// 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);
}
// 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);
}
public void ValidateWiggleParserPublicProperties()
{
// Gets the filepath from the Xml
string filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: File Exists in the Path '{0}'.", filePath));
//Get the expected values from configuration file.
string expectedDescription = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.ParserDescriptionNode);
string expectedName = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.NameNode);
string expectedFileType = this.utilityObj.xmlUtil.GetTextValue(Constants.
SimpleWiggleWithFixedStepNodeName, Constants.FileTypesNode);
WiggleParser parser = new WiggleParser();
//Parse the file
var annotation = parser.Parse(filePath);
Assert.IsNotNull(annotation);
Assert.AreEqual(expectedDescription, parser.Description);
Assert.AreEqual(expectedName, parser.Name);
Assert.AreEqual(expectedFileType, parser.SupportedFileTypes);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Wiggle Parser BVT: Validation of all public properties is successful"));
}
public void TestWiggleFormatter()
{
string filepathTmp = Path.GetTempFileName();
using (WiggleFormatter formatter = new WiggleFormatter(filepathTmp))
{
formatter.Write(CreateDummyAnnotation());
}
WiggleParser parser = new WiggleParser();
VerifyDummyAnnotation(parser.Parse(filepathTmp));
}
public void TestWiggleFormatter()
{
string filepathTmp = Path.GetTempFileName();
WiggleFormatter formatter = new WiggleFormatter();
using (formatter.Open(filepathTmp))
{
formatter.Format(CreateDummyAnnotation());
}
WiggleParser parser = new WiggleParser();
VerifyDummyAnnotation(parser.Parse(filepathTmp).First());
}
// 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;
}
// 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;
}
/// <summary>
/// Validate Exceptions from Wiggle Parser with invalid metadata.
/// </summary>
/// <param name="nodeName">Node containing the invalid file name.</param>
public void ValidateFormatException(string nodeName)
{
// Gets the filepath.
String filePath = this.utilityObj.xmlUtil.GetTextValue(Constants.
InValidFileNamesNode, nodeName);
Assert.IsTrue(File.Exists(filePath));
WiggleParser parser=new WiggleParser();
try
{
parser.Parse(filePath);
}
catch (FormatException exception)
{
ApplicationLog.WriteLine(
"Wiggle P2 test cases : Successfully validated Format exception:", exception.Message);
}
}
