/****************************************************************************
* Copyright (C) 2009 Peter Mortensen *
* This file is part of MSQuant. *
* *
* MSQuant is distributed under the terms of *
* the GNU General Public License. See src/COPYING.TXT or *
* for details. *
* *
* MSQuant is free software; you can redistribute it *
* and/or modify it under the terms of the GNU *
* General Public License as published by the Free *
* Software Foundation; either version 2 of the *
* License, or (at your option) any later version. *
* *
* MSQuant is distributed in the hope that it will be *
* useful, but WITHOUT ANY WARRANTY; without even the *
* implied warranty of MERCHANTABILITY or FITNESS FOR *
* A PARTICULAR PURPOSE. See the GNU General Public *
* License for more details. *
* *
* You should have received a copy of the GNU General *
* Public License along with MSQuant; if not, write to *
* the Free Software Foundation, Inc., 59 Temple *
* Place, Suite 330, Boston, MA 02111-1307 USA *
* *
* Purpose: tryout for using the new interface, IXRawfile3, in *
* the Finnigan COM component XRawFile2.dll. *
* *
****************************************************************************/
/****************************************************************************
* CEBI *
* Software Development Group *
* Peter Mortensen *
* E-mail, through: *
* WWW: http://www.cebi.sdu.dk/ *
* *
* Program for post-processing of result from search in mass *
* spectrometric data. *
* *
* FILENAME: XCaliburAccess.cs *
* TYPE: CSHARP *
* *
* CREATED: PM 2009-10-13 First attempt. *
* UPDATED: PM 2009-xx-xx *
* *
* *
* *
****************************************************************************/
using System; //For Object, etc.
//using System.Collections.Generic;
//using System.Linq;
//using System.Text;
using XRAWFILE2Lib;
namespace massSpectrometryBase
{
class XCaliburAccess
{
XRawfile mRawfile;
XRAWFILE2Lib.IXRawfile3 mRawfile3;
public XCaliburAccess()
{
// SFinniganRawfile2Wrap.cpp is using the same,
// 0x5FE970B2,0x29C3,0x11D3,{0x81,0x1D,0x00,0x10,0x4B,0x30,0x48,0x96
//This error happend:
// COMException was unhandled.
// Retrieving the COM class factory for component with CLSID
// {5FE970B2-29C3-11D3-811D-00104B304896} failed due to the
// following error: 80040154
//
// 80040154 is ERROR_CLASS_NOTREGISTERED
//
//Reason:
// Project NewXCalibur/Properties/Build/General/Platform target
// was set to "Any". It should be set to "x86" as COM components
// are 32 bit only ("Any" will run as 64 bit on a 64 bit
// version of Windows.)
//
mRawfile = new XRawfile();
string filename =
//@"H:\toDelete\2009-09-28\BAB-BM-JVO-NE-1-5-20-T-A02.RAW";
@"L:\tempCollection\temp19,LyrisYeast\2005-03-04,LGYeastSILACtest\Lyris-YeastSILAC_Lys8-MS3.RAW";
mRawfile.Open(filename);
mRawfile.SetCurrentController(0, 1); //Mass spec device, first MS device.
int lastSpectrumNumber = -17;
mRawfile.GetLastSpectrumNumber(ref lastSpectrumNumber);
//Input
//int spectrumNumber = 9213; //A "SIM" spectrum.
int spectrumNumber = 9206; //A "Full MS" spectrum.
//Common for the two calls
string noFilter = null;
int noCutOff_Type = 0;
int noCutOff = 0;
int allPeaksReturned = 0;
int doNotCentroid = 0;
//Cut-off configuration
int effective_CutOff_Type = 0;
int effective_CutOff = 0;
effective_CutOff_Type = noCutOff_Type;
effective_CutOff = noCutOff;
//Classic call. GetMassListFromScanNum()
{
//int absoluteCutOff_Type = 1;
//int minimumCutOff = 1;
//Outputs
int outArraySize = -1;
Object outRawData = null; //Keep compiler happy.
double outCentroidWidth = 0.0;
object outPeakFlags = null; //Keep compiler happy.
mRawfile.GetMassListFromScanNum(
ref spectrumNumber,
noFilter,
effective_CutOff_Type,
effective_CutOff,
allPeaksReturned,
doNotCentroid,
ref outCentroidWidth,
ref outRawData,
ref outPeakFlags,
ref outArraySize);
int peter2 = 2;
}
//New call. GetMassListFromScanNum()
{
//mRawfile3 = new XRAWFILE2Lib.IXRawfile3();
//mRawfile3 = new XRawfile();
mRawfile3.Open(filename);
mRawfile3.SetCurrentController(0, 1); //Mass spec device, first MS device.
int lastSpectrumNumber2 = -17;
mRawfile3.GetLastSpectrumNumber(ref lastSpectrumNumber2);
//Output
int outArraySize = -1;
Object outRawData = null; //Keep compiler happy.
double outCentroidWidth = 0.0;
object outPeakFlags = null; //Keep compiler happy.
//606.84 Th: highest peak in 9206, Full ms.
//[606.00;608.50]
string massRangeStr = "606.00-608.50";
//Compiles, but an instance of mRawfile3 can not be created...
mRawfile3.GetMassListRangeFromScanNum(
ref spectrumNumber,
noFilter,
effective_CutOff_Type,
effective_CutOff,
allPeaksReturned,
doNotCentroid,
ref outCentroidWidth,
ref outRawData,
ref outPeakFlags,
massRangeStr,
ref outArraySize);
//Compile error:
// Error 1 'XRAWFILE2Lib.XRawfile' does not contain a
// definition for 'GetMassListRangeFromScanNum' and no
// extension method 'GetMassListRangeFromScanNum' accepting a
// first argument of type 'XRAWFILE2Lib.XRawfile' could be
// found (are you missing a using directive or an assembly
// reference?)
// D:\dproj\tryouts\NewXCalibur\NewXCalibur\src\XCaliburAccess\
// XCaliburAccess.cs 133 26 NewXCalibur
mRawfile.GetMassListRangeFromScanNum(
ref spectrumNumber,
noFilter,
effective_CutOff_Type,
effective_CutOff,
allPeaksReturned,
doNotCentroid,
ref outCentroidWidth,
ref outRawData,
ref outPeakFlags,
massRangeStr,
ref outArraySize);
int peter2 = 2;
}
int peter3 = 3;
} //Constructor.
} //class XCaliburAccess
} //namespace massSpectrometryBase