public void Filter(MassTagDatabaseOptions options)
{
var massTags = MassTags.Where(t => t.Net >= options.MinimumNet)
.Where(t => t.Net <= options.MaximumNet)
.Where(t => t.MassMonoisotopic >= options.MinimumMass)
.Where(t => t.MassMonoisotopic <= options.MaximumMass).ToList();
this.MassTags.Clear();
this.AddMassTagsAndProteins(massTags, this.Proteins);
}
/// <summary>
/// Loads the mass tags and populates the protein information.
/// </summary>
/// <param name="massTags"></param>
/// <param name="massTagToProteinMap"></param>
public void AddMassTagsAndProteins(List <MassTagLight> massTags,
Dictionary <int, List <Protein> > massTagToProteinMap)
{
MassTags.AddRange(massTags);
var massTagMap = new Dictionary <int, MassTagLight>();
foreach (var tag in massTags)
{
if (massTagMap.ContainsKey(tag.Id) == false)
{
massTagMap.Add(tag.Id, tag);
}
}
ProteinsToMassTags = new Dictionary <int, List <MassTagLight> >();
var proteinMap = new Dictionary <int, Protein>();
AllProteins = new List <Protein>();
foreach (var key in massTagToProteinMap.Keys)
{
var proteins = massTagToProteinMap[key];
if (massTagMap.ContainsKey(key) == false)
{
continue;
}
var tag = massTagMap[key];
foreach (var p in proteins)
{
if (!proteinMap.ContainsKey(p.RefId))
{
AllProteins.Add(p);
proteinMap.Add(p.RefId, p);
}
if (!ProteinsToMassTags.ContainsKey(p.ProteinId))
{
ProteinsToMassTags.Add(p.ProteinId, new List <MassTagLight>());
}
ProteinsToMassTags[p.ProteinId].Add(tag);
}
}
Proteins = massTagToProteinMap;
DetermineIfContainsDriftTime(massTags);
}
/// <summary>
/// Handles converting the rows to factor objects.
/// </summary>
/// <param name="sender"></param>
/// <param name="args"></param>
public void HandleDataRow(object sender, MageDataEventArgs args)
{
if (args == null)
{
throw new NullReferenceException("The mass tags are invalid.");
}
if (args.Fields == null)
{
return;
throw new NullReferenceException("The mass tag database rows are invalid.");
}
if (args.Fields.Length < 11)
{
return;
throw new ArgumentException("The number of columns for the mass tags are invalid.");
}
var tag = new MassTagLight();
if (m_columnMapping.ContainsKey("Mass"))
{
tag.MassMonoisotopic = Convert.ToDouble(args.Fields[m_columnMapping["Mass"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("NET"))
{
tag.NetAverage = Convert.ToDouble(args.Fields[m_columnMapping["NET"]]);
tag.Net = tag.NetAverage;
}
else
{
return;
}
if (m_columnMapping.ContainsKey("Dataset_Member_Count"))
{
tag.ObservationCount = Convert.ToInt32(args.Fields[m_columnMapping["Dataset_Member_Count"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("Cluster_ID"))
{
tag.Id = Convert.ToInt32(args.Fields[m_columnMapping["Cluster_ID"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("Drift_Time"))
{
tag.DriftTime = Convert.ToDouble(args.Fields[m_columnMapping["Drift_Time"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("Charge"))
{
tag.ChargeState = Convert.ToInt32(args.Fields[m_columnMapping["Charge"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("Score"))
{
tag.Score = Convert.ToDouble(args.Fields[m_columnMapping["Score"]]);
}
else
{
return;
}
MassTags.Add(tag);
}
