// Test wiggle fixed step
private static WiggleAnnotation TestParserFixedStep(string filename)
{
WiggleParser p = new WiggleParser();
WiggleAnnotation an = p.Parse(filename).First();
Assert.IsTrue(an.Chromosome == "chr19");
Assert.IsTrue(an.BasePosition == 59307401);
Assert.IsTrue(an.Step == 300);
Assert.IsTrue(an.Span == 200);
Assert.IsTrue(an.Metadata["type"] == "wiggle_0");
Assert.IsTrue(an.Metadata["name"] == "ArrayExpt1");
Assert.IsTrue(an.Metadata["description"] == "20 degrees, 2 hr");
float[] values = an.GetValueArray(0, 3);
Assert.IsTrue(values[0] == 1000);
Assert.IsTrue(values[1] == 900);
Assert.IsTrue(values[2] == 800);
values = an.GetValueArray(7, 3);
Assert.IsTrue(values[0] == 300);
Assert.IsTrue(values[1] == 200);
Assert.IsTrue(values[2] == 100);
return(an);
}
// Test wiggle variable step
private static WiggleAnnotation TestParserVariableStep(string filename)
{
WiggleParser p = new WiggleParser();
WiggleAnnotation an = p.Parse(filename).First();
Assert.IsTrue(an.Chromosome == "chr19");
Assert.IsTrue(an.Step == 0);
Assert.IsTrue(an.BasePosition == 0);
Assert.IsTrue(an.Span == 150);
Assert.IsTrue(an.Metadata["type"] == "wiggle_0");
Assert.IsTrue(an.Metadata["name"] == "ArrayExpt1");
Assert.IsTrue(an.Metadata["description"] == "20 degrees, 2 hr");
var x = an.GetEnumerator();
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59304701); Assert.IsTrue(x.Current.Value == 10.0);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59304901); Assert.IsTrue(x.Current.Value == 12.5);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 59305401); Assert.IsTrue(x.Current.Value == 15.0);
x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext(); x.MoveNext();
Assert.IsTrue(x.Current.Key == 59307871); Assert.IsTrue(x.Current.Value == 10.0);
return(an);
}
/// <summary>
/// Writes a single sequence to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="annotation">Wiggle Annotation</param>
public static void Format(this WiggleFormatter formatter, WiggleAnnotation annotation)
{
var fs = ParserFormatterExtensions<WiggleFormatter>.GetOpenStream(formatter, true);
if (fs != null)
formatter.Format(fs, annotation);
else
throw new Exception("You must open a formatter before calling Write.");
}
/// <summary>
/// Verifies an annotation object against a pre-defined set of values.
/// </summary>
/// <param name="an"></param>
private static void VerifyDummyAnnotation(WiggleAnnotation an)
{
Assert.IsTrue(an.Chromosome == "chromeee");
Assert.IsTrue(an.Span == 100);
try
{
an.GetValueArray(0, 3);
Assert.Fail();
}
catch(NotSupportedException)
{ }
var x = an.GetEnumerator();
x.MoveNext();
Assert.IsTrue(x.Current.Key == 100); Assert.IsTrue(x.Current.Value == 10);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 200); Assert.IsTrue(x.Current.Value == 20);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 300); Assert.IsTrue(x.Current.Value == 30);
}
/// <summary>
/// Verifies an annotation object against a pre-defined set of values.
/// </summary>
/// <param name="an"></param>
private static void VerifyDummyAnnotation(WiggleAnnotation an)
{
Assert.IsTrue(an.Chromosome == "chromeee");
Assert.IsTrue(an.Span == 100);
try
{
an.GetValueArray(0, 3);
Assert.Fail();
}
catch (NotSupportedException)
{ }
var x = an.GetEnumerator();
x.MoveNext();
Assert.IsTrue(x.Current.Key == 100); Assert.IsTrue(x.Current.Value == 10);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 200); Assert.IsTrue(x.Current.Value == 20);
x.MoveNext();
Assert.IsTrue(x.Current.Key == 300); Assert.IsTrue(x.Current.Value == 30);
}
public void TestAnnotationObject()
{
WiggleAnnotation an = CreateDummyAnnotation();
VerifyDummyAnnotation(an);
}
/// <summary>
/// Writes a single sequence to the formatter.
