/// <summary>
///
/// </summary>
/// <param name="args">
/// Arg0: FilePath
/// Arg1: FileType switch
/// raw
/// mzxml
/// Arg2: Function switch
/// R:ReadScan
/// N:Number of Scan
/// H: Get HCD info
/// C: Checked if it is CID scan
/// S: Scan header Description
/// M: Get MS Level
/// Arg3:
/// Switch R: int scan number
/// Switch N: none
///
/// Arg4: PeakProcessorParameter _singleToNoiseRatio
/// Arg5: PeakProcessorParameter _peakBackgroundRatio
/// Arg6: TransformParameter _peptideMinBackgroundRatio
/// Arg7: TransformParameter _maxCharge
/// </param>
///
static int Main(string[] args)
{
string FunctionSwitch;// = args[2].ToLower();
GlypID.Readers.clsRawData Raw;
//Debug
//End Debug
try
{
do
{
Console.WriteLine(
"@@\nR:ReadScan\n" +
"N:Number of Scan\n" +
"H: Get HCD info\n" +
"C: Checked if it is CID scan\n" +
"S: Scan header Description\n" +
"M: Get MS Level\n" +
"Q: Quit\n" +
"Please select function:");
FunctionSwitch = Console.In.ReadLine().ToLower().Substring(0, 1);
if (FunctionSwitch == "q")
{
return(0);
}
else
{
Console.WriteLine("Please input file location:");
string _fullFilePath = Console.In.ReadLine();
Console.WriteLine("FIle Type(r: Raw, x:mzXML)");
if (Console.In.ReadLine().ToLower().StartsWith("x"))
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
}
else
{
Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
}
//PipeClient pipeClt = new PipeClient();
//pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
if (FunctionSwitch == "r")//Read Scan
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
Console.WriteLine("Please input Single to Noise ratio (default:3.0):");
double parsedResult = 3.0;
double _singleToNoiseRatio = 3.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_singleToNoiseRatio = parsedResult;
}
Console.WriteLine("Please input Peak background ratio (default:5.0):");
parsedResult = 5.0;
double _peakBackgroundRatio = 5.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_peakBackgroundRatio = parsedResult;
}
Console.WriteLine("Please input Minimum background ratio (default:5.0):");
parsedResult = 5.0;
double _peptideMinBackgroundRatio = 5.0;
if (double.TryParse(Console.In.ReadLine(), out parsedResult))
{
_peptideMinBackgroundRatio = parsedResult;
}
Console.WriteLine("Please input Max charge (defatlt:10):");
short paredCharge = 10;
short _maxCharge = 10;
if (short.TryParse(Console.In.ReadLine(), out paredCharge))
{
_maxCharge = paredCharge;
}
Console.WriteLine("Reading Scan");
MSScan scan = GetScanFromFile(ScanNo, _singleToNoiseRatio, _peakBackgroundRatio, _peptideMinBackgroundRatio, _maxCharge, Raw);
string responseMsg = SendScanViaNamedPipe(scan);
//scan = null;
//if (pipeClt.Connected)
//{
// while (!pipeClt.SendMessage(memStream.ToArray())) ;
// Console.WriteLine("Named pipe sent");
// pipeClt.Disconnect();
//}
//else
//{
// throw new Exception("Named Pipe not found");
//}
Console.WriteLine("ANS:Read Scan: " + ScanNo + " finish;MSScan bytes-" + responseMsg);
}
else if (FunctionSwitch == "n") //Get total scans
{
Console.WriteLine("ANS:" + Raw.GetNumScans().ToString());
}
else if (FunctionSwitch == "h") //Check HCD
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
HCDInfo HCDinfo = GetHCDInfo(Raw, ScanNo);
if (HCDinfo != null)
{
Console.WriteLine("ANS:" + HCDinfo.ScanNum.ToString() + ";" +
HCDinfo.GlycanType.ToString() + ";" +
HCDinfo.HCDScore.ToString());
}
else
{
Console.WriteLine("ANS:" + "false");
}
}
else if (FunctionSwitch == "c") //Check CID
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
if (Raw.IsCIDScan(ScanNo) == true)
{
Console.WriteLine("ANS:" + "true");
}
else
{
Console.WriteLine("ANS:" + "false");
}
}
else if (FunctionSwitch == "s") //Check description
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
string description = Raw.GetScanDescription(ScanNo);
Console.WriteLine("ANS:" + description);
}
else if (FunctionSwitch == "m")//Get MS Level
{
Console.WriteLine("Please input scan num:");
int ScanNo = Convert.ToInt32(Console.In.ReadLine());
Console.WriteLine("ANS:" + Raw.GetMSLevel(ScanNo));
