/// <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 factors are invalid.");
}
if (args.Fields == null)
{
return;
throw new NullReferenceException("The factor rows are invalid.");
}
if (args.Fields.Length < 4)
{
return;
throw new ArgumentException("The number of columns for the factors are invalid.");
}
var sequence = new DatabaseSearchSequence();
if (m_columnMapping.ContainsKey("Peptide"))
{
sequence.Sequence = Convert.ToString(args.Fields[m_columnMapping["Peptide"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("ScanNum"))
{
sequence.Scan = Convert.ToInt32(args.Fields[m_columnMapping["ScanNum"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("XCorr"))
{
sequence.Score = Convert.ToDouble(args.Fields[m_columnMapping["XCorr"]]);
}
else
{
return;
}
sequence.Id = m_count++;
sequence.GroupId = DatasetID;
m_sequences.Add(sequence);
}
/// <summary>
/// Handles the definitions of data rows.
/// </summary>
/// <param name="sender"></param>
/// <param name="args"></param>
public void HandleDataRow(object sender, MageDataEventArgs args)
{
if (!args.DataAvailable)
{
return;
}
var value = args.Fields[m_archiveFolderPath].ToString();
m_folders.Add(value);
}
/// <summary>
/// Handles the definitions of data rows.
/// </summary>
/// <param name="sender"></param>
/// <param name="args"></param>
public void HandleDataRow(object sender, MageDataEventArgs args)
{
if (!args.DataAvailable)
{
return;
}
var database = new InputDatabase();
database.DatabaseName = args.Fields[m_databaseNameColumn].ToString();
database.DatabaseServer = args.Fields[m_serverNameColumn].ToString();
database.Description = args.Fields[m_description].ToString();
database.Organism = args.Fields[m_organism].ToString();
database.Jobs = Convert.ToInt32(args.Fields[m_msmsJobs]);
m_databases.Add(database);
}
public void HandleDataRow(object sender, MageDataEventArgs args)
{
}
/// <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);
}
public void HandleDataRow(object sender, MageDataEventArgs args)
{
}
/// <summary>
/// Handles the definitions of data rows.
/// </summary>
/// <param name="sender"></param>
/// <param name="args"></param>
public void HandleDataRow(object sender, MageDataEventArgs args)
{
if (!args.DataAvailable)
{
return;
}
var database = new InputDatabase();
database.DatabaseName = args.Fields[m_databaseNameColumn].ToString();
database.DatabaseServer = args.Fields[m_serverNameColumn].ToString();
database.Description = args.Fields[m_description].ToString();
database.Organism = args.Fields[m_organism].ToString();
database.Jobs = Convert.ToInt32(args.Fields[m_msmsJobs]);
m_databases.Add(database);
}
/// <summary>
/// Handles the definitions of data rows.
/// </summary>
/// <param name="sender"></param>
/// <param name="args"></param>
public void HandleDataRow(object sender, MageDataEventArgs args)
{
if (!args.DataAvailable)
{
return;
}
var value = args.Fields[m_archiveFolderPath].ToString();
m_folders.Add(value);
}
/// <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 factors are invalid.");
}
if (args.Fields == null)
{
return;
throw new NullReferenceException("The factor rows are invalid.");
}
if (args.Fields.Length < 4)
{
return;
throw new ArgumentException("The number of columns for the factors are invalid.");
}
var datasetName = "";
if (m_columnMapping.ContainsKey("Dataset"))
{
datasetName = Convert.ToString(args.Fields[m_columnMapping["Dataset"]]).ToLower().Replace("\"", "");
}
else
{
return;
}
var datasetId = -1;
if (m_columnMapping.ContainsKey("Dataset_ID"))
{
datasetId = Convert.ToInt32(args.Fields[m_columnMapping["Dataset_ID"]].ToString().Replace("\"", ""));
}
else
{
return;
}
var factor = "";
if (m_columnMapping.ContainsKey("Factor"))
{
factor = Convert.ToString(args.Fields[m_columnMapping["Factor"]]).Replace("\"", "");
}
else
{
return;
}
var value = "";
if (m_columnMapping.ContainsKey("Value"))
{
value = Convert.ToString(args.Fields[m_columnMapping["Value"]]).Replace("\"", "");
}
else
{
return;
}
var factorMap = new ExperimentalFactor();
factorMap.Value = value;
factorMap.Name = factor;
DatasetInformation info = null;
// Update the dataset ID.
