public void TestWrite() { TextFileDefinition def = new TextFileDefinition(); def.Delimiter = '\t'; def.Description = "Test File ..."; def.Add(new FileDefinitionItem() { AnnotationName = "AnnoKey1", PropertyName = "PropName1", ValueType = "double", Format = "{0:0.0000}" }); def.Add(new FileDefinitionItem() { AnnotationName = "AnnoKey2", PropertyName = "PropName2", ValueType = "int" }); def.Add(new FileDefinitionItem() { AnnotationName = "AnnoKey3", PropertyName = "PropName3", ValueType = "string" }); var newfile = @"../../../data/TextFileDefinition2.xml"; def.WriteToFile(newfile); AssertUtils.AssertFileEqual(DefinitionFile, newfile); File.Delete(newfile); }
public PropertyMappingParser(string mappingFile) { var maps = new TextFileDefinition(); maps.ReadFromFile(mappingFile); InitializeByDefinition(maps); }
public void TestRead() { TextFileDefinition def = new TextFileDefinition(); def.ReadFromFile(DefinitionFile); Assert.AreEqual('\t', def.Delimiter); Assert.AreEqual("Test File ...", def.Description); Assert.AreEqual(3, def.Count); Assert.AreEqual("AnnoKey1", def[0].AnnotationName); Assert.AreEqual("PropName1", def[0].PropertyName); Assert.AreEqual("double", def[0].ValueType); Assert.AreEqual("{0:0.0000}", def[0].Format); Assert.AreEqual("AnnoKey2", def[1].AnnotationName); Assert.AreEqual("PropName2", def[1].PropertyName); Assert.AreEqual("int", def[1].ValueType); Assert.AreEqual("AnnoKey3", def[2].AnnotationName); Assert.AreEqual("PropName3", def[2].PropertyName); Assert.AreEqual("string", def[2].ValueType); }
private void InitializeByDefinition(TextFileDefinition maps) { Type t = typeof(BreastCancerSampleItem); var properties = t.GetProperties(); foreach (var item in maps) { if (!String.IsNullOrEmpty(item.PropertyName)) { converters[item.AnnotationName] = ConverterUtils.GetPropertConverters<BreastCancerSampleItem>(properties, item.PropertyName); } } foreach (var df in maps.DefaultValues) { var ct = ConverterUtils.GetPropertConverters<BreastCancerSampleItem>(properties, df.PropertyName); defaultConverters[ct] = df.Value; } }
private void InitializeByDefinition(TextFileDefinition maps) { Type t = typeof(BreastCancerSampleItem); var properties = t.GetProperties(); foreach (var item in maps) { if (!String.IsNullOrEmpty(item.PropertyName)) { converters[item.AnnotationName] = ConverterUtils.GetPropertConverters <BreastCancerSampleItem>(properties, item.PropertyName); } } foreach (var df in maps.DefaultValues) { var ct = ConverterUtils.GetPropertConverters <BreastCancerSampleItem>(properties, df.PropertyName); defaultConverters[ct] = df.Value; } }
private void btnNewSample_Click(object sender, EventArgs e) { TextFileDefinition def = new TextFileDefinition(); def.ReadFromFile(formats.SelectedItem.GetFormatFile()); string ext = "csv"; if (def.Delimiter != ',') { ext = "txt"; } dlgSave.Filter = "Sample File|*." + ext + "|All Files|*.*"; if (dlgSave.ShowDialog() == System.Windows.Forms.DialogResult.OK) { def.WriteSampleFile(dlgSave.FileName); MessageBox.Show(this, "File saved to : " + dlgSave.FileName); } }
public void NewFromData(string subdir) { try { var siformat = Directory.GetFiles(subdir, "*.siformat"); TextFileDefinition prefile = new TextFileDefinition(); if (siformat.Length > 0) { prefile.ReadFromFile(siformat[0]); } var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(subdir); LastDirectory = subdir; lastFile = String.Empty; var files = new HashSet <string>(from f in CelFile.GetCelFiles(subdir, false) select GeoUtils.GetGsmName(f)); Dictionary <string, HashSet <string> > headers = new Dictionary <string, HashSet <string> >(); foreach (var m in map) { var gsm = m.Key.ToUpper(); if (!files.Contains(gsm)) { continue; } var curmap = m.Value; foreach (var entry in curmap) { if (!headers.ContainsKey(entry.Key)) { headers[entry.Key] = new HashSet <string>(); } headers[entry.Key].UnionWith(entry.Value); } } ClearDataSource(); items.Clear(); foreach (var part in headers) { items.Add(new FileDefinitionItem() { AnnotationName = part.Key, Example = (from v in