}
else
{
Console.WriteLine("Function error");
}
}
} while (true);
}
catch (Exception e)
{
Console.WriteLine(e.Message);
return(-1);
}
//if (args == null || args.Length == 0)
//{
// Console.WriteLine("args is null"); // Check for null array
// return -1;
//}
//if (FunctionSwitch == "r" && args.Length != 8)
//{
// Console.WriteLine("args is not enough"); // Check for null array
// return -1;
//}
//else
//{
// string _fullFilePath = Console.In.ReadLine();
// Console.WriteLine("Init GlypID");
// if (args[1].ToLower() == "raw")
// {
// Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.FINNIGAN);
// }
// else
// {
// Raw = new GlypID.Readers.clsRawData(_fullFilePath, GlypID.Readers.FileType.MZXMLRAWDATA);
// }
// if (FunctionSwitch == "n") //Get Total scans
// {
// Console.WriteLine(Raw.GetNumScans().ToString());
// return Raw.GetNumScans();
// }
// else if (FunctionSwitch == "m") //Get MS Level
// {
// int ScanNo = Convert.ToInt32(args[3]);
// return Raw.GetMSLevel(ScanNo);
// }
// else if (FunctionSwitch == "c") //IsCID Scan
// {
// int ScanNo = Convert.ToInt32(args[3]);
// if (Raw.IsCIDScan(ScanNo) == true)
// {
// return 1;
// }
// return 0;
// }
// else if (FunctionSwitch == "s") //Get Description
// {
// int ScanNo = Convert.ToInt32(args[3]);
// //Console.WriteLine("Get Description info");
// string description = Raw.GetScanDescription(ScanNo);
// Console.WriteLine(description);
// //System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// //MemoryStream memStream = new MemoryStream();
// //f.Serialize(memStream, description);
// //PipeClient pipeClt = new PipeClient();
// //pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(memStream.ToArray())) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return 1;
// }
// else if (FunctionSwitch == "h") //Get HCD
// {
// int ScanNo = Convert.ToInt32(args[3]);
// HCDInfo HCDinfo = GetHCDInfo(Raw, ScanNo);
// //Console.WriteLine("Get HCD info");
// //System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// //PipeClient pipeClt = new PipeClient();
// //pipeClt.Connect("\\\\.\\pipe\\GlypIDPipeHCD");
// if (HCDinfo != null)
// {
// Console.WriteLine(HCDinfo.ScanNum.ToString() + ";" +
// HCDinfo.GlycanType.ToString() + ";" +
// HCDinfo.HCDScore.ToString());
// //MemoryStream memStream = new MemoryStream();
// //f.Serialize(memStream, HCDinfo);
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(memStream.ToArray())) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return 1;
// }
// else
// {
// //if (pipeClt.Connected)
// //{
// // while (!pipeClt.SendMessage(Encoding.ASCII.GetBytes("No HCD Info found"))) ;
// // Console.WriteLine("Named pipe sent");
// //}
// //else
// //{
// // throw new Exception("Named Pipe not found");
// //}
// return -1;
// }
// }
// else //ReadScan
// {
// int ScanNo = Convert.ToInt32(args[3]);
// double _singleToNoiseRatio = Convert.ToDouble(args[4]);
// double _peakBackgroundRatio = Convert.ToDouble(args[5]);
// double _peptideMinBackgroundRatio = Convert.ToDouble(args[6]);
// short _maxCharge = Convert.ToInt16(args[7]);
// Console.WriteLine("Read Scan");
// MSScan scan = GetScanFromFile(ScanNo, _singleToNoiseRatio, _peakBackgroundRatio, _peptideMinBackgroundRatio, _maxCharge);
// System.Runtime.Serialization.IFormatter f = new System.Runtime.Serialization.Formatters.Binary.BinaryFormatter();
// MemoryStream memStream = new MemoryStream();
// f.Serialize(memStream, scan);
// PipeClient pipeClt = new PipeClient();
// pipeClt.Connect("\\\\.\\pipe\\GlypIDPipe");
// if (pipeClt.Connected)
// {
// while (!pipeClt.SendMessage(memStream.ToArray())) ;
// Console.WriteLine("Named pipe sent");
// }
// else
// {
// throw new Exception("Named Pipe not found");
// }
// /*NamedPipeClientStream PipeClient = new NamedPipeClientStream(".", "ReadMSScan", PipeDirection.Out);
// PipeClient.Connect();
// f.Serialize(PipeClient, scan);
// PipeClient.Close();*/
// Console.WriteLine("Read Scan: " + args[3] + " finish");
// }
// //End Read Scan
// return 1;
//}
}