if (m_datasets.ContainsKey(datasetName))
{
info = m_datasets[datasetName];
m_datasets[datasetName].DMSDatasetID = datasetId;
}
else
{
return;
}
// Make sure we haven't seen this factor map before.
var shouldAdd = true;
if (m_factorMaps.ContainsKey(factor))
{
if (m_factorMaps[factor].ContainsKey(value))
{
shouldAdd = false;
}
}
else
{
m_factorMaps.Add(factor, new Dictionary<string, int>());
}
var factorID = 0;
// Add it to the list and map of factors to dump into the database.
if (shouldAdd)
{
factorMap.FactorID = m_factorCount++;
m_factorMaps[factor].Add(value, factorMap.FactorID);
factorID = factorMap.FactorID;
m_factors.Add(factorMap);
}
else
{
factorID = m_factorMaps[factor][value];
}
var datasetFactorMap = new DatasetToExperimentalFactorMap();
datasetFactorMap.DatasetID = info.DatasetId;
datasetFactorMap.FactorID = factorID;
m_factorAssignments.Add(datasetFactorMap);
}
/// <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 factors are invalid.");
}
if (args.Fields == null)
{
return;
throw new NullReferenceException("The factor rows are invalid.");
}
if (args.Fields.Length < 4)
{
return;
throw new ArgumentException("The number of columns for the factors are invalid.");
}
var datasetName = "";
if (m_columnMapping.ContainsKey("Dataset"))
{
datasetName = Convert.ToString(args.Fields[m_columnMapping["Dataset"]]).ToLower().Replace("\"", "");
}
else
{
return;
}
var datasetId = -1;
if (m_columnMapping.ContainsKey("Dataset_ID"))
{
datasetId = Convert.ToInt32(args.Fields[m_columnMapping["Dataset_ID"]].ToString().Replace("\"", ""));
}
else
{
return;
}
var factor = "";
if (m_columnMapping.ContainsKey("Factor"))
{
factor = Convert.ToString(args.Fields[m_columnMapping["Factor"]]).Replace("\"", "");
}
else
{
return;
}
var value = "";
if (m_columnMapping.ContainsKey("Value"))
{
value = Convert.ToString(args.Fields[m_columnMapping["Value"]]).Replace("\"", "");
}
else
{
return;
}
var factorMap = new ExperimentalFactor();
factorMap.Value = value;
factorMap.Name = factor;
DatasetInformation info = null;
// Update the dataset ID.
if (m_datasets.ContainsKey(datasetName))
{
info = m_datasets[datasetName];
m_datasets[datasetName].DMSDatasetID = datasetId;
}
else
{
return;
}
// Make sure we haven't seen this factor map before.
var shouldAdd = true;
if (m_factorMaps.ContainsKey(factor))
{
if (m_factorMaps[factor].ContainsKey(value))
{
shouldAdd = false;
}
}
else
{
m_factorMaps.Add(factor, new Dictionary <string, int>());
}
var factorID = 0;
// Add it to the list and map of factors to dump into the database.
if (shouldAdd)
{
factorMap.FactorID = m_factorCount++;
m_factorMaps[factor].Add(value, factorMap.FactorID);
factorID = factorMap.FactorID;
m_factors.Add(factorMap);
}
else
{
factorID = m_factorMaps[factor][value];
}
var datasetFactorMap = new DatasetToExperimentalFactorMap();
datasetFactorMap.DatasetID = info.DatasetId;
datasetFactorMap.FactorID = factorID;
m_factorAssignments.Add(datasetFactorMap);
}
/// <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);
}
/// <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 factors are invalid.");
}
if (args.Fields == null)
{
return;
throw new NullReferenceException("The factor rows are invalid.");
}
if (args.Fields.Length < 4)
{
return;
throw new ArgumentException("The number of columns for the factors are invalid.");
}
var sequence = new DatabaseSearchSequence();
if (m_columnMapping.ContainsKey("Peptide"))
{
sequence.Sequence = Convert.ToString(args.Fields[m_columnMapping["Peptide"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("ScanNum"))
{
sequence.Scan = Convert.ToInt32(args.Fields[m_columnMapping["ScanNum"]]);
}
else
{
return;
}
if (m_columnMapping.ContainsKey("XCorr"))
{
sequence.Score = Convert.ToDouble(args.Fields[m_columnMapping["XCorr"]]);
}
else
{
return;
}
sequence.Id = m_count ++;
sequence.GroupId = DatasetID;
m_sequences.Add(sequence);
}
