private static void GetBalanceData(List <QuantitationPeak> argQuantPeaks)
{
QuantitationPeak processingGlycan = null;
try
{
int minScanCount = 0;
List <QuantitationPeak> qPeaks = argQuantPeaks.Where(x => x.ProtonatedPeaks.Count > 0).ToList();
if (qPeaks.Count > 0)
{
minScanCount = qPeaks.Min(x => x.ProtonatedPeaks.Count);
foreach (QuantitationPeak qPeak in argQuantPeaks)
{
processingGlycan = qPeak;
while (qPeak.ProtonatedPeaks.Count > minScanCount)
{
if (qPeak.ProtonatedPeaks[0].Item2 > qPeak.ProtonatedPeaks[qPeak.ProtonatedPeaks.Count - 1].Item2)
{
qPeak.ProtonatedPeaks.RemoveAt(qPeak.ProtonatedPeaks.Count - 1);
}
else
{
qPeak.ProtonatedPeaks.RemoveAt(0);
}
}
}
}
}
catch
{
throw new InvalidDataException("GetBalanceData exception " + processingGlycan.GlycanKey);
}
}
public static void MergeFullList(List<string> argFiles, string argOutputFile, bool argProtonatedResult = false)
{
List<string> ResultFiles = argFiles;
List<string> AllGlycans = new List<string>();
Dictionary<string, List<QuantitationPeak>> AllResult = new Dictionary<string, List<QuantitationPeak>>();
for (int i = 0; i < ResultFiles.Count; i++)
{
//Glycan, Adduct
Dictionary<string, Dictionary<string, List<Tuple<float, float>>>> Result = ReadFullResultCSV(ResultFiles[i]);
//Impute data
ImputationData(Result);
foreach (string glycanKey in Result.Keys)
{
if (!AllGlycans.Contains(glycanKey))
{
AllGlycans.Add(glycanKey);
}
if (!AllResult.ContainsKey(glycanKey))
{
AllResult.Add(glycanKey, new List<QuantitationPeak>());
}
QuantitationPeak qPeak = new QuantitationPeak(Path.GetFileNameWithoutExtension(ResultFiles[i]).Replace("_FullList", ""), glycanKey);
qPeak.AssignPeaks(Result[glycanKey]);
if (!AllResult.ContainsKey(glycanKey))
{
AllResult.Add(glycanKey, new List<QuantitationPeak>());
}
AllResult[glycanKey].Add(qPeak);
}
}
//Export File
using (StreamWriter sw = new StreamWriter(argOutputFile))
{
string tmpStr = "";
tmpStr = "Glycan,";
//Title
foreach (string filename in ResultFiles)
{
tmpStr = tmpStr + Path.GetFileNameWithoutExtension(filename) + ",";
}
sw.WriteLine(tmpStr);
foreach (string GlycanKey in AllResult.Keys)
{
GetBalanceData(AllResult[GlycanKey]);
//Protonated
tmpStr = GlycanKey + " Protonated,";
int ZeroAndNACount = 0;
double smallestIntensity = 9999999999999;
int fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
ZeroAndNACount++;
}
tmpStr = tmpStr + AllResult[GlycanKey][i].TotalProtonatedIntensity.ToString("0.00") + ",";
if (AllResult[GlycanKey][i].TotalProtonatedIntensity == 0)
{
ZeroAndNACount++;
}
fileIdx++;
if (smallestIntensity >= AllResult[GlycanKey][i].TotalProtonatedIntensity && AllResult[GlycanKey][i].TotalProtonatedIntensity > 0)
{
smallestIntensity = AllResult[GlycanKey][i].TotalProtonatedIntensity;
}
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
ZeroAndNACount++;
}
if (ZeroAndNACount == ResultFiles.Count)
{
continue;
}
sw.WriteLine(tmpStr);
tmpStr = GlycanKey + " Protonated Ratio,";
fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
}
tmpStr = tmpStr + (AllResult[GlycanKey][i].TotalProtonatedIntensity / smallestIntensity).ToString("0.00") + ",";
fileIdx++;
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
}
sw.WriteLine(tmpStr);
//All
tmpStr = GlycanKey + " All Adducts,";
smallestIntensity = 9999999999999;
fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
}
tmpStr = tmpStr + AllResult[GlycanKey][i].TotalIntensity.ToString("0.00") + ",";
fileIdx++;
if (smallestIntensity >= AllResult[GlycanKey][i].TotalIntensity && AllResult[GlycanKey][i].TotalIntensity > 0)
{
smallestIntensity = AllResult[GlycanKey][i].TotalIntensity;
}
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
}
sw.WriteLine(tmpStr);
tmpStr = GlycanKey + " All Ratio,";
fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
}
tmpStr = tmpStr + (AllResult[GlycanKey][i].TotalIntensity / smallestIntensity).ToString("0.00") + ",";
fileIdx++;
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
}
sw.WriteLine(tmpStr);
}
}
//Debug
if (argProtonatedResult)
{
StreamWriter swDebug = new StreamWriter(Path.GetDirectoryName(argOutputFile) + "\\MergeResult_Debug.csv");
string tmpDebugStr = "";
tmpDebugStr = "Glycan,";
//Title
foreach (string filename in ResultFiles)
{
tmpDebugStr = tmpDebugStr + Path.GetFileNameWithoutExtension(filename) + "_Time," + Path.GetFileNameWithoutExtension(filename) + "_Intensity,";
}
swDebug.WriteLine(tmpDebugStr);
foreach (string GlycanKey in AllResult.Keys)
{
GetBalanceData(AllResult[GlycanKey]);
swDebug.WriteLine(GlycanKey + " Protonated");
int ProtonatedPeakCount = AllResult[GlycanKey][0].ProtonatedPeaks.Count;
for (int i = 0; i < ProtonatedPeakCount; i++)
{
tmpDebugStr = ",";
int fileIdx = 0;
for (int j = 0; j < ResultFiles.Count; j++)
{
if (AllResult[GlycanKey].Count <= fileIdx || AllResult[GlycanKey][fileIdx].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", "") || AllResult[GlycanKey][fileIdx].ProtonatedPeaks.Count == 0)
{
tmpDebugStr += "N/A,N/A,";
}
else
{
tmpDebugStr += AllResult[GlycanKey][fileIdx].ProtonatedPeaks[i].Item1.ToString("0.00") + "," + AllResult[GlycanKey][fileIdx].ProtonatedPeaks[i].Item2.ToString("0.00") + ",";
fileIdx++;
}
}
swDebug.WriteLine(tmpDebugStr);
}
}
swDebug.Close();
}
}
public static void MergeFullList(List <string> argFiles, string argOutputFile, bool argProtonatedResult = false)
{
List <string> ResultFiles = argFiles;
List <string> AllGlycans = new List <string>();
Dictionary <string, List <QuantitationPeak> > AllResult = new Dictionary <string, List <QuantitationPeak> >();
for (int i = 0; i < ResultFiles.Count; i++)
{
//Glycan, Adduct
Dictionary <string, Dictionary <string, List <Tuple <float, float> > > > Result = ReadFullResultCSV(ResultFiles[i]);
//Impute data
ImputationData(Result);
foreach (string glycanKey in Result.Keys)
{
if (!AllGlycans.Contains(glycanKey))
{
AllGlycans.Add(glycanKey);
}
if (!AllResult.ContainsKey(glycanKey))
{
AllResult.Add(glycanKey, new List <QuantitationPeak>());
}
QuantitationPeak qPeak = new QuantitationPeak(Path.GetFileNameWithoutExtension(ResultFiles[i]).Replace("_FullList", ""), glycanKey);
qPeak.AssignPeaks(Result[glycanKey]);
if (!AllResult.ContainsKey(glycanKey))
{
AllResult.Add(glycanKey, new List <QuantitationPeak>());
}
AllResult[glycanKey].Add(qPeak);
}
}
//Export File
using (StreamWriter sw = new StreamWriter(argOutputFile))
{
string tmpStr = "";
tmpStr = "Glycan,";
//Title
foreach (string filename in ResultFiles)
{
tmpStr = tmpStr + Path.GetFileNameWithoutExtension(filename) + ",";
}
sw.WriteLine(tmpStr);
foreach (string GlycanKey in AllResult.Keys)
{
