public void PhylogeneticTreeP1ParserValidateAllProperties()
{
// Gets the expected sequence from the Xml
string filePath = _utilityObj.xmlUtil.GetTextValue(Constants.OneNodePhyloTreeNodeName,
Constants.FilePathNode);
Assert.IsTrue(File.Exists(filePath));
// Logs information to the log file
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Parser P1: File Exists in the Path '{0}'.", filePath));
using (NewickParser parