public void WriteToFile(string proteinFile, IIdentifiedResult mr)
{
if (this.proteinConverter == null)
{
this.proteinConverter =
IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(
"Locus\tSequence Count\tSpectrum Count\tSequence Coverage\tLength\tMolWt\tpI\tValidation Status\tDescriptive Name",
'\t', "Dtaselect");
this.peptideConverter =
IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(
"Unique\tFileName\tScore\tDeltCN\tM+H+\tCalcM+H+\tTotalIntensity\tSpRank\tSpScore\tIonProportion\tRedundancy\tSequence",
'\t', "Dtaselect");
}
using (var sw = new StreamWriter(proteinFile))
{
sw.WriteLine("DTASelect v1.9");
sw.WriteLine();
sw.WriteLine("true Use criteria");
sw.WriteLine();
sw.WriteLine(this.proteinConverter.Name);
sw.WriteLine(this.peptideConverter.Name);
foreach (IdentifiedProteinGroup mpg in mr)
{
for (int proteinIndex = 0; proteinIndex < mpg.Count; proteinIndex++)
{
IIdentifiedProtein mpro = mpg[proteinIndex];
sw.WriteLine(this.proteinConverter.GetProperty(mpro));
}
mpg.GetSortedPeptides().ForEach(m => sw.WriteLine(this.peptideConverter.GetProperty(m)));
}
}
}
/// <summary>
/// If supported, convert the provided value into a <see cref="IPropertyToken"/>.
/// </summary>
/// <param name="converter">Converter for conversion of additional values.</param>
/// <param name="value">The value to convert.</param>
/// <param name="result">Value converted to <see cref="IPropertyToken"/> if conversion was successful.</param>
/// <returns><c>true</c> if the value could be converted under this policy; <c>false</c> otherwise.</returns>
public bool TryConvert(IPropertyConverter converter, object value, out IPropertyToken result)
{
result = null;
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
var enumerable = value as IEnumerable;
if (enumerable == null)
{
return(false);
}
if (value.GetType().IsDictionary())
{
return(false);
}
var elements = enumerable.Cast <object>();
if (_config.ItemLimit > 0)
{
elements = elements.Take(_config.ItemLimit);
}
result = new SequenceToken(elements.Select(converter.Convert));
return(true);
}
public void TestNoredundant()
{
string header = " Reference PepCount UniquePepCount CoverPercent MW PI IdentifiedName";
IPropertyConverter <IIdentifiedProtein> converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(header, '\t');
Assert.AreEqual(header, converter.Name);
string line = "\tIPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088 Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial 84 19 43.46% 61054.43 5.70 IPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088 Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial";
IIdentifiedProtein protein = new IdentifiedProtein();
converter.SetProperty(protein, line);
Assert.AreEqual("IPI:IPI00784154.1|SWISS-PROT:P10809|TREMBL:B2R5M6;Q53QD5;Q53SE2;Q96RI4;Q9UCR6|ENSEMBL:ENSP00000340019;ENSP00000373620|REFSEQ:NP_002147;NP_955472|H-INV:HIT000031088", protein.Name);
Assert.AreEqual("Tax_Id=9606 Gene_Symbol=HSPD1 60 kDa heat shock protein, mitochondrial", protein.Description);
Assert.AreEqual(19, protein.UniquePeptideCount);
Assert.AreEqual(43.46, protein.Coverage);
Assert.AreEqual(61054.43, protein.MolecularWeight);
Assert.AreEqual(5.7, protein.IsoelectricPoint);
for (int i = 0; i < 84; i++)
{
protein.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum()));
}
Assert.AreEqual(line, converter.GetProperty(protein));
}
public void TestDtaselect()
{
string header = "Locus Sequence Count Spectrum Count Sequence Coverage Length MolWt pI Validation Status Descriptive Name";
IPropertyConverter <IIdentifiedProtein> converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(header, '\t');
