public static LCTrace CreateTrace(LCMSGroup Group, MZData Start)
{
if (Group == null)
{
return(null);
}
if (Start == null)
{
Start = Group.Points[0];
foreach (MZData P in Group.Points)
{
if (P.Intensity > Start.Intensity)
{
Start = P;
}
}
}
return(new LCTrace(Group, Start));
}
private MZData TakeFreePoint(int Scan, double Mass, LCMSGroup Group)
{
MZData Point = RawFile.RawSpectra[Scan].FindNearestPeak(Mass, Program.MassError);
if (Point.Mass != 0.0)
{
if (Point.Group == null)
{
Point.Group = Group;
Group.Points.Add(Point);
return(Point);
}
else
{
if (Point.Group != Group)
{
//Console.WriteLine("Warning: Group conflict {0}",ConflictCounter++);
ConflictCounter++;
}
}
}
return(null);
}
LCTrace(LCMSGroup Group, MZData Start)
{
this.Group = Group;
this.StartPoint = Start;
}
static int Main(string[] args)
{
//Data Sources
//args[0] - database
//args[1] - Raw File Name
//args[2] - ID for file
try{
Console.ReadLine();
Console.WriteLine("Information: Loading...", args[1]);
//Load Parameters
string DBName = args[0];
int FileID = Convert.ToInt32(args[2]);
//against database locking at start time
int RepeatCount = 0;
while (RepeatCount < 10)
{
try{
DBInt = new DBInterface();
DBInt.InitDB(DBName);
LoadParameters();
break;
}catch (System.Data.SQLite.SQLiteException sqle) {
if (sqle.ErrorCode == System.Data.SQLite.SQLiteErrorCode.Busy && RepeatCount < 10)
{
//здесь возможна генерация идентичных features (- с точностью до границ пика)
Console.WriteLine("Warning: {0}", sqle.Message);
System.Threading.Thread.Sleep(10000);
RepeatCount++;
}
else
{
throw sqle;
}
}
}
RawFileService = new FileService(args[1]);
Target T = null;
MZData P = null;
double MaxI = 0;
Console.WriteLine("Information: Building data map");
RawFileService.BuildDataMap();
P = RawFileService.BiggestUnused();
T = Target.TargetFromPoint(P, 0);
MaxI = P.Intensity;
Console.WriteLine("Information: Targets processing...", args[1]);
List <Feature> ReadyFeatures = new List <Feature>();
int i = 0;
int ICount = 1;
while (T != null)
{
//Progress indicator
if ((int)Math.Pow(100, (Math.Log10(MaxI / DataThres) - Math.Log10(P.Intensity / DataThres)) / (Math.Log10(MaxI / DataThres))) > ICount)
{
Console.WriteLine("Information: Targets - {0}; Intensity - {1} ", i, P.Intensity);
Console.WriteLine("{0}%...", (int)Math.Pow(100, (Math.Log10(MaxI / DataThres) - Math.Log10(P.Intensity / DataThres)) / (Math.Log10(MaxI / DataThres))));
ICount++;
}
Feature F = FeatureForTarget(T, P);
if (F != null)
{
ReadyFeatures.Add(F);
}
i++;
//make a features from additional peaks
if (F != null)
{
for (int j = 0; j < F.TPeaks.Peaks.Count; j++)
{
if (F.TPeaks.TargetPeak != F.TPeaks.Peaks[j])
{
T = Target.TargetFromPeak(F.TPeaks.Peaks[j], i);
Feature NF = FeatureForTarget(T, P);
ReadyFeatures.Add(NF); //!!!!! ReadyFeatures.Add(F);
i++;
}
}
}
P = RawFileService.BiggestUnused();
if (P == null)
{
break;
}
T = Target.TargetFromPoint(P, i);
}
RepeatCount = 0;
while (RepeatCount < 10000)
{
try{
DBInt.tr = DBInt.con.BeginTransaction();
DBInt.SaveFile(args[1], FileID, RawFileService.RawFile.Mode);
LCMSGroup.GroupBase = DBInt.GetGroupBase();
foreach (Feature F in ReadyFeatures)
{
if (F != null && DBInt != null)
{
F.Write(DBInt.con, FileID);
}
}
RawFileService.SaveRTs(DBInt.con, FileID);
LCMSGroup.SaveGroups(DBInt.con, FileID);
DBInt.tr.Commit();
break;
}catch (System.Data.SQLite.SQLiteException sqle) {
if (sqle.ErrorCode == System.Data.SQLite.SQLiteErrorCode.Busy && RepeatCount < 1000)
{
Console.WriteLine("Warning: {0}", sqle.Message);
System.Threading.Thread.Sleep(1000);
RepeatCount++;
}
else
{
throw sqle;
}
}
}
Console.WriteLine("Completed");
Console.ReadLine();
}catch (Exception e) {
