public void Test()
{
List<QueryItem> items = new QueryItemListFormat().ReadFromFile(@"../../../data/LipidProductIon.txt");
Assert.AreEqual(2, items.Count);
Assert.AreEqual(185.1029, items[0].ProductIonMz, 0.0001);
Assert.AreEqual(0.3, items[0].MinRelativeIntensity, 0.1);
Assert.AreEqual(157.3049, items[1].ProductIonMz, 0.0001);
Assert.AreEqual(0.5, items[1].MinRelativeIntensity, 0.1);
}
protected override void ShowReturnInfo(IEnumerable <string> returnInfo)
{
base.ShowReturnInfo(returnInfo);
QueryItemListFormat format = new QueryItemListFormat();
var queryItems = format.ReadFromFile(lastQueryFileName);
UpdateQueryItems(queryItems);
}
public override IEnumerable <string> Process(string fileName)
{
var result = new List <string>();
QueryItemListFormat format = new QueryItemListFormat();
FileInfo rawFile = new FileInfo(rawFileName);
Progress.SetMessage("Reading query product ion from " + fileName);
var queryItems = format.ReadFromFile(fileName);
using (IRawFile reader = RawFileFactory.GetRawFileReader(rawFileName))
{
reader.Open(rawFileName);
int firstSpectrumNumber = reader.GetFirstSpectrumNumber();
LipidPrecursorQuery queryFunc = new LipidPrecursorQuery(reader);
queryFunc.Progress = this.Progress;
char[] chars = new char[] { '\t' };
int curIndex = 0;
foreach (var query in queryItems)
{
Progress.SetMessage(MyConvert.Format("{0}/{1} - Querying precursor ions for product ion {2} ...", ++curIndex, queryItems.Count, query.ProductIonMz));
string savedQueryFile = GetQueryFileName(rawFileName, query.ProductIonMz, productIonPPM, precursorPPM);
PrecursorItemListXmlFormat pilFormat = new PrecursorItemListXmlFormat();
List <PrecursorItem> precursors;
if (!File.Exists(savedQueryFile))
{
precursors = queryFunc.QueryPrecursorFromProductIon(query, productIonPPM, precursorPPM);
pilFormat.WriteToFile(savedQueryFile, precursors);
}
else
{
precursors = pilFormat.ReadFromFile(savedQueryFile);
}
result.Add(savedQueryFile);
var precursorMzs = (from item in precursors
group item by item.PrecursorMZ into mzGroup
let count = mzGroup.Where(m => m.PrecursorIntensity > 0).Count()
orderby count descending
select new PrecursorArea {
PrecursorMz = mzGroup.Key, ScanCount = count, Area = 0.0
}).ToList();
//去掉冗余的precursor
for (int i = precursorMzs.Count - 1; i >= 0; i--)
{
if (precursorMzs[i].ScanCount >= 5)
{
break;
}
for (int j = 0; j < i; j++)
{
if (precursorMzs[j].ScanCount < 5)
{
break;
}
double ppm = PrecursorUtils.mz2ppm(precursorMzs[i].PrecursorMz, Math.Abs(precursorMzs[i].PrecursorMz - precursorMzs[j].PrecursorMz));
if (ppm < precursorPPM)
{
precursorMzs.RemoveAt(i);
break;
}
}
}
string savedDetailDir = FileUtils.ChangeExtension(savedQueryFile, "");
if (!Directory.Exists(savedDetailDir))
{
Directory.CreateDirectory(savedDetailDir);
}
for (int i = 0; i < precursorMzs.Count; i++)
{
Progress.SetMessage(MyConvert.Format("{0}/{1} {2} - {3}/{4} Get chromotograph for precursor {5} ...", curIndex, queryItems.Count, query.ProductIonMz, i + 1, precursorMzs.Count, precursorMzs[i].PrecursorMz));
string targetFile = savedDetailDir + "\\" + GetDetailFileName(rawFileName, precursorMzs[i].PrecursorMz);
var itemFormat = new LabelFreeSummaryItemXmlFormat();
LabelFreeSummaryItem item;
if (File.Exists(targetFile))
{
item = itemFormat.ReadFromFile(targetFile);
}
else
{
var ions = queryFunc.QueryChromotograph(precursorMzs[i].PrecursorMz, precursorPPM);
int continueCount = 0;
int firstIndex = -1;
for (int j = 0; j < ions.Count; j++)
{
if (ions[j].Intensity > 0)
{
if (firstIndex == -1)
{
firstIndex = j;
continueCount = 1;
}
else
{
continueCount++;
if (continueCount >= 5)
{
break;
}
}
}
else
{
firstIndex = -1;
continueCount = 0;
}
}
if (continueCount >= 5)
{
ions.RemoveRange(0, firstIndex);
}
continueCount = 0;
int lastIndex = -1;
for (int j = ions.Count - 1; j >= 0; j--)
{
if (ions[j].Intensity > 0)
{
if (lastIndex == -1)
{
lastIndex = j;
continueCount = 1;
}
else
{
continueCount++;
if (continueCount >= 5)
{
break;
}
}
}
else
{
lastIndex = -1;
continueCount = 0;
}
}
if (continueCount >= 5)
{
ions.RemoveRange(lastIndex + 1, ions.Count - lastIndex - 1);
}
//get full ms corresponding to identified ms/ms
var identified = new HashSet <int>();
foreach (var p in precursors)
{
if (p.PrecursorMZ == precursorMzs[i].PrecursorMz)
{
for (int j = p.Scan - 1; j >= firstSpectrumNumber; j--)
{
if (reader.GetMsLevel(j) == 1)
{
identified.Add(j);
break;
}
}
}
}
ions.ForEach(m =>
{
m.Identified = identified.Contains(m.Scan);
m.Enabled = true;
});
Debug.Assert(ions.FindAll(m => m.Identified == true).Count == identified.Count);
item = new LabelFreeSummaryItem()
{
RawFilename = rawFileName,
Sequence = MyConvert.Format("{0:0.0000}; {1:0.00}", query.ProductIonMz, query.MinRelativeIntensity)
};
item.AddRange(ions);
item.CalculatePPM(precursorMzs[i].PrecursorMz);
new LabelFreeSummaryItemXmlFormat().WriteToFile(targetFile, item);
}
precursorMzs[i].Area = item.GetArea();
string savedAreaFile = GetAreaFileName(rawFileName, query.ProductIonMz, productIonPPM, precursorPPM);
new PrecursorAreaListTextFormat().WriteToFile(savedAreaFile, precursorMzs);
}
}
return(result);
}
}
