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 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 PropertyMappingParser(TextFileDefinition maps)
{
InitializeByDefinition(maps);
}
public SampleItemParser(TextFileDefinition maps)
{
this.maps = maps;
}
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());
}
public SampleItemParser(string mappingFile)
{
this.maps = new TextFileDefinition();
maps.ReadFromFile(mappingFile);
}