Assert.AreEqual(header, converter.Name);
string line = "YDR050C 495 495 81.10% 249 26795.41 5.74 U YDR050C TPI1 SGDID:S000002457, Chr IV from 556470-555724, reverse complement, Verified ORF, \"Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5' non-coding region\"";
IIdentifiedProtein protein = new IdentifiedProtein();
converter.SetProperty(protein, line);
Assert.AreEqual("YDR050C", protein.Name);
Assert.AreEqual("TPI1 SGDID:S000002457, Chr IV from 556470-555724, reverse complement, Verified ORF, \"Triose phosphate isomerase, abundant glycolytic enzyme; mRNA half-life is regulated by iron availability; transcription is controlled by activators Reb1p, Gcr1p, and Rap1p through binding sites in the 5' non-coding region\"", protein.Description);
Assert.AreEqual(495, protein.UniquePeptideCount);
Assert.AreEqual(81.1, protein.Coverage);
Assert.AreEqual(26795.41, protein.MolecularWeight);
Assert.AreEqual(5.74, protein.IsoelectricPoint);
for (int i = 0; i < 495; i++)
{
protein.Peptides.Add(new IdentifiedPeptide(new IdentifiedSpectrum()));
}
Assert.AreEqual(line, converter.GetProperty(protein));
}
private XElement ToXml(object obj, PropertyInfo pInfo)
{
if (pInfo == null)
{
return(null);
}
object[] atts = pInfo.GetCustomAttributes(typeof(XmlPersistAttribute), false);
if (atts == null || atts.Length == 0)
{
return(ValueTypePropertyToXml(obj, pInfo));
}
XmlPersistAttribute xlmPersistAtt = atts[0] as XmlPersistAttribute;
IPropertyConverter convter = null;
try
{
convter = Activator.CreateInstance(xlmPersistAtt.PropertyConverter) as IPropertyConverter;
object propertyValue = obj.GetType().InvokeMember(pInfo.Name, BindingFlags.GetProperty, null, obj, null);
if (propertyValue != null)
{
return(convter.ToXml(pInfo.Name, propertyValue));
}
return(null);
}
catch (Exception ex)
{
Console.WriteLine(ex.Message);
return(null);
}
}
public PropertyAliasConverter(IPropertyConverter <T> source, string aliasName)
{
this.source = source;
this.aliasName = aliasName;
InitializeAliasName(aliasName);
}
/// <summary>
/// Initializes a new instance of the <see cref="EntityProperty"/> class.
/// </summary>
/// <param name="propertyContext">The property info that object is associated with.</param>
/// <param name="item">The data item.</param>
/// <param name="converter">The converter. Optionally you can convert your source property to a different format depending on the UI and scenario.</param>
public EntityProperty(object propertyContext, object item, IPropertyConverter converter)
{
this.PropertyContext = propertyContext;
this.Errors = new ObservableCollection <object>();
this.DataItem = item;
this.PropertyConverter = converter;
}
private IEnumerable <PropertyToken> GetProperties(object value, IPropertyConverter converter)
{
foreach (var property in value.GetType().GetDerivedProperties())
{
object propertyValue;
try
{
propertyValue = property.GetValue(value);
}
catch (TargetParameterCountException)
{
// These properties will be ignored since they never produce values they're not
// of concern to auditing and exceptions can be suppressed.
_logger.Warning(
$"The property accessor '{property.DeclaringType.FullName}.{property.Name}' is a non-default indexer");
continue;
}
catch (TargetInvocationException ex)
{
_logger.Error(ex,
$"The property accessor '{property.DeclaringType.FullName}.{property.Name}' threw an {ex.InnerException.GetType().Name}");
propertyValue = $"The property accessor threw an exception: {ex.InnerException.GetType().Name}";
}
yield return(new PropertyToken(property.Name, converter.Convert(propertyValue)));
}
}
/// <summary>
/// If supported, convert the provided value into a <see cref="IPropertyToken"/>.
/// </summary>
/// <param name="converter">Converter for conversion of additional values.</param>
/// <param name="value">The value to convert.</param>
/// <param name="result">Value converted to <see cref="IPropertyToken"/> if conversion was successful.</param>
/// <returns><c>true</c> if the value could be converted under this policy; <c>false</c> otherwise.</returns>
public bool TryConvert(IPropertyConverter converter, object value, out IPropertyToken result)
{
result = null;
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
var bytes = value as byte[];
if (bytes == null)
{
return(false);
}
//Enforce limit on size of array
if (_config.ByteArrayLimit > 0 && bytes.Length > _config.ByteArrayLimit)
{
string hexValue = string.Concat(bytes.Take(16).Select(b => b.ToString("X2")));
string description = $"0x: {hexValue}... ({bytes.Length} bytes)";
result = new ScalarToken(description);
return(true);
}
result = new ScalarToken(bytes.ToArray());
return(true);
}
private static DynamoDBEntry ToDynamoDBEntry(Type type, object value, IPropertyConverter converter, bool canReturnPrimitiveInsteadOfList)
{
if (value == null)
{
return(null);
}
if (converter != null)
{
return(converter.ToEntry(value));
}
Primitive primitive;
if (TryToPrimitive(type, value, out primitive))
{
return(primitive);
}
DynamoDBEntry primitiveList;
if (TryToPrimitiveList(type, value, canReturnPrimitiveInsteadOfList, out primitiveList))
{
return(primitiveList);
}
throw new InvalidOperationException("Unable to convert value of type " + value.GetType().FullName + ", type is not primitive or primitive collection and does not define a converter");
}
public void TestDtaselect()
{
string header = "Unique FileName Score DeltCN M+H+ CalcM+H+ TotalIntensity SpRank SpScore IonProportion Redundancy Sequence";
IPropertyConverter <IIdentifiedSpectrum> converter = IdentifiedSpectrumPropertyConverterFactory.GetInstance().GetConverters(header, '\t');
Assert.AreEqual(header, converter.Name);
}
/// <summary>
/// Adds a type converter
/// </summary>
/// <param name="converter"></param>
/// <typeparam name="TProperty"></typeparam>
/// <returns></returns>
public IConnectionStringUtility <T> AddTypeConverter <TProperty>(IPropertyConverter converter)
where TProperty : struct
{
_converters.Add(converter);
return(this);
}
public void RegisterConverter(IPropertyConverter <T> item, params string[] aliasNames)
{
itemMap.Add(item);
foreach (var name in aliasNames)
{
itemMap.Add(new PropertyAliasConverter <T>(item, name));
}
}
public PropertyViewModel(IGenericProperty <TProperty> property, IEqualityComparer <TProperty> equalityComparer, IPropertyConverter <TProperty> converter)
{
_property = property;
_equalityComparer = equalityComparer;
_converter = converter;
_objectProperty = _property.Value;
Validate();
}
public ConditionPropertyDescriptor(string name, IPropertyConverter <T1, T2> converter)
{
this.converter = converter;
field = AccessTools.Field(typeof(Condition), name);
if (!typeof(T1).IsAssignableFrom(field.FieldType))
{
throw new ArgumentException("Bad T1!");
}
}
public bool IsMessagePropertyConverter <T>(out IPropertyConverter <TProperty, T> propertyConverter)
{
if (_converter is ITypeConverter <TProperty, T> converter)
{
propertyConverter = new ConvertPropertyConverter <TProperty, T>(converter);
return(true);
}
propertyConverter = null;
return(false);
}
public bool TryGetConverter(out IPropertyConverter <TMessage, TMessage> converter)
{
if (Count > 0)
{
converter = new TransformPropertyConverter <TMessage>(Build());
return(true);
}
converter = default;
return(false);
}
/// <summary>
/// If supported, convert the provided value into a <see cref="IPropertyToken"/>.
/// </summary>
/// <param name="converter">Converter for conversion of additional values.</param>
/// <param name="value">The value to convert.</param>
/// <param name="result">Value converted to <see cref="IPropertyToken"/> if conversion was successful.</param>
/// <returns><c>true</c> if the value could be converted under this policy; <c>false</c> otherwise.</returns>
public bool TryConvert(IPropertyConverter converter, object value, out IPropertyToken result)
{
result = null;
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
var enumerable = value as IEnumerable;
if (enumerable == null)
{
return(false);
}
// Only dictionaries with 'scalar' keys are permitted, as
// more complex keys may not serialize to unique values for
// representation in targets. This check strengthens the expectation
// that resulting dictionary is representable in JSON as well
// as richer formats (e.g. XML, .NET type-aware...).
