private List <string> GenerateGlycoPeptide()
{
List <ProteinInfo> PInfos = FastaReader.ReadFasta(_fastaFile);
List <string> GlycoPeptide = new List <string>();
foreach (ProteinInfo Prot in PInfos)
{
GlycoPeptide.AddRange(Prot.NGlycopeptide(_MissCLeavage, _ProteaseType, _peptideMutation));
}
return(GlycoPeptide);
}
/// <summary>
/// Input GlycanCompostion (From Glycan list)
/// </summary>
/// <param name="argStartScan"></param>
/// <param name="argEndScan"></param>
/// <param name="argMSMSTol"></param>
/// <param name="argPrecursorTol"></param>
/// <param name="argNGlycan"></param>
/// <param name="argHuman"></param>
/// <param name="argGlycanCompounds"></param>
/// <param name="argMassGlycanMapping"></param>
/// <param name="argGlycanCompoundMassList"></param>
/// <param name="argRawFilePath"></param>
/// <param name="argFastaFile"></param>
/// <param name="argProteaseType"></param>
/// <param name="argMissCleavage"></param>
/// <param name="argAverageMass"></param>
/// <param name="argUseHCD"></param>
/// <param name="argExportFilename"></param>
/// <param name="argGetTopRank"></param>
/// <param name="argCompletedOnly"></param>
/// <param name="argCompletedReward"></param>
public frmInvokeProcesses(int argStartScan,
int argEndScan,
float argMSMSTol,
float argPrecursorTol,
bool argNGlycan,
bool argHuman,
List <GlycanCompound> argGlycanCompounds,
Dictionary <double, GlycanCompound> argMassGlycanMapping,
List <float> argGlycanCompoundMassList,
string argGlycanFile,
string argRawFilePath,
string argFastaFile,
List <Protease.Type> argProteaseType,
int argMissCleavage,
bool argAverageMass,
bool argUseHCD,
bool argSeqHCD,
string argExportFile,
int argGetTopRank,
bool argCompletedOnly,
float argCompletedReward
)
{
InitializeComponent();
AAMW = new AminoAcidMass();
_StartScan = argStartScan;
_EndScan = argEndScan;
_MSMSTol = argMSMSTol;
_PrecursorTol = argPrecursorTol;
_NGlycan = argNGlycan;
_Human = argHuman;
_GlycanCompounds = argGlycanCompounds;
_MassGlycanMapping = argMassGlycanMapping;
_GlycanCompoundMassList = argGlycanCompoundMassList;
_glycanFile = argGlycanFile;
_rawFilePath = argRawFilePath;
Proteins = FastaReader.ReadFasta(argFastaFile);
_fastaFile = argFastaFile;
_ProteaseType = argProteaseType;
_MissCLeavage = argMissCleavage;
_AverageMass = argAverageMass;
_UseGlycanList = true;
_exportFile = argExportFile;
_GetTopRank = argGetTopRank;
_UseHCD = argUseHCD;
_SeqHCD = argSeqHCD;
_CompletedOnly = argCompletedOnly;
_CompletedReward = argCompletedReward;
WorkThread = new Thread(RunWork);
WorkThread.Start();
}
/// <summary>
/// Input Number of Glycans (blind search)
/// </summary>
/// <param name="argStartScan"></param>
/// <param name="argEndScan"></param>
/// <param name="argMSMSTol"></param>
/// <param name="argPrecursorTol"></param>
/// <param name="argNGlycan"></param>
/// <param name="argHuman"></param>
/// <param name="argNoHexNAc"></param>
/// <param name="argNoHex"></param>
/// <param name="argNoDeHex"></param>
/// <param name="argNoSia"></param>
/// <param name="argRawFilePath"></param>
/// <param name="argFastaFile"></param>
/// <param name="argProteaseType"></param>
/// <param name="argMissCleavage"></param>
/// <param name="argAverageMass"></param>
/// <param name="argUseHCD"></param>
/// <param name="argExportFilename"></param>
/// <param name="argGetTopRank"></param>
/// <param name="argCompletedOnly"></param>
/// <param name="argCompletedReward"></param>
public frmInvokeProcesses(int argStartScan,
int argEndScan,
float argMSMSTol,
float argPrecursorTol,
bool argNGlycan,
bool argHuman,
int argNoHexNAc,
int argNoHex,
int argNoDeHex,
int argNoSia,
string argRawFilePath,
string argFastaFile,
List <Protease.Type> argProteaseType,
int argMissCleavage,
bool argAverageMass,
bool argUseHCD,
bool argSeqHCD,
string argExportFile,
int argGetTopRank,
bool argCompletedOnly,
float argCompletedReward
)
{
InitializeComponent();
AAMW = new AminoAcidMass();
_StartScan = argStartScan;
_EndScan = argEndScan;
_MSMSTol = argMSMSTol;
_PrecursorTol = argPrecursorTol;
_NGlycan = argNGlycan;
_Human = argHuman;
_NoHexNAc = argNoHexNAc;
_NoHex = argNoHex;
_NoDeHex = argNoDeHex;
_NoSia = argNoSia;
_rawFilePath = argRawFilePath;
Proteins = FastaReader.ReadFasta(argFastaFile);
_fastaFile = argFastaFile;
_ProteaseType = argProteaseType;
_MissCLeavage = argMissCleavage;
_AverageMass = argAverageMass;
_UseGlycanList = false;
_UseHCD = argUseHCD;
_SeqHCD = argSeqHCD;
_CompletedOnly = argCompletedOnly;
_CompletedReward = argCompletedReward;
_exportFile = argExportFile;
_GetTopRank = argGetTopRank;
WorkThread = new Thread(RunWork);
WorkThread.Start();
}