 数据可能因为质量不好的原因，造成 Get 不到谱图号
spec.m_spectrum = spec.m_msExperiment.GetMassSpectrum(j);
}catch (System.Exception e){
continue;
}
spec.details = spec.m_msExperiment.Details;
spec.m_spectrumInfo = spec.m_msExperiment.GetMassSpectrumInfo(j);
spec.pointsAreContinuous = !spec.m_spectrumInfo.CentroidMode;
if (spec.GetDataSize(doCentroid) > 0){
List<double> centermzs = new List<double>();
List<double> centerint = new List<double>();
spec.GetData(doCentroid, out centermzs, out centerint);
if (para.cent == true){
PeakDetection.WindowCentroid(centermzs, centerint, out spec.mz, out spec.intensity, spec);
}else{
spec.mz = centermzs;
spec.intensity = centerint;
}
spec.retentionTime = (double)totalIonChromatogram.GetXValue(j);
spec.precursor_mz = 0.0;
spec.charge = 0;
if (spec.m_spectrumInfo.IsProductSpectrum){
spec.precursor_mz = spec.m_spectrumInfo.ParentMZ;
spec.charge = spec.m_spectrumInfo.ParentChargeState;
}
spec.scan++;
//scan从1开始
if (spec.GetMSLevel() == 1 && para.ms1 == 1){
spec.WriteMS1(writerms1);
}else if(spec.GetMSLevel() > 1){
if (para.ms2 == 1){
spec.WriteMS2(writerms2);
}
if (para.mgf == 1){
spec.WriteMGF(wifffile,writermgf);
}
// 输出 locus2scan 哈希表
string wifftitle = "Locus:" + "1.1.1." + spec.cycle + "." + spec.experiment;
//Console.WriteLine("WiffTitle:"+wifftitle);
//Console.WriteLine("Scan:"+spec.scan);
//Console.Read();
writerLocus2Scan.WriteLine(wifftitle+" "+spec.scan);
}
}
}
}
}
if (para.ms1 == 1){
writerms1.Close();
}
if (para.ms2 == 1){
writerms2.Close();
}
if (para.mgf == 1){
writermgf.Close();
}
//写出.Xtract文件作为导出flag.
FileStream flagMsFile = new FileStream(flagMsFileName, FileMode.Create, FileAccess.Write);
flagMsFile.Close();
writerLocus2Scan.Close();
Console.WriteLine();
}
static void Main(string[] args)
{
Application.EnableVisualStyles();
//此方法为应用程序启用可视样式，如果控件和操作系统支持视觉样式，则控件将以视觉样式进行绘制
Stopwatch watch = new Stopwatch();
watch.Start(); //计时
List<string> files = new List<string>();
Param para = new Param();
para.ParseParam(args);
para.getAllInputFile(ref files);
if (files.Count == 0 && args.Length != 0){
Console.WriteLine("[wiff] <Exception>: Warning: No input files.");
return;
}else{
for (int i = 0; i < files.Count; i++){
extract(files[i], para);
// 用了批处理，但 pParse 调用 WiffReader 时使用的是一次一个文件；
}
}
watch.Stop();
string runtime = (watch.ElapsedMilliseconds / 1000).ToString();
Console.WriteLine("{0} {1}", "[wiff] == == == Time elapsed: ", runtime + "s. == == ==");
return;
}
