private clsMassTag convertDeconToolsMassTagToMultialignMassTag(TargetBase mt)
{
var multialignMassTag = new clsMassTag();
multialignMassTag.Id = mt.ID;
multialignMassTag.Charge1FScore = 0;
multialignMassTag.Charge2FScore = 0;
multialignMassTag.Charge3FScore = 0;
multialignMassTag.ChargeState = mt.ChargeState;
multialignMassTag.CleavageState = -1;
multialignMassTag.DiscriminantMax = 0;
//multialignMassTag.DriftTime = 0;
multialignMassTag.HighPeptideProphetProbability = 0;
multialignMassTag.Mass = mt.MonoIsotopicMass;
multialignMassTag.ModCount = -1;
multialignMassTag.Modifications = String.Empty;
multialignMassTag.MSGFSpecProbMax = 0;
multialignMassTag.MSMSObserved = mt.ObsCount;
multialignMassTag.NetAverage = mt.NormalizedElutionTime;
multialignMassTag.NetPredicted = -1;
multialignMassTag.NetStandardDeviation = 0;
multialignMassTag.Peptide = mt.Code;
multialignMassTag.PeptideEx = String.Empty;
multialignMassTag.XCorr = -1;
return(multialignMassTag);
}
private clsMassTag[] convertDeconToolsMassTagsToMultialignMassTags(List <MassTag> massTagList)
{
List <clsMassTag> massTags = new List <clsMassTag>();
foreach (var mt in massTagList)
{
clsMassTag multialignMassTag = convertDeconToolsMassTagToMultialignMassTag(mt);
massTags.Add(multialignMassTag);
}
return(massTags.ToArray());
}
/// <summary>
/// Reads the XAMT file.
/// </summary>
/// <param name="filepath">Path of XAMT in flat file form.</param>
/// <returns>Mass Tag Database. Null if file does not exist.</returns>
public clsMassTagDB ReadXAMTDatabase(string filepath)
{
if (System.IO.File.Exists(filepath) == false)
return null;
///
/// Create a new database.
///
clsMassTagDB xamt = new clsMassTagDB();
///
/// Read the file - We could use a read line by line
/// method here, but the files are small.
///
string[] lines = System.IO.File.ReadAllLines(filepath);
///
/// Read the column headers
///
string header = lines[0];
ConstructHeaderMapping(header);
///
/// Parse the rest of the file now.
///
List<clsMassTag> massTags = new List<clsMassTag>();
for(int i = 1; i < lines.Length; i++)
{
string line = lines[i];
massTags.Add(ParseLine(line));
}
///
/// Transfer the data to the XAMT.
///
clsMassTag[] tags = new clsMassTag[massTags.Count];
massTags.CopyTo(tags);
xamt.AddMassTags(tags);
return xamt;
}
/// <summary>
/// Parses a line of data from the XAMT File and returns a mass tag.
/// </summary>
/// <param name="line"></param>
/// <returns></returns>
private clsMassTag ParseLine(string line)
{
string[] data = line.Split(CONST_CHAR_DELIMITER);
clsMassTag tag = new clsMassTag();
tag.Id = Convert.ToInt32(data[m_headerDictionary[CONST_MASS_TAG_ID]]);
tag.Mass = Convert.ToDouble(data[m_headerDictionary[CONST_MONO_MASS]]);
tag.NetAverage = Convert.ToDouble(data[m_headerDictionary[CONST_NET]]);
tag.NetPredicted = Convert.ToDouble(data[m_headerDictionary[CONST_NET]]);
tag.DriftTime = Convert.ToDouble(data[m_headerDictionary[CONST_PREDICTED_DRIFT_TIME]]);
tag.mstrPeptide = data[m_headerDictionary[CONST_PEPTIDE]];
return tag;
}