/// </summary>
/// <param name="formatter">Formatter</param>
/// <param name="annotation">Wiggle Annotation</param>
/// <param name="filename">Filename</param>
public static void Format(this WiggleFormatter formatter, WiggleAnnotation annotation, string filename)
{
using (var fs = File.Create(filename))
formatter.Format(fs,annotation);
}
/// <summary>
/// Validate Exceptions from Wiggle Parser and Formatter for General test cases.
/// </summary>
/// <param name="exceptionType"></param>
public void ValidateArgumentNullException(ExceptionType exceptionType)
{
// Gets the filepath.
String filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
WiggleAnnotation annotation =null;
try
{
switch (exceptionType)
{
case ExceptionType.NullFormatter:
WiggleFormatter formatter = new WiggleFormatter();
formatter.Format(null, annotation);
break;
case ExceptionType.NullParser:
WiggleParser parser = new WiggleParser();
string valueForParse = null;
parser.ParseOne(valueForParse);
break;
case ExceptionType.NullAnnotationWithData:
annotation = new WiggleAnnotation(null, Constants.StringByteArray);
break;
case ExceptionType.NullAnnotationWithChromosomeName:
float[] data = new float[2] { 1.0F, 2.0F };
annotation = new WiggleAnnotation(data, null,0,0);
break;
}
}
catch (ArgumentNullException exception)
{
ApplicationLog.WriteLine(
"Wiggle P2 test cases : Successfully validated the exception:", exception.Message);
}
}
public void ValidateGetValueArray()
{
string[] expectedValues = this.utilityObj.xmlUtil.GetTextValue(Constants.
AnnotationValuesNode, Constants.ExpectedValuesNode).Split(',');
string stepValue = this.utilityObj.xmlUtil.GetTextValue(Constants.
AnnotationValuesNode, Constants.ExpectedStepNode);
string startValue = this.utilityObj.xmlUtil.GetTextValue(Constants.
AnnotationValuesNode, Constants.ExpectedStartNode);
int index = 0;
float[] data = new float[expectedValues.Length];
for (index = 0; index < expectedValues.Length; index++)
{
data[index] = float.Parse(expectedValues[index], CultureInfo.InvariantCulture);
}
WiggleAnnotation annotation = new WiggleAnnotation(data, Constants.
ChromosomeNode, long.Parse(startValue, CultureInfo.InvariantCulture), int.Parse(stepValue, CultureInfo.InvariantCulture));
//Get the values.
float[] dataNew = annotation.GetValueArray(0, expectedValues.Length);
index = 0;
//Validate the values from GetValueArray.
foreach (float value in dataNew)
{
Assert.AreEqual(data[index], value);
index++;
}
}
public void ValidateWiggleAnnotation()
{
string[] expectedValues = this.utilityObj.xmlUtil.GetTextValue(Constants.
AnnotationValuesNode, Constants.ExpectedValuesNode).Split(',');
string[] annotationKeys = this.utilityObj.xmlUtil.GetTextValue(Constants.
AnnotationValuesNode, Constants.ExpectedKeysNode).Split(',');
string stepValue = this.utilityObj.xmlUtil.GetTextValue(Constants.
AnnotationValuesNode, Constants.ExpectedStepNode);
string startValue = this.utilityObj.xmlUtil.GetTextValue(Constants.
AnnotationValuesNode, Constants.ExpectedStartNode);
int index = 0;
float[] data = new float[expectedValues.Length];
for (index = 0; index < expectedValues.Length; index++)
{
data[index] = float.Parse(expectedValues[index], CultureInfo.InvariantCulture);
}
WiggleAnnotation annotation = new WiggleAnnotation(data, Constants.
ChromosomeNode, long.Parse(startValue, CultureInfo.InvariantCulture),
int.Parse(stepValue, CultureInfo.InvariantCulture));
index = 0;
//Validate keys and values of the parsed file.
foreach (KeyValuePair<long, float> keyvaluePair in annotation)
{
Assert.AreEqual(float.Parse(annotationKeys[index],
CultureInfo.InvariantCulture), keyvaluePair.Key);
Assert.AreEqual(long.Parse(expectedValues[index],
CultureInfo.InvariantCulture), keyvaluePair.Value);
index++;
}
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Annotation BVT: Validation of Annotation creation is successfull"));
}
