/// <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); }
/// <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 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); }