public static void RunTheCode(string seq1File, string seq2File, int matchWeight, int misMatchWeight, int indlWeight)
{
ScoringParameterDto scoringParameter = new ScoringParameterDto(matchWeight, misMatchWeight, indlWeight);
var seq1 = LoadProteinDatabase.GetProteins(seq1File);
var seq2 = LoadProteinDatabase.GetProteins(seq2File);
SequencesDto sequences = new SequencesDto(seq1[0].Seq, seq2[0].Seq);
EvaluateDto evaluation = GridEvaluateFunction.Evaluate(scoringParameter, sequences);
ResultsDto results = Traceback.Trace(evaluation, sequences);
WriteAlignment.Write(results, scoringParameter);
}
/// <summary>
/// This function is being used in place of Main(~) and will be called from the RunMe GUI. Moreover, the Protein
/// Database "uniprot_human.fasta" only contain 2 proteins. One will be filtered by Protein mass
/// filter. So, the alignment is only performed on the Histone H4 (P62805).
/// </summary>
/// <param name="peakListFileAddress">Contains MS data (*.txt) file address</param>
/// <param name="databaseFileAddress">Conatins protein database (*.fasta) file address</param>
/// <param name="mwTolerance">Tolerance for filtering Proteins having theoretical mass in comparison with MS1</param>
/// <param name="fragmentTolerance">Tolerance for aligning theoretical and experimental spectra</param>
/// <param name="maximumNoOfModifications">Maximum number of mass shifts allowed in an alignment</param>
public static void RunTheCode(string peakListFileAddress, string databaseFileAddress, double mwTolerance,
double fragmentTolerance, int maximumNoOfModifications)
{
// Load Mass Spectrometry Data from *.txt data file
var massSpectrometryData = PeakListReader.ReadPeakListFile(peakListFileAddress);
// Load proteins from *.fasta protein database
var proteinList = LoadProteinDatabase.GetProteins(databaseFileAddress);
// Applying Terminal Modification, cuurently only handles NME_Accetylation
var modifiedProteinList = TerminalModification.ModifyProteins(proteinList);
// Filter Proteins using user provided MW Tolerance
var filteredProteinList = FilterCandidateProteinsByMs1.FilterProteinDb(modifiedProteinList,
massSpectrometryData.WholeProteinMolecularWeight, mwTolerance);
// Evaluate Spectral Alignment and Print the Results in Console
SpectralAlignment.Align(massSpectrometryData, filteredProteinList, fragmentTolerance,
maximumNoOfModifications);
}