GetBalanceData(AllResult[GlycanKey]);
//Protonated
tmpStr = GlycanKey + " Protonated,";
int ZeroAndNACount = 0;
double smallestIntensity = 9999999999999;
int fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
ZeroAndNACount++;
}
tmpStr = tmpStr + AllResult[GlycanKey][i].TotalProtonatedIntensity.ToString("0.00") + ",";
if (AllResult[GlycanKey][i].TotalProtonatedIntensity == 0)
{
ZeroAndNACount++;
}
fileIdx++;
if (smallestIntensity >= AllResult[GlycanKey][i].TotalProtonatedIntensity && AllResult[GlycanKey][i].TotalProtonatedIntensity > 0)
{
smallestIntensity = AllResult[GlycanKey][i].TotalProtonatedIntensity;
}
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
ZeroAndNACount++;
}
if (ZeroAndNACount == ResultFiles.Count)
{
continue;
}
sw.WriteLine(tmpStr);
tmpStr = GlycanKey + " Protonated Ratio,";
fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
}
tmpStr = tmpStr + (AllResult[GlycanKey][i].TotalProtonatedIntensity / smallestIntensity).ToString("0.00") + ",";
fileIdx++;
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
}
sw.WriteLine(tmpStr);
//All
tmpStr = GlycanKey + " All Adducts,";
smallestIntensity = 9999999999999;
fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
}
tmpStr = tmpStr + AllResult[GlycanKey][i].TotalIntensity.ToString("0.00") + ",";
fileIdx++;
if (smallestIntensity >= AllResult[GlycanKey][i].TotalIntensity && AllResult[GlycanKey][i].TotalIntensity > 0)
{
smallestIntensity = AllResult[GlycanKey][i].TotalIntensity;
}
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
}
sw.WriteLine(tmpStr);
tmpStr = GlycanKey + " All Ratio,";
fileIdx = 0;
for (int i = 0; i < AllResult[GlycanKey].Count; i++)
{
while (AllResult[GlycanKey][i].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", ""))
{
tmpStr = tmpStr + "N/A,";
fileIdx++;
}
tmpStr = tmpStr + (AllResult[GlycanKey][i].TotalIntensity / smallestIntensity).ToString("0.00") + ",";
fileIdx++;
}
while (tmpStr.Count(t => t == ',') < ResultFiles.Count + 1)
{
tmpStr += "N/A,";
}
sw.WriteLine(tmpStr);
}
}
//Debug
if (argProtonatedResult)
{
StreamWriter swDebug = new StreamWriter(Path.GetDirectoryName(argOutputFile) + "\\MergeResult_Debug.csv");
string tmpDebugStr = "";
tmpDebugStr = "Glycan,";
//Title
foreach (string filename in ResultFiles)
{
tmpDebugStr = tmpDebugStr + Path.GetFileNameWithoutExtension(filename) + "_Time," + Path.GetFileNameWithoutExtension(filename) + "_Intensity,";
}
swDebug.WriteLine(tmpDebugStr);
foreach (string GlycanKey in AllResult.Keys)
{
GetBalanceData(AllResult[GlycanKey]);
swDebug.WriteLine(GlycanKey + " Protonated");
int ProtonatedPeakCount = AllResult[GlycanKey][0].ProtonatedPeaks.Count;
for (int i = 0; i < ProtonatedPeakCount; i++)
{
tmpDebugStr = ",";
int fileIdx = 0;
for (int j = 0; j < ResultFiles.Count; j++)
{
if (AllResult[GlycanKey].Count <= fileIdx || AllResult[GlycanKey][fileIdx].DataSetName != Path.GetFileNameWithoutExtension(ResultFiles[fileIdx]).Replace("_FullList", "") || AllResult[GlycanKey][fileIdx].ProtonatedPeaks.Count == 0)
{
tmpDebugStr += "N/A,N/A,";
}
else
{
tmpDebugStr += AllResult[GlycanKey][fileIdx].ProtonatedPeaks[i].Item1.ToString("0.00") + "," + AllResult[GlycanKey][fileIdx].ProtonatedPeaks[i].Item2.ToString("0.00") + ",";
fileIdx++;
}
}
swDebug.WriteLine(tmpDebugStr);
}
}
swDebug.Close();
}
}
