private void LoadPeaks(ZedGraphControl zgcScan, List <ZedGraphSmallMoleculeFilePeak> zgcPeaks, string[] fileNames, Color color)
{
var sigPeaks = from p in significantPeaks select p.Peak;
List <FileData2> datas = FileData2.ReadFiles(fileNames, sigPeaks);
SmallMoleculeZedGraphUtils.LoadPeaks(zgcScan, zgcPeaks, datas, color);
zgcScan.MasterPane.SetLayout(zgcScan.CreateGraphics(), PaneLayout.SquareRowPreferred);
zgcScan.AxisChange();
}
private void AddGraphPane(ZedGraphControl zgcScan, FileData2 data, Color color)
{
var items = data[peakName];
GraphPane myPane = new GraphPane();
var points = new PointPairList();
items.ConvertAll(m => new PointPair(m.Scan, m.Intensity)).ForEach(m => points.Add(m));
myPane.AddCurve(data.FileName, points, color, SymbolType.None);
zgcScan.MasterPane.PaneList.Add(myPane);
}
public override IEnumerable <string> Process(string fileName)
{
var result = new List <string>();
var peakNames = GetPeakInfos(fileName);
var peaks = from p in peakNames
select p.Substring(1);
string[] positiveSampleFiles = GetFiles(dir1);
string[] positiveReferencesFiles = GetFiles(dir2);
List <FileData2> sampleDatas = FileData2.ReadFiles(positiveSampleFiles, peaks);
List <FileData2> referencesDatas = FileData2.ReadFiles(positiveReferencesFiles, peaks);
foreach (var peakName in peakNames)
{
var file = targetDir + "\\" + peakName + ".png";
if (File.Exists(file))
{
continue;
}
Console.WriteLine(file);
var peak = peakName.Substring(1);
var maxIntensity = (from m in sampleDatas
from p in m[peak]
select p.Intensity).Union(from m in referencesDatas
from p in m[peak]
select p.Intensity).Max();
SmallMoleculeSignificantPeakImageBuilder2 builder2 = new SmallMoleculeSignificantPeakImageBuilder2(peak, sampleDatas, referencesDatas, Color.Red, Color.Blue);
result.AddRange(builder2.Process(file));
}
sampleDatas.Clear();
referencesDatas.Clear();
GC.Collect();
GC.WaitForFullGCComplete();
return(result);
}
public override IEnumerable <string> Process(string rootDirectory)
{
string[] files = Directory.GetFiles(rootDirectory, "*.d.100.400.txt");
List <Item> items = new List <Item>();
Progress.SetRange(1, files.Length);
int count = 0;
double totalIntensity = 0.0;
foreach (var file in files)
{
Progress.SetPosition(count++);
var pureName = new FileInfo(file).Name;
Match m = nameReg.Match(pureName);
if (!m.Success || m.Groups.Count < 2)
{
throw new ArgumentException("Regex pattern doesn't match to file : " + file);
}
string name = "";
for (int i = 1; i < m.Groups.Count; i++)
{
name = name + m.Groups[i].Value;
}
if (name.StartsWith("_"))
{
name = name.Substring(1);
}
Progress.SetMessage("Parsing " + file + " for " + name + "...");
string mode = pureName.Contains("neg") ? "N" : "P";
FileData2 data = new FileData2();
data.Read(file);
if (totalIntensity == 0.0)
{
totalIntensity = data.TotalIntensity;
}
double ratio = 1;
if (normalizeByTotalIntensity)
{
ratio = totalIntensity / data.TotalIntensity;
}
var map = data.MaxIntensityMap;
foreach (var entry in map)
{
items.Add(new Item()
{
FileName = name,
MZ = mode + entry.Key,
Intensity = entry.Value * ratio
});
}
}
var dic = items.ToDoubleDictionary(m => m.MZ, m => m.FileName);
dic.Remove("P400");
dic.Remove("N400");
var peaks = dic.Keys.ToList();
peaks.Sort();
var fileNames = dic.Values.FirstOrDefault().Keys.ToList();
fileNames.Sort();
var resultFile = new DirectoryInfo(rootDirectory).FullName;
if (resultFile.EndsWith(@"\"))
{
resultFile = resultFile.Substring(0, resultFile.Length - 1);
}
resultFile = resultFile + ".data";
using (StreamWriter sw = new StreamWriter(resultFile))
{
sw.Write("Peak/File");
foreach (var file in fileNames)
{
sw.Write("\t" + file);
}
sw.WriteLine();
foreach (var peak in peaks)
{
sw.Write(peak);
var dic2 = dic[peak];
foreach (var file in fileNames)
{
if (!dic2.ContainsKey(file))
{
throw new Exception(MyConvert.Format("Cannot find peak {0} of file {1}", peak, file));
}
sw.Write("\t{0:0.0}", dic2[file].Intensity);
}
sw.WriteLine();
}
}
return(new string[] { resultFile });
}