// Only actual dictionaries are supported, as arbitrary types
// can implement multiple IDictionary interfaces and thus introduce
// multiple different interpretations.
var type = value.GetType();
if (!type.IsDictionary())
{
return(false);
}
var typeInfo = typeof(KeyValuePair <,>).MakeGenericType(type.GenericTypeArguments).GetTypeInfo();
var keyProperty = typeInfo.GetDeclaredProperty("Key");
var valueProperty = typeInfo.GetDeclaredProperty("Value");
var items = enumerable.Cast <object>();
if (_config.ItemLimit > 0)
{
items = items.Take(_config.ItemLimit);
}
var elements = items
.Select(kvp =>
new KeyValuePair <ScalarToken, IPropertyToken>(
(ScalarToken)converter.Convert(keyProperty.GetValue(kvp)),
converter.Convert(valueProperty.GetValue(kvp))
)
)
.Where(kvp => kvp.Key.Value != null);
result = new DictionaryToken(elements);
return(true);
}
private XElement ToXml(object obj, PropertyInfo pInfo)
{
if (pInfo == null)
{
return(null);
}
object[] atts = pInfo.GetCustomAttributes(typeof(GeoDo.Core.XmlPersistAttribute), true);
if (atts == null || atts.Length == 0)
{
return(ValueTypePropertyToXml(obj, pInfo));
}
GeoDo.Core.XmlPersistAttribute xmlPersistAtt = atts[0] as GeoDo.Core.XmlPersistAttribute;
if (!xmlPersistAtt.IsNeedPersisted)
{
return(null);
}
IPropertyConverter convter = null;
try
{
object propertyValue = obj.GetType().InvokeMember(pInfo.Name, BindingFlags.GetProperty, null, obj, null);
if (propertyValue != null)
{
if (xmlPersistAtt.PropertyConverter != null)
{
convter = Activator.CreateInstance(xmlPersistAtt.PropertyConverter) as IPropertyConverter;
}
if (pInfo.PropertyType.IsArray)
{
XElement containerXml = new XElement(pInfo.Name);
Array array = propertyValue as Array;
GenerateCollectionItemXElement(pInfo, array as IList, convter, xmlPersistAtt, containerXml);
return(containerXml);
}
else if (PropertyIsList(pInfo))
{
XElement containerXml = new XElement(pInfo.Name);
IList lst = propertyValue as IList;
GenerateCollectionItemXElement(pInfo, lst, convter, xmlPersistAtt, containerXml);
return(containerXml);
}
else
{
return(convter.ToXml(pInfo.Name, propertyValue));
}
}
return(null);
}
catch (Exception ex)
{
Console.WriteLine(ex.Message);
return(null);
}
}
private void ReadComplexProperty(XElement pElement, object obj)
{
string proName = pElement.Name.LocalName;
PropertyInfo pInfo = obj.GetType().GetProperty(proName);
object[] atts = pInfo.GetCustomAttributes(typeof(XmlPersistAttribute), false);
XmlPersistAttribute xmlPersisitAtt = atts[0] as XmlPersistAttribute;
IPropertyConverter convter = Activator.CreateInstance(xmlPersisitAtt.PropertyConverter) as IPropertyConverter;
object value = convter.FromXml(pElement);
obj.GetType().InvokeMember(proName, BindingFlags.SetProperty, null, obj, new object[] { value });
}
public FieldConfiguration(string propertyName, Type type, bool isComplexType = false,
ICollection <FieldConfiguration> fieldConfigurations = null,
IPropertyConverter propertyConverter = null,
AccessStrategy accessStrategy = AccessStrategy.Default)
{
Type = type;
PropertyName = propertyName;
IsComplexType = isComplexType;
FieldConfigurations = fieldConfigurations ?? new List <FieldConfiguration>();
PropertyConverter = propertyConverter;
AccessStrategy = accessStrategy;
}
public IdentifiedProteinTextWriter(string proteinHeader, IEnumerable <IIdentifiedProtein> proteins)
{
this._proteins = proteins;
this._annotationKeys = AnnotationUtils.GetAnnotationKeys(this._proteins);
var sb = new StringBuilder();
sb.Append(proteinHeader);
foreach (string key in this._annotationKeys)
{
sb.Append("\t" + key);
}
this.converter = IdentifiedProteinPropertyConverterFactory.GetInstance().GetConverters(sb.ToString(), '\t');
}
public void Apply(ITransformConfigurator <TInput> configurator)
{
if (_transformConfigurator.TryGetConverter(out var converter))
{
var inputPropertyProvider = new InputPropertyProvider <TInput, TProperty>(_property);
IPropertyConverter <TProperty, TProperty> arrayConverter = typeof(TProperty).IsArray
