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();
}
public void WriteMGF(WiffFile wifffile, StreamWriter writer)
{
string title = wifffile.name + "." + scan + "." + scan + "." + "2.0.dta";
writer.WriteLine("BEGIN IONS");
writer.WriteLine("TITLE=" + title);
//string wifftitle = "Locus:" + "1.1.1." + this.cycle + "." + this.experiment;
//Console.WriteLine("pFindTitle:" + title);
//Console.WriteLine("WIFFTITILE=" + wifftitle);
//Console.Read();
//if (this.charge != 0)
//{
// writer.WriteLine("CHARGE=" + this.charge + "+");
//}
writer.WriteLine("CHARGE=2+");
writer.WriteLine("RTINSECONDS=" + this.retentionTime.ToString("F6"));
writer.WriteLine("PEPMASS=" + this.precursor_mz.ToString("G10"));
//去噪，统计频率最高的谱峰，不输出
Dictionary<int, int> dic = new Dictionary<int, int>();
for (int i = 0; i < mz.Count; i++)
{
if (dic.ContainsKey((int)intensity[i]))
dic[(int)intensity[i]] += 1;
else
dic.Add((int)intensity[i], 1);
}
//int mostInten = 0;
int[] mostInten = new int[4];
int countMost = 0;
var aaaa = dic.OrderByDescending(a => a.Value); //按照value降序排序；
foreach (KeyValuePair<int, int> a in aaaa)
{
//Console.WriteLine(a.Key + " " + a.Value);
mostInten[countMost++] = a.Key;
if (countMost == 2)
break;
}
//Console.WriteLine(mostInten[0] + " " + mostInten[1] + " " + mostInten[2]);
//Console.Read();
//输出，但避开强度频率最高的峰
for (int i = 0; i < mz.Count; ++i)
{
if ((int)intensity[i] != mostInten[0] && (int)intensity[i] != mostInten[1])
writer.WriteLine(mz[i].ToString("F5") + "\t" + intensity[i]);
}
writer.WriteLine("END IONS\n");
}
