/// <summary>
/// Base-Constructor. Performs the initalizations common to all experiments.
/// </summary>
/// <param name="wiffFile">A <see cref="FMANWiffFileClass"/> instance. The source from where to
/// read the periods properties and data.</param>
/// <param name="wiffPeriod">The <see cref="WiffPeriod"/> instance this experiment belongs to.</param>
/// <param name="experimentIndex">The <b>zero-based</b> index of this experiment in the associated period.</param>
public WiffExperiment(FMANWiffFileClass wiffFile, WiffPeriod wiffPeriod, int experimentIndex)
{
if (wiffFile == null)
{
throw new ArgumentNullException("wiffFile");
}
if (wiffPeriod == null)
{
throw new ArgumentNullException("wiffPeriod");
}
this.wiffPeriod = wiffPeriod;
this.index = experimentIndex;
Initialize(wiffFile);
}
/// <summary>
/// Constructor. Creates and initializes a Q1ScanExperiment instance.
/// </summary>
/// <param name="wiffFile">A <see cref="FMANWiffFileClass"/> instance. The source from where to
/// read the periods properties and data.</param>
/// <param name="wiffPeriod">The <see cref="WiffPeriod"/> instance this experiment belongs to.</param>
/// <param name="experimentIndex">The <b>zero-based</b> index of this experiment in the associated period.</param>
public Q1ScanExperiment(FMANWiffFileClass wiffFile, WiffPeriod wiffPeriod, int experimentIndex)
: base(wiffFile, wiffPeriod, experimentIndex)
{
}
// Private Methods (1)
/// <summary>
/// Fills this instance data members with the information read from <paramref name="wiffFile"/>.
/// </summary>
/// <param name="wiffFile">A <see cref="FMANWiffFileClass"/> instance. The data source.</param>
private void Initialize(FMANWiffFileClass wiffFile)
{
// retrieve this sample's name
name = wiffFile.GetSampleName(index);
// get the position information for the selected sample
// the position data exists in a seperate file ( one per sample )
// and is read from that file 'manually'
AppContext.ProgressStart("reading path file");
try
{
string pathFile = wiffFileContent.FileName + " (" + index.ToString() + ").path";
FileStream positionStream = new FileStream(@pathFile, FileMode.Open, FileAccess.Read);
// calculate the count of position entries
positionDataLength = positionStream.Length / 12; // 12 Byte per position entry
// the array to hold the position information
positionData = new uint[positionDataLength, 3];
BinaryReader positionReader = new BinaryReader(positionStream);
for (long i = 0; i < positionDataLength; i++)
{
positionData[i, 0] = positionReader.ReadUInt32();
positionData[i, 1] = positionReader.ReadUInt32();
positionData[i, 2] = positionReader.ReadUInt32();
if ((i % (positionDataLength / 100.0)) == 0) // hundred progress ticks
{
AppContext.ProgressSetValue(100.0 * i / positionDataLength);
}
}
positionReader.Close();
positionStream.Close();
}
finally
{
AppContext.ProgressClear();
}
#if (false)
string csvPosFile = wiffFileContent.FileName + " (" + index.ToString() + ").path" + ".csv";
using (FileStream csvPosStream = new FileStream(@csvPosFile, FileMode.Create, FileAccess.Write))
{
using (StreamWriter sw = new StreamWriter(csvPosStream))
{
for (long i = 0; i < positionDataLength; i++)
{
sw.Write(positionData[i, 0]);
sw.Write(',');
sw.Write(positionData[i, 1]);
sw.Write(',');
sw.Write(positionData[i, 2]);
sw.WriteLine();
}
}
}
#endif
// get user data of the selected sample
string userData = wiffFile.GetUserData(index);
if (!string.IsNullOrEmpty(userData))
{
//width in mm
x2 = float.Parse(userData.Split(',')[2]);
x1 = float.Parse(userData.Split(',')[0]);
width = x2 - x1;
//height in mm
y2 = float.Parse(userData.Split(',')[3]);
y1 = float.Parse(userData.Split(',')[1]);
height = y2 - y1;
}
// get the number of periods
int nrPeriods = wiffFile.GetActualNumberOfPeriods(index);
// loop through the periods; the index of the periods is zero based!!
for (int actPeriod = 0; actPeriod < nrPeriods; actPeriod++)
{
WiffPeriod period = new WiffPeriod(wiffFile, this, actPeriod);
periods.Add(period);
}
}
/// <summary>
/// Determines with what kind of experiment we're dealing with and instatiates
/// an object of the accurate subclass derived from the abstract baseclass
/// <see cref="WiffExperiment"/>.
/// </summary>
/// <param name="wiffFile">A <see cref="FMANWiffFileClass"/> instance. The source from where to
/// read the experiments properties and data.</param>
/// <param name="wiffPeriod">The <see cref="WiffPeriod"/> instance this the experiment belongs to.</param>
/// <param name="experimentIndex">The <b>zero-based</b> index of the experiment in the associated period.</param>
/// <returns>The newly created, <see cref="WiffExperiment"/> dirived object.</returns>
public static WiffExperiment CreateWiffExperiment(FMANWiffFileClass wiffFile, WiffPeriod wiffPeriod, int experimentIndex)
{
Experiment experiment = (Experiment)wiffFile.GetExperimentObject(wiffPeriod.Sample.Index, wiffPeriod.Index, experimentIndex);
// get scan type
short scanType = experiment.ScanType;
WiffExperiment theExperiment = null;
switch (scanType)
{
case 0: // Q1 scan
{
theExperiment = new Q1ScanExperiment(wiffFile, wiffPeriod, experimentIndex);
}
break;
case 1: // Q1 MI scan
case 2: // Q3 scan
case 3: // Q3 MI scan
break;
case 4: // MRM scan
{
theExperiment = new MRMScanExperiment(wiffFile, wiffPeriod, experimentIndex);
}
break;
case 5: // precursor scan
case 6: // product ion scan
case 7: // neural loss scan
break;
default:
{
// TODO -- Check if this is really, really intended...
theExperiment = new MRMScanExperiment(wiffFile, wiffPeriod, experimentIndex);
}
break;
}
return(theExperiment);
}
