private void Parse(string tagFilePath)
{
var tagParser = new TsvFileParser(tagFilePath);
var scan = tagParser.GetData("ScanNum").Select(s => Convert.ToInt32(s)).ToArray();
var sequence = tagParser.GetData("SequenceTag").ToArray();
var isPrefix = tagParser.GetData("IsPrefix").Select(s => s.Equals("1")).ToArray();
var flankingMass = tagParser.GetData("FlankingMass").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < tagParser.NumData; i++)
{
if (sequence[i].Length < _minTagLength)
{
continue;
}
var tag = new SequenceTag(scan[i], sequence[i], isPrefix[i], flankingMass[i]);
IList <SequenceTag> tagList;
if (_scanToTags.TryGetValue(scan[i], out tagList))
{
if (tagList.Count < _numTagsPerScan)
{
tagList.Add(tag);
}
}
else
{
_scanToTags.Add(scan[i], new List <SequenceTag> {
tag
});
}
}
}
public MatchedTag(SequenceTag tag, int startIndex, double?featureMass)
{
StartIndex = startIndex;
EndIndex = startIndex + tag.Sequence.Length;
NumMergedSequenceTags = 1;
NTermFlankingMass = tag.GetNTermFlankingMass(featureMass - Composition.H2O.Mass);
CTermFlankingMass = tag.GetCTermFlankingMass(featureMass - Composition.H2O.Mass);
NumReliableNTermFlankingMasses = tag.IsPrefix ? 1 : 0;
NumReliableCTermFlankingMasses = tag.IsPrefix ? 0 : 1;
}
private void Parse(string tagFilePath)
{
var tagParser = new TsvFileParser(tagFilePath);
var scan = tagParser.GetData("ScanNum").Select(s => Convert.ToInt32(s)).ToArray();
var sequence = tagParser.GetData("SequenceTag").ToArray();
var isPrefix = tagParser.GetData("IsPrefix").Select(s => s.Equals("1")).ToArray();
var flankingMass = tagParser.GetData("FlankingMass").Select(Convert.ToDouble).ToArray();
for (var i = 0; i < tagParser.NumData; i++)
{
if (sequence[i].Length < _minTagLength) continue;
var tag = new SequenceTag(scan[i], sequence[i], isPrefix[i], flankingMass[i]);
IList<SequenceTag> tagList;
if (_scanToTags.TryGetValue(scan[i], out tagList))
{
if (tagList.Count < _numTagsPerScan) tagList.Add(tag);
}
else
{
_scanToTags.Add(scan[i], new List<SequenceTag> { tag });
}
}
}
//public static List<InitialAA> RemoveModifications(List<InitialAA> values, bool direction, List<double> modifications)
//{
// List<InitialAA> newvalues = new List<InitialAA>();
// List<InitialAA> vals = new List<InitialAA>();
// vals.AddRange(values.OrderBy(a => a.Start).ToList());
// foreach (var va in vals)
// {
// //modifications.Where(a => a == vals.Select(b => b.Start - va.))
// }
// return newvalues;
//}
public static void findprlltags(List <InitialAA> values, List <SequenceTag> sequences)
{
try
{
int h = 0;
List <double> start = new List <double>();
List <SequenceTag> startse = new List <SequenceTag>();
List <double> end = new List <double>();
double singleend = new double();
foreach (InitialAA val in values)
{
var m = from SequenceTag sq in sequences
where sq.Index.Contains("-" + val.Index + "-")
select sq;
if (m.Any())
{
h++; continue;
}
List <SequenceTag> seq = new List <SequenceTag>();
List <AminoAcids> aas = new List <AminoAcids>();
aas.Add(new AminoAcids
{
End = val.End,
Name = val.Name,
Start = val.Start,
Score = val.Delta + 50 / ((val.StartDelta + val.EndDelta) / 2),
StartScore = val.StartDelta,
EndScore = val.EndDelta,
AverageMonoMassIntensities = val.AverageMonoMassIntensity,
SumofMonoMassIntensities = val.SumofMonoMassIntensities
});
seq.Add(new SequenceTag
{
End = val.End,
Start = val.Start,
totalScore = val.Delta,
RawSequence = val.Name,
MaxScore = val.Delta,
NumberofAA = 1,