part.Value orderby v select v).Merge(";") }); } foreach (var olditem in prefile) { if (!string.IsNullOrEmpty(olditem.PropertyName)) { var newitem = items.Find(m => m.AnnotationName.Equals(olditem.AnnotationName)); if (newitem != null) { newitem.PropertyName = olditem.PropertyName; } } } items.DefaultValues.Clear(); items.Sort((m1, m2) => m1.AnnotationName.CompareTo(m2.AnnotationName)); UpdateDataSource(); label1.Text = "Annotation/property mapping - " + Path.GetFileName(subdir); dlgOpenDirectory.SelectedPath = subdir; dlgSaveFormatFile.FileName = Path.Combine(subdir, Path.GetFileName(subdir) + ".siformat"); } catch (Exception ex) { MessageBox.Show(this, ex.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error); } }
public void NewFromData(string subdir) { var siformat = Directory.GetFiles(subdir, "*.siformat"); TextFileDefinition prefile = new TextFileDefinition(); if (siformat.Length > 0) { prefile.ReadFromFile(siformat[0]); bool bFound = false; prefile.ForEach(m => { if (m.PropertyName.Equals("TumorStage")) { m.PropertyName = "TumorStatus"; bFound = true; } if (m.PropertyName.Equals("Metastasis")) { m.PropertyName = "MetastasisStatus"; bFound = true; } }); if (bFound) { prefile.WriteToFile(siformat[0]); } } var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(subdir); lastDirectory = subdir; lastFile = String.Empty; var files = new HashSet <string>(from f in CelFile.GetCelFiles(subdir, false) select GeoUtils.GetGsmName(f)); Dictionary <string, HashSet <string> > headers = new Dictionary <string, HashSet <string> >(); foreach (var m in map) { var gsm = m.Key.ToLower(); if (!files.Contains(gsm)) { continue; } var curmap = m.Value; foreach (var entry in curmap) { if (!headers.ContainsKey(entry.Key)) { headers[entry.Key] = new HashSet <string>(); } headers[entry.Key].UnionWith(entry.Value); } } ClearDataSource(); items.Clear(); foreach (var part in headers) { items.Add(new FileDefinitionItem() { AnnotationName = part.Key, Example = (from v in part.Value orderby v select v).Merge(";") }); } foreach (var olditem in prefile) { if (!string.IsNullOrEmpty(olditem.PropertyName)) { var newitem = items.Find(m => m.AnnotationName.Equals(olditem.AnnotationName)); if (newitem != null) { newitem.PropertyName = olditem.PropertyName; } } } items.DefaultValues.Clear(); foreach (var olddv in prefile.DefaultValues) { if (propertyNames.Contains(olddv.PropertyName)) { items.DefaultValues.Add(new DefaultValue() { PropertyName = olddv.PropertyName, Value = olddv.Value }); } } items.Sort((m1, m2) => m1.AnnotationName.CompareTo(m2.AnnotationName)); UpdateDataSource(); this.Text = title + " - " + Path.GetFileName(subdir); }
public PropertyMappingParser(TextFileDefinition maps) { InitializeByDefinition(maps); }
public void NewFromData(string subdir) { var siformat = Directory.GetFiles(subdir, "*.siformat"); TextFileDefinition prefile = new TextFileDefinition(); if (siformat.Length > 0) { prefile.ReadFromFile(siformat[0]); bool bFound = false; prefile.ForEach(m => { if (m.PropertyName.Equals("TumorStage")) { m.PropertyName = "TumorStatus"; bFound = true; } if (m.PropertyName.Equals("Metastasis")) { m.PropertyName = "MetastasisStatus"; bFound = true; } }); if (bFound) { prefile.WriteToFile(siformat[0]); } } var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(subdir); lastDirectory = subdir; lastFile = String.Empty; var files = new HashSet<string>(from f in CelFile.GetCelFiles(subdir, false) select GeoUtils.GetGsmName(f)); Dictionary<string, HashSet<string>> headers = new Dictionary<string, HashSet<string>>(); foreach (var m in map) { var gsm = m.Key.ToLower(); if (!files.Contains(gsm)) { continue; } var curmap = m.Value; foreach (var entry in curmap) { if (!headers.ContainsKey(entry.Key)) { headers[entry.Key] = new HashSet<string>(); } headers[entry.Key].UnionWith(entry.Value); } } ClearDataSource(); items.Clear(); foreach (var part in headers) { items.Add(new FileDefinitionItem() { AnnotationName = part.Key, Example = (from v in part.Value orderby v select