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.SequenceTag(scan[i], sequence[i], isPrefix[i], flankingMass[i]);
IList <SequenceTag.SequenceTag> tagList;
if (_scanToTags.TryGetValue(scan[i], out tagList))
{
if (tagList.Count < _numTagsPerScan)
{
tagList.Add(tag);
}
}
else
{
_scanToTags.Add(scan[i], new List <SequenceTag.SequenceTag> {
tag
});
}
}
}
public MatchedTag(SequenceTag.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.SequenceTag tag, int startIndex) : this(tag, startIndex, null)
{
}
