/// <summary>
/// Name: FindExperiment
/// Description: This function will find the experimental data (in the form of a list) that matches the given experimental code.
/// </summary>
/// <param name="experimentCode">
/// Input: The experimentCode is a code that can reference a given experiment that is in the current opened mz data file.
/// </param>
/// <returns>
/// Output: The output is a List of ActualElement, where actual elements are containers with all possible data that can be in the current file.
/// </returns>
public List <ActualElement> FindExperiment(int experimentCode)
{
//Initialize a new experimentalData list to return.
List <ActualElement> experimentData = new List <ActualElement>();
//update the new experimentCode to the inputed experiment code, so we can get the right Parent Ion number.
this.m_experimentCode = experimentCode;
if (this.m_isFileOpened)
{
//We need to Cache the entire file into memory (which puts it into MZList) to look at the data in the file.
m_fileToRead.ReadAndCacheEntireFile();
//narrow the number of Spectrums down to all the data sets that match the experimentCode.
bool result = m_fileToRead.GetSpectrumByScanNumber(m_experimentCode, ref m_currentSpectrum);
this.m_mZIndex = 0;
//We will run through each data that is in memory and convert that data into
// an ActualElement structure and then all the element to the experimentData List.
while (m_mZIndex < this.m_currentSpectrum.MZList.Count())
{
ActualElement inputForList = new ActualElement();
inputForList.MZValue = this.m_currentSpectrum.MZList[m_mZIndex];
inputForList.Intensity = (double)this.m_currentSpectrum.LookupIonIntensityByMZ(inputForList.MZValue, (float)0, (float)0.04);
experimentData.Add(inputForList);
++m_mZIndex;
}
}
return(experimentData);
}
/// <summary>
/// The constructor of this parser will attempt to open any files that
/// end in ".mzXML" or ".mzData". If a null string is passed in or a
/// a string without a ".mzXML" or ".mzData" file extension then an exception
/// will be thrown.
/// </summary>
/// <param name="fileLocation">This must be a file Location to a ".mzXML" or ".mzData" file.</param>
public MzParser(string fileLocation)
{
this.m_fileLocation = fileLocation;
if (m_fileLocation != null)
{
if (m_fileLocation.ToLower().EndsWith(".mzXML".ToLower()) ||
m_fileLocation.ToLower().EndsWith(".mzData".ToLower()))
{
m_fileToRead = new clsMzXMLFileAccessor();
m_fileOpened = m_fileToRead.OpenFile(m_fileLocation);
}
else
{
throw new System.InvalidProgramException("Invalid File Type, must be .mzXML or .mzData");
}
m_fileToRead.ReadAndCacheEntireFile();
}
else
{
throw new System.InvalidOperationException("The file location passed was equal to null");
}
}