Console.Write("Error:");
Console.Write(e.Message);
Console.WriteLine("STACKINFO:" + e.StackTrace);
Console.WriteLine("Completed");
Console.ReadLine();
return(1);
}
return(0);
}
public LCMSGroup GroupFromPoint(MZData Point)
{
if (Point.Group != null)
{
return(Point.Group as LCMSGroup);
}
LCMSGroup Group = new LCMSGroup();
Point.Group = Group;
Group.Points.Add(Point);
Queue <MZData> QPoints = new Queue <MZData>();
QPoints.Enqueue(Point);
do
{
MZData CurrentPoint = QPoints.Dequeue();
int ForwardScan = RawFile.IndexDir[CurrentPoint.Scan];
int BackwardScan = RawFile.IndexRev[CurrentPoint.Scan];
for (int i = 0; i < Program.ZeroScans + 1; i++)
{
if (ForwardScan > 0)
{
MZData NextPoint = TakeFreePoint(ForwardScan, CurrentPoint.Mass, Group);
if (NextPoint != null)
{
QPoints.Enqueue(NextPoint);
}
ForwardScan = RawFile.IndexDir[ForwardScan];
}
if (BackwardScan > 0)
{
MZData NextPoint = TakeFreePoint(BackwardScan, CurrentPoint.Mass, Group);
if (NextPoint != null)
{
QPoints.Enqueue(NextPoint);
}
BackwardScan = RawFile.IndexRev[BackwardScan];
}
}
} while(QPoints.Count > 0);
Group.Points.Sort((p1, p2) => p1.Scan.CompareTo(p2.Scan));
//Add zero points
Group.Points.Add(MZData.CreateZero(RawFile.IndexDir[Group.Points[Group.Points.Count - 1].Scan]));
Group.Points.Add(MZData.CreateZero(RawFile.IndexRev[Group.Points[0].Scan]));
for (int i = Group.Points.Count - 3; i > 0; i--)
{
int CurrentScan = RawFile.IndexRev[Group.Points[i].Scan];
while (CurrentScan > Group.Points[i - 1].Scan)
{
Group.Points.Add(MZData.CreateZero(CurrentScan));
CurrentScan = RawFile.IndexRev[CurrentScan];
}
}
Group.Points.Sort((p1, p2) => p1.Scan.CompareTo(p2.Scan));
if (Group.Points[Group.Points.Count - 1].RT - Group.Points[0].RT < Program.PeakMinWidth)
{
return(null);
}
LCMSGroup.Global.Add(Group);
return(Group);
}
public LCMSGroup GroupFromArea(double StartRT, double EndRT, double MZ, double MassError = 0.0)
{
LCMSGroup Group = new LCMSGroup();
if (MassError == 0.0)
{
MassError = Program.MassError;
}
int StartScan = RawFile.ScanNumFromRT(StartRT);
int EndScan = RawFile.ScanNumFromRT(EndRT);
for (int Scan = RawFile.IndexDir[StartScan]; Scan <= EndScan; Scan = RawFile.IndexDir[Scan])
{
if (Scan == -1)
{
break;
}
MZData Next = RawFile.RawSpectra[Scan].FindBiggestPeak(MZ, MassError);
Group.Points.Add(Next);
}
//Заполнение дыр
//из начала в конец
int LastIndex = -Program.ZeroScans - 1;
for (int i = 0; i < Group.Points.Count; i++)
{
if (Group.Points[i].Intensity == 0.0)
{
if (i - LastIndex < Program.ZeroScans)
{
double LastMZ = Group.Points[LastIndex].Mass;
MZData Next = RawFile.RawSpectra[Group.Points[i].Scan].FindBiggestPeak(LastMZ, MassError);
Group.Points[i] = Next;
if (Next.Intensity != 0.0)
{
LastIndex = i;
}
}
}
else
{
LastIndex = i;
}
}
//из конца в начало
LastIndex = Group.Points.Count + Program.ZeroScans + 1;
for (int i = Group.Points.Count - 1; i >= 0; i--)
{
if (Group.Points[i].Intensity == 0.0)
{
if (LastIndex - i < Program.ZeroScans)
{
double LastMZ = Group.Points[LastIndex].Mass;
MZData Next = RawFile.RawSpectra[Group.Points[i].Scan].FindBiggestPeak(LastMZ, MassError);
Group.Points[i] = Next;
if (Next.Intensity != 0.0)
{
LastIndex = i;
}
}
}
else
{
LastIndex = i;
}
}
//leading and tailing zeros (except one)
while (Group.Points.Count > 1 &&
Group.Points[0].Intensity == 0.0 &&
Group.Points[1].Intensity == 0.0)
{
Group.Points.RemoveAt(0);
}
while (Group.Points.Count > 1 &&
Group.Points[Group.Points.Count - 1].Intensity == 0.0 &&
Group.Points[Group.Points.Count - 2].Intensity == 0.0)
{
Group.Points.RemoveAt(Group.Points.Count - 1);
}
if (Group.Points.Count <= 1)
{
return(null);
}
LCMSGroup.Global.Add(Group);
return(Group);
}