v).Merge(";") }); } foreach (var olditem in prefile) { if (!string.IsNullOrEmpty(olditem.PropertyName)) { var newitem = items.Find(m => m.AnnotationName.Equals(olditem.AnnotationName)); if (newitem != null) { newitem.PropertyName = olditem.PropertyName; } } } items.DefaultValues.Clear(); foreach (var olddv in prefile.DefaultValues) { if (propertyNames.Contains(olddv.PropertyName)) { items.DefaultValues.Add(new DefaultValue() { PropertyName = olddv.PropertyName, Value = olddv.Value }); } } items.Sort((m1, m2) => m1.AnnotationName.CompareTo(m2.AnnotationName)); UpdateDataSource(); this.Text = title + " - " + Path.GetFileName(subdir); }
public SampleItemParser(string mappingFile) { this.maps = new TextFileDefinition(); maps.ReadFromFile(mappingFile); }
public SampleItemParser(TextFileDefinition maps) { this.maps = maps; }
public void NewFromData(string subdir) { try { var siformat = Directory.GetFiles(subdir, "*.siformat"); TextFileDefinition prefile = new TextFileDefinition(); if (siformat.Length > 0) { prefile.ReadFromFile(siformat[0]); } var map = new RawSampleInfoReader().ReadDescriptionFromDirectory(subdir); LastDirectory = subdir; lastFile = String.Empty; var files = new HashSet<string>(from f in CelFile.GetCelFiles(subdir, false) select GeoUtils.GetGsmName(f)); Dictionary<string, HashSet<string>> headers = new Dictionary<string, HashSet<string>>(); foreach (var m in map) { var gsm = m.Key.ToUpper(); if (!files.Contains(gsm)) { continue; } var curmap = m.Value; foreach (var entry in curmap) { if (!headers.ContainsKey(entry.Key)) { headers[entry.Key] = new HashSet<string>(); } headers[entry.Key].UnionWith(entry.Value); } } ClearDataSource(); items.Clear(); foreach (var part in headers) { items.Add(new FileDefinitionItem() { AnnotationName = part.Key, Example = (from v in part.Value orderby v select v).Merge(";") }); } foreach (var olditem in prefile) { if (!string.IsNullOrEmpty(olditem.PropertyName)) { var newitem = items.Find(m => m.AnnotationName.Equals(olditem.AnnotationName)); if (newitem != null) { newitem.PropertyName = olditem.PropertyName; } } } items.DefaultValues.Clear(); items.Sort((m1, m2) => m1.AnnotationName.CompareTo(m2.AnnotationName)); UpdateDataSource(); label1.Text = "Annotation/property mapping - " + Path.GetFileName(subdir); dlgOpenDirectory.SelectedPath = subdir; dlgSaveFormatFile.FileName = Path.Combine(subdir, Path.GetFileName(subdir) + ".siformat"); } catch (Exception ex) { MessageBox.Show(this, ex.Message, "Error", MessageBoxButtons.OK, MessageBoxIcon.Error); } }
public SrmTransitionDefinitionForm() { InitializeComponent(); items = new TextFileDefinition(); headers = new List <FileDefinitionItem>(); headers.Add(new FileDefinitionItem() { PropertyName = "ObjectName", ValueType = "string", Required = false }); headers.Add(new FileDefinitionItem() { PropertyName = "PrecursorFormula", ValueType = "string", Required = true }); headers.Add(new FileDefinitionItem() { PropertyName = "PrecursorMZ", ValueType = "double", Format = "{0:0.0000}", Required = true }); headers.Add(new FileDefinitionItem() { PropertyName = "PrecursorCharge", ValueType = "integer", Required = false }); headers.Add(new FileDefinitionItem() { PropertyName = "ProductIon", ValueType = "double", Format = "{0:0.0000}", Required = true }); headers.Add(new FileDefinitionItem() { PropertyName = "ExpectCenterRetentionTime", ValueType = "double", Format = "{0:0.00}", Required = false }); headers.Add(new FileDefinitionItem() { PropertyName = "IsHeavy", ValueType = "boolean", Required = false }); headers.Add(new FileDefinitionItem() { PropertyName = "IsLight", ValueType = "boolean", Required = false }); headers.Add(new FileDefinitionItem() { PropertyName = "IonType", ValueType = "string", Required = false }); headers.Add(new FileDefinitionItem() { PropertyName = "IonIndex", ValueType = "integer", Required = false }); propertyNames = (from h in headers select h.PropertyName).ToList(); propertyNames.Insert(0, string.Empty); colPropertyName.Items.AddRange(propertyNames.ToArray()); }