? new ArrayPropertyConverter <TElement, TElement>(converter) as IPropertyConverter <TProperty, TProperty>
: new ListPropertyConverter <TElement, TElement>(converter) as IPropertyConverter <TProperty, TProperty>;
var provider = new PropertyConverterPropertyProvider <TInput, TProperty, TProperty>(arrayConverter, inputPropertyProvider);
configurator.Transform(_property, provider);
}
}
public PropertyConvertInputValuePropertyProvider(IPropertyConverter <TProperty, TInputProperty> converter, string inputPropertyName)
{
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
if (inputPropertyName == null)
{
throw new ArgumentNullException(nameof(inputPropertyName));
}
_converter = converter;
_inputProperty = ReadPropertyCache <TInput> .GetProperty <TInputProperty>(inputPropertyName);
}
internal object GetConvertBackValue(object value)
{
object result;
IPropertyConverter propertyConverter = this.PropertyConverter;
if (propertyConverter != null)
{
result = propertyConverter.ConvertBack(value);
}
else
{
result = value;
}
return(result);
}
public PropertyConverterPropertyProvider(IPropertyConverter <TProperty, TInputProperty> converter,
IPropertyProvider <TInput, TInputProperty> inputProvider)
{
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
if (inputProvider == null)
{
throw new ArgumentNullException(nameof(inputProvider));
}
_converter = converter;
_inputProvider = inputProvider;
}
/// <summary>
/// If supported, convert the provided value into a <see cref="IPropertyToken"/>.
/// </summary>
/// <param name="converter">Converter for conversion of additional values.</param>
/// <param name="value">The value to convert.</param>
/// <param name="result">Value converted to <see cref="IPropertyToken"/> if conversion was successful.</param>
/// <returns><c>true</c> if the value could be converted under this policy; <c>false</c> otherwise.</returns>
public bool TryConvert(IPropertyConverter converter, object value, out IPropertyToken result)
{
result = null;
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
if (value == null)
{
return(false);
}
var type = value.GetType();
string typeName = type.IsCompilerGenerated() ? null : type.Name;
result = new StructureToken(GetProperties(value, converter), typeName);
return(true);
}
private void GenerateCollectionItemXElement(PropertyInfo pInfo, IList items, IPropertyConverter convter, XmlPersistAttribute persistAtt, XElement containerXml)
{
foreach (object it in items)
{
XElement ele = null;
if (convter != null)
{
ele = convter.ToXml(persistAtt.CollectionItemName, it);
}
else
{
ele = ToXml(it);
}
if (ele != null)
{
containerXml.Add(ele);
}
}
}
public ConvertObjectPropertyInitializer(IPropertyConverter <TProperty, TInputProperty> converter, string messagePropertyName,
string inputPropertyName = null)
{
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
if (messagePropertyName == null)
{
throw new ArgumentNullException(nameof(messagePropertyName));
}
_converter = converter;
_inputProperty = ReadPropertyCache <TInput> .GetProperty <TInputProperty>(inputPropertyName ?? messagePropertyName);
_messageProperty = WritePropertyCache <TMessage> .GetProperty <TProperty>(messagePropertyName);
}
/// <summary>
/// If supported, convert the provided value into a <see cref="IPropertyToken"/>.
/// </summary>
/// <param name="converter">Converter for conversion of additional values.</param>
/// <param name="value">The value to convert.</param>
/// <param name="result">Value converted to <see cref="IPropertyToken"/> if conversion was successful.</param>
/// <returns><c>true</c> if the value could be converted under this policy; <c>false</c> otherwise.</returns>
public bool TryConvert(IPropertyConverter converter, object value, out IPropertyToken result)
{
result = null;
if (converter == null)
{
throw new ArgumentNullException(nameof(converter));
}
var del = value as Delegate;
if (del == null)
{
return(false);
}
result = new ScalarToken(del.GetMethodInfo().ToString());
return(true);
}