/// <summary>
/// Phylogenetic Tree Formatter General Tests
/// </summary>
/// <param name="nodeName">Xml node Name.</param>
/// <param name="formatParam">Additional parameter</param>
void PhylogeneticTreeFormatterGeneralTests(string nodeName,
FormatterParameters formatParam)
{
// Gets the expected sequence from the Xml
string filePath = string.Empty;
NewickParser parser = new NewickParser();
{
Tree rootTree;
switch (formatParam)
{
case FormatterParameters.Object:
rootTree = GetFormattedObject();
break;
default:
filePath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: File Exists in the Path '{0}'.",
filePath));
rootTree = parser.Parse(filePath);
break;
}
string outputFilepath = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.OutputFilePathNode);
NewickFormatter format = new NewickFormatter();
switch (formatParam)
{
case FormatterParameters.Stream:
using (var writer = File.Create(outputFilepath))
{
format.Format(writer, rootTree);
}
break;
case FormatterParameters.FormatString:
// Validate format String
var formatString = format.FormatString(rootTree);
string expectedFormatString =
_utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FormatStringNode);
Assert.AreEqual(expectedFormatString, formatString);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: Format string '{0}' is as expected.",
formatString));
break;
default:
format.Format(rootTree, outputFilepath);
break;
}
// Validate only if not a Format String
if (FormatterParameters.FormatString != formatParam)
{
// Re-parse the created file and validate the tree.
NewickParser newparserObj = new NewickParser();
{
Tree newrootTreeObj = null;
Assert.IsTrue(File.Exists(outputFilepath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: New File Exists in the Path '{0}'.",
outputFilepath));
newrootTreeObj = newparserObj.Parse(outputFilepath);
Node rootNode = newrootTreeObj.Root;
string rootBranchCount = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.RootBranchCountNode);
// Validate the root branch count
Assert.AreEqual(rootBranchCount,
rootNode.Children.Count.ToString((IFormatProvider)null));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser BVT: Number of Root Branches found are '{0}'.",
rootNode.Children.Count.ToString((IFormatProvider)null)));
List<string> leavesName = new List<string>();
List<double> leavesDistance = new List<double>();
// Gets all the leaves in the root node list
GetAllNodesAndEdges(rootNode, ref leavesName, ref leavesDistance);
string[] expectedLeavesName = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.NodeNamesNode).Split(',');
string[] expectedLeavesDistance = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.EdgeDistancesNode).Split(',');
for (int i = 0; i < expectedLeavesName.Length; i++)
{
Assert.AreEqual(expectedLeavesName[i], leavesName[i]);
}
for (int i = 0; i < expectedLeavesDistance.Length; i++)
{
Assert.AreEqual(expectedLeavesDistance[i],
leavesDistance[i].ToString((IFormatProvider)null));
}
}
ApplicationLog.WriteLine(
"Phylogenetic Tree Parser BVT: The Node Names and Distance are as expected.");
}
if (File.Exists(outputFilepath))
File.Delete(outputFilepath);
}
}
public void PhylogeneticTreeP1FormatterValidateAllProperties()
{
NewickFormatter formatter = new NewickFormatter();
string name = formatter.Name;
string fileTypes = formatter.SupportedFileTypes;
string description = formatter.Description;
Assert.AreEqual(Constants.ParserName, name);
Assert.AreEqual(Constants.ParserFileTypes, fileTypes);
Assert.AreEqual(Constants.FormatDescription, description);
ApplicationLog.WriteLine(
"Phylogenetic Tree Formatter P1: Validated all properties in Formatter class.");
}
