private static void FormatCsvArray(TextWriter writer, IList<float> floatArray, CultureInfo cultureInfo) { char intensitySeparator = TextUtil.GetCsvSeparator(cultureInfo); for (int i = 0; i < floatArray.Count; ++i) { if (i > 0) writer.Write(intensitySeparator); writer.WriteDsvField(System.Convert.ToString(floatArray[i], cultureInfo), intensitySeparator); } }
private static void FormatHeader(TextWriter writer, IList<string> fieldNames) { for (int i = 0; i < fieldNames.Count; ++i) { if (i > 0) writer.Write(MAIN_SEPARATOR); writer.WriteDsvField(fieldNames[i], MAIN_SEPARATOR); } writer.WriteLine(); }
protected override void WriteTransition(TextWriter writer, XmlFastaSequence sequence, XmlPeptide peptide, XmlTransition transition) { char separator = TextUtil.GetCsvSeparator(_cultureInfo); writer.Write(transition.PrecursorMz.ToString(_cultureInfo)); writer.Write(separator); writer.Write(transition.ProductMz.ToString(_cultureInfo)); writer.Write(separator); if (MethodType == ExportMethodType.Standard) writer.Write(Math.Round(DwellTime, 2).ToString(_cultureInfo)); else { if (!peptide.PredictedRetentionTime.HasValue) throw new InvalidOperationException(Resources.XmlThermoMassListExporter_WriteTransition_Attempt_to_write_scheduling_parameters_failed); writer.Write(peptide.PredictedRetentionTime.Value.ToString(_cultureInfo)); } writer.Write(separator); // Write special ID for ABI software var fastaSequence = new FastaSequence(sequence.Name, sequence.Description, null, peptide.Sequence); var newPeptide = new Peptide(fastaSequence, peptide.Sequence, 0, peptide.Sequence.Length, peptide.MissedCleavages); var nodePep = new PeptideDocNode(newPeptide); string modifiedPepSequence = AbiMassListExporter.GetSequenceWithModsString(nodePep, _document.Settings); // Not L10N; string extPeptideId = string.Format("{0}.{1}.{2}.{3}", // Not L10N sequence.Name, modifiedPepSequence, GetTransitionName(transition), "light"); // Not L10N : file format writer.WriteDsvField(extPeptideId, separator); writer.Write(separator); writer.Write(Math.Round(transition.DeclusteringPotential ?? 0, 1).ToString(_cultureInfo)); writer.Write(separator); writer.Write(Math.Round(transition.CollisionEnergy, 1).ToString(_cultureInfo)); writer.WriteLine(); }
private static void FormatChromLine(TextWriter writer, IEnumerable<string> fieldArray, IList<float> times, IList<float> intensities, CultureInfo cultureInfo) { foreach (string field in fieldArray) { writer.WriteDsvField(field, MAIN_SEPARATOR); writer.Write(MAIN_SEPARATOR); } FormatCsvArray(writer, times, cultureInfo); writer.Write(MAIN_SEPARATOR); FormatCsvArray(writer, intensities, cultureInfo); writer.WriteLine(); }
private static void WriteHeader(TextWriter writer) { const char separator = TextUtil.SEPARATOR_TSV; // ReSharper disable NonLocalizedString var namesArray = new List<string> { "FileName", "PeptideModifiedSequence", "Apex", "annotation_Score", "annotation_QValue", "decoy" }; // ReSharper restore NonLocalizedString bool first = true; foreach (var name in namesArray) { if (first) first = false; else writer.Write(separator); writer.WriteDsvField(name, separator); } writer.WriteLine(); }
private static void WriteLine(TextWriter writer, CultureInfo cultureInfo, string file, string modifiedSequence, double rt, double score, double qValue, bool decoy) { const char separator = TextUtil.SEPARATOR_TSV; var fieldsArray = new List<string> { file, modifiedSequence, Convert.ToString(rt, cultureInfo), Convert.ToString(score, cultureInfo), Convert.ToString(qValue, cultureInfo), Convert.ToString(decoy, cultureInfo) }; bool first = true; foreach (var name in fieldsArray) { if (first) first = false; else writer.Write(separator); writer.WriteDsvField(name, separator); } writer.WriteLine(); }
