/// <summary>
/// Writes the incremental results to a txt file and clears the RAM of existing results.
/// </summary>
/// <param name="outputFile"></param>
internal void FlushResultsToSQTFile(string outputFile, RegexGeneration.RegexGenerationParams regexParams)
{
StreamWriter sw = new StreamWriter(outputFile);
sw.WriteLine("#ScanNo\tDeltaCN\tScore\tName\tMeasuredMZ\tEstPrecursorZ\tSequence");
sw.WriteLine("Database searched:" + fastaParser.DBName);
string header = regexParams.PrintHeader();
sw.WriteLine(header);
foreach (SearchResult sr in mySearchResults)
{
sw.WriteLine("M\t" + sr.ScanNumber + "\t" + Math.Round(sr.DeltaCN, 3) + "\t" + sr.TheResults[0].Score + "\t" + sr.TheResults[0].Name + "\t" + sr.MeasuredPrecursorMZ + "\t" + sr.EstimatedPrecursorCharge + "\t" + sr.TheResults[0].Sequence);
foreach (PatternTools.T_ReXS.RegexGenerationTools.SearchResult.RegexAndPath rp in sr.TheResults[0].RegexAndPaths)
{
string path = "";
foreach (int i in rp.NodePath)
{
path += i + ":";
}
path.Remove(path.Length - 1, 1);
sw.WriteLine("R\t" + rp.TheRegex + "\t" + path);
}
}
sw.Close();
mySearchResults.Clear();
}
internal void IncrementalBatchSearch(MSParser.MSFull ms, List <PathCandidate> pathCandidates, RegexGeneration.RegexGenerationParams regexParams)
{
//Handle the precursor stuff
double precursor = -1;
double precursorCharge = -1;
double lowerSearchBound = -1;
double upperSearchBound = -1;
if (ms.ZLines.Count > 0 && regexParams.UsePrecursorInformation)
{
string[] zLine = tabSplitterRegex.Split(ms.ZLines[0]);
precursorCharge = double.Parse(zLine[1]);
precursor = PatternTools.pTools.DechargeMSPeakToPlus1(ms.ChargedPrecursor, precursorCharge);
if (precursorCharge <= regexParams.MinTrustedCharge)
{
lowerSearchBound = precursor - regexParams.PrecursorLowerBound;
upperSearchBound = precursor + regexParams.PrecursorUpperBound;
}
else
{
lowerSearchBound = PatternTools.pTools.DechargeMSPeakToPlus1(ms.ChargedPrecursor, regexParams.MinTrustedCharge);
upperSearchBound = -1;
}
}
else if (regexParams.UsePrecursorInformation && ms.ZLines.Count == 0)
{
lowerSearchBound = (regexParams.MinTrustedCharge * ms.ChargedPrecursor) - 500;
upperSearchBound = -1;
}
else if (!regexParams.UsePrecursorInformation)
{
lowerSearchBound = ms.MSData[(int)(ms.MSData.Count * 0.8)].MZ;
upperSearchBound = -1;
}
SearchResult sr = Search(lowerSearchBound, upperSearchBound, pathCandidates, regexParams.MaxRegexes, ms.ScanNumber, ms.ChargedPrecursor, precursorCharge);
sr.TheResults.Sort((a, b) => b.Score.CompareTo(a.Score));
if (sr.TheResults.Count > 0)
{
if (sr.DeltaCN > 0)
{
mySearchResults.Add(sr);
}
}
}