/// <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);
}
/// <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)
{
//get the number of cycles
cycles = wiffFile.GetActualNumberOfCycles(sample.Index, index);
// get the period object
Period period = (Period)wiffFile.GetPeriodObject(sample.Index, index);
// get the cycle time
cycleTime = period.CycleTime;
// get number of experiments
int nrExperiments = wiffFile.GetNumberOfExperiments(sample.Index, index);
// loop through the experiments; the index of the experiments is zero based!!
for (int actExperiment = 0; actExperiment < nrExperiments; actExperiment++)
{
WiffExperiment experiment = WiffExperimentFactory.CreateWiffExperiment(wiffFile, this, actExperiment);
experiments.Add(experiment);
}
}
/// <summary>
/// Fills this instance data members with the information read from <paramref name="wiffFile"/>.
/// </summary>
/// <param name="wiffFile">A <see cref="Batch"/> instance. The data source.</param>
private void Initialize(Batch wiffFile)
{
Sample sample = wiffFile.GetSample(this.index);
// retrieve this sample's name
this.name = sample.Details.SampleName;
// 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
{
// 1) Set the various WiffSample Parameters
string pathFile = this.wiffFileContent.FileName + " (" + (this.index + 1).ToString(CultureInfo.InvariantCulture) + ").path";
// Make sure the path file exists
if (!File.Exists(pathFile))
{
MessageBox.Show(pathFile + " is missing", "Missing File");
return;
}
var positionStream = new FileStream(@pathFile, FileMode.Open, FileAccess.Read);
// calculate the count of position entries (12 bytes per position entry)
this.positionDataLength = positionStream.Length / 12;
this.x1 = 1e10;
this.x2 = 0.0;
this.y1 = 1e10;
this.y2 = 0.0;
// the array to hold the position information
this.positionData = new uint[this.positionDataLength, 3];
var positionReader = new BinaryReader(positionStream);
for (long posindex = 0; posindex < this.positionDataLength; posindex++)
{
this.positionData[posindex, 0] = positionReader.ReadUInt32();
this.positionData[posindex, 1] = positionReader.ReadUInt32();
this.positionData[posindex, 2] = positionReader.ReadUInt32();
// hundred progress ticks
if (Equals(posindex % (this.positionDataLength / 100.0), 0.0))
{
AppContext.ProgressSetValue(100.0 * posindex / this.positionDataLength);
}
if (this.positionData[posindex, 1] < this.x1)
{
this.x1 = this.positionData[posindex, 1];
}
if (this.positionData[posindex, 1] > this.x2)
{
this.x2 = this.positionData[posindex, 1];
}
if (this.positionData[posindex, 2] < this.y1)
{
this.y1 = this.positionData[posindex, 2];
}
if (this.positionData[posindex, 2] > this.y2)
{
this.y2 = this.positionData[posindex, 2];
}
}
positionReader.Close();
positionStream.Close();
this.x1 /= 1000;
this.x2 /= 1000;
this.y1 /= 1000;
this.y2 /= 1000;
this.width = this.x2 - this.x1;
this.height = this.y2 - this.y1;
}
finally
{
AppContext.ProgressClear();
}
// 2) Get the size of the scan file set scanfilesize
string scanpathFile = this.wiffFileContent.FileName + ".scan";
var fileinfo = new FileInfo(scanpathFile);
this.scanfilesize = fileinfo.Length;
MassSpectrometerSample massSpecSample = sample.MassSpectrometerSample;
int numberOfExperiments = massSpecSample.ExperimentCount;
// 3) Get number of experiments and create WiffExperiments for each
// loop through the experiments; the index of the experiments is zero based!!
for (int actExperiment = 0; actExperiment < numberOfExperiments; actExperiment++)
{
MSExperiment msexperiment = massSpecSample.GetMSExperiment(actExperiment);
WiffExperiment experiment = WiffExperimentFactory.CreateWiffExperiment(msexperiment, this);
this.experiments.Add(experiment);
}
}