public void WriteLine(TextWriter writer, string dataset, string toolName, double peptides01, double peptides05, double peptidesAll, double qValue01, double qValue05) { const char separator = TextUtil.SEPARATOR_TSV; var fieldsArray = new List<string> { dataset, toolName, Convert.ToString(peptides01, CultureInfo.InvariantCulture), Convert.ToString(peptides05, CultureInfo.InvariantCulture), Convert.ToString(peptidesAll, CultureInfo.InvariantCulture), Convert.ToString(qValue01, CultureInfo.InvariantCulture), Convert.ToString(qValue05, CultureInfo.InvariantCulture), }; bool first = true; foreach (var name in fieldsArray) { if (first) first = false; else writer.Write(separator); writer.WriteDsvField(name, separator); } writer.WriteLine(); }
public void WriteHeader(TextWriter writer) { const char separator = TextUtil.SEPARATOR_TSV; // ReSharper disable NonLocalizedString var namesArray = new List<string> { "DataSet", "ToolName", "Peptides01", "Peptides05", "PeptdesAll", "QValue01", "QValue05" }; // ReSharper restore NonLocalizedString bool first = true; foreach (var name in namesArray) { if (first) first = false; else writer.Write(separator); writer.WriteDsvField(name, separator); } writer.WriteLine(); }
private static void WriteRow(TextWriter writer, PeakTransitionGroupFeatures features, PeakGroupFeatures peakGroupFeatures, CultureInfo cultureInfo, double mProphetScore, double pValue, double qValue) { char separator = TextUtil.GetCsvSeparator(cultureInfo); string fileName = SampleHelp.GetFileName(features.Id.FilePath); var fieldsArray = new List<string> { Convert.ToString(features.Id, cultureInfo), Convert.ToString(features.Id.Run, cultureInfo), fileName, Convert.ToString(peakGroupFeatures.RetentionTime, cultureInfo), Convert.ToString(peakGroupFeatures.StartTime, cultureInfo), Convert.ToString(peakGroupFeatures.EndTime, cultureInfo), features.Id.NodePep.RawUnmodifiedTextId, // Unmodified sequence, or custom ion name features.Id.NodePep.RawTextId, // Modified sequence, or custom ion name features.Id.NodePepGroup.Name, Convert.ToString(features.Id.NodePep.IsDecoy ? 1 : 0, cultureInfo), ToFieldString((float) mProphetScore, cultureInfo), ToFieldString((float) pValue, cultureInfo), ToFieldString((float) qValue, cultureInfo) }; if (IsFilterTestData) { fieldsArray.Add(peakGroupFeatures.GetFilterPairsText(cultureInfo)); } foreach (var name in fieldsArray) { writer.WriteDsvField(name, separator); writer.Write(separator); } bool first = true; foreach (float featureColumn in peakGroupFeatures.Features) { if (!first) writer.Write(separator); writer.WriteDsvField(ToFieldString(featureColumn, cultureInfo), separator); first = false; } writer.WriteLine(); }
private static void WriteHeaderRow(TextWriter writer, IEnumerable<IPeakFeatureCalculator> calcs, CultureInfo cultureInfo) { char separator = TextUtil.GetCsvSeparator(cultureInfo); // ReSharper disable NonLocalizedString var namesArray = new List<string> { "transition_group_id", "run_id", "FileName", "RT", "MinStartTime", "MaxEndTime", "Sequence", "PeptideModifiedSequence", "ProteinName", "PrecursorIsDecoy", "mProphetScore", "pValue", "qValue" }; if (IsFilterTestData) { namesArray.Add("FoundIonFilters"); } // ReSharper restore NonLocalizedString foreach (var name in namesArray) { writer.WriteDsvField(name, separator); writer.Write(separator); } bool first = true; foreach (var peakFeatureCalculator in calcs) { if (!first) writer.Write(separator); writer.Write(first ? "main_var_{0}" : "var_{0}", peakFeatureCalculator.HeaderName.Replace(" ", "_")); // Not L10N first = false; } writer.WriteLine(); }
public static void WriteReportHelper(ResultSet results, char separator, TextWriter writer, CultureInfo ci) { for (int i = 0; i < results.ColumnInfos.Count; i++) { var columnInfo = results.ColumnInfos[i]; if (columnInfo.IsHidden) continue; if (i > 0) writer.Write(separator); writer.WriteDsvField(columnInfo.Caption, separator); } writer.WriteLine(); for (int iRow = 0; iRow < results.RowCount; iRow++) { for (int iColumn = 0; iColumn < results.ColumnInfos.Count; iColumn++) { var columnInfo = results.ColumnInfos[iColumn]; if (columnInfo.IsHidden) continue; if (iColumn > 0) writer.Write(separator); string value = results.FormatValue(iRow, iColumn, ci); writer.WriteDsvField(value, separator); } writer.WriteLine(); } }