Index = "-" + val.Index + "-",
IndividualAAs = aas
});
end.Add(val.End);
singleend = val.End;
foreach (InitialAA v in values.GetRange(h, values.Count - h))
{
if (v.Index == val.Index)
{
continue;
}
if (end.Where(a => a == v.Start).Any())
{
if (!(start.Where(a => a == v.Start).Any()))
{
var xx = (seq.Where(a => a.End == v.Start).ToList());
foreach (var z in xx)
{
int x = seq.IndexOf(z);
end.Add(v.End);
start.Add(v.Start);
AminoAcids aa = new AminoAcids();
aa.End = v.End;
aa.Start = v.Start;
aa.EndScore = v.EndDelta;
aa.Name = v.Name;
aa.StartScore = v.StartDelta;
aa.AverageMonoMassIntensities = v.AverageMonoMassIntensity;
aa.SumofMonoMassIntensities = v.SumofMonoMassIntensities;
if (v.StartDelta == 0 && v.EndDelta == 0)
{
aa.Score = v.Delta;
}
else
{
aa.Score = v.Delta + 50 / ((v.StartDelta + v.EndDelta) / 2);
}
List <AminoAcids> aaa = new List <AminoAcids>();
aaa.AddRange(seq[x].IndividualAAs);
startse.Add(new SequenceTag
{
RawSequence = seq[x].Sequence,
Start = v.Start,
Index = seq[x].Index,
IndividualAAs = aaa,
totalScore = seq[x].Score + (float)aa.Score,
Score = seq[x].Score + (float)aa.Score,
End = v.End
});
seq[x].Start = v.Start;
seq[x].End = v.End;
seq[x].RawSequence += v.Name;
seq[x].totalScore = (float)aa.Score + startse[startse.Count - 1].totalScore;
seq[x].Index += "-" + v.Index + "-";
seq[x].IndividualAAs.Add(aa);
}
}
else
{
var ses = startse.Where(b => b.Start == v.Start).ToList();
foreach (var se in ses)
{
if (se.realEnd != v.Start)
{
continue;
}
SequenceTag sequence = new SequenceTag();
AminoAcids aa = new AminoAcids();
aa.End = v.End;
aa.Start = v.Start;
aa.EndScore = v.EndDelta;
aa.Name = v.Name;
if (v.StartDelta == 0 && v.EndDelta == 0)
{
aa.Score = v.Delta;
}
else
{
aa.Score = v.Delta + 50 / ((v.StartDelta + v.EndDelta) / 2);
}
aa.StartScore = v.StartDelta;
aa.AverageMonoMassIntensities = v.AverageMonoMassIntensity;
aa.SumofMonoMassIntensities = v.SumofMonoMassIntensities;
seq.Add(new SequenceTag
{
Index = se.Index + "-" + v.Index + "-",
Start = se.Start,
RawSequence = se.Sequence + v.Name,
End = v.End,
totalScore = se.totalScore + (float)aa.Score,
Score = se.totalScore + (float)aa.Score
});
int count = seq.Count - 1;
end.Add(v.End);
start.Add(v.Start);
List <AminoAcids> aaa = new List <AminoAcids>();
aaa.AddRange(se.IndividualAAs);
startse.Add(new SequenceTag
{
RawSequence = se.Sequence + v.Name,
Start = se.Start,
Index = v.Index,
IndividualAAs = aaa,
End = v.End
});
int cnt = startse.Count - 1;
startse[cnt].IndividualAAs.Add(aa);
seq[count].IndividualAAs = new List <AminoAcids>();
seq[count].IndividualAAs = startse[cnt].IndividualAAs;
seq[count].totalScore = v.Delta + seq[count].totalScore;
}
}
}
}
sequences.AddRange(seq);
end.Clear();
start.Clear();
startse.Clear();
h++;
}
}
catch (Exception ex)
{
Debug.Print("Exception in findprlltags(): " + ex.Message);
}
}
public MatchedTag(SequenceTag tag, int startIndex) : this(tag, startIndex, null)
{
}
public MatchedTag(SequenceTag tag, int startIndex, double? featureMass)
{
StartIndex = startIndex;
EndIndex = startIndex + tag.Sequence.Length;
NumMergedSequenceTags = 1;
NTermFlankingMass = tag.GetNTermFlankingMass(featureMass - Composition.H2O.Mass);
CTermFlankingMass = tag.GetCTermFlankingMass(featureMass - Composition.H2O.Mass);
NumReliableNTermFlankingMasses = tag.IsPrefix ? 1 : 0;
NumReliableCTermFlankingMasses = tag.IsPrefix ? 0 : 1;
}
public MatchedTag(SequenceTag tag, int startIndex): this(tag, startIndex, null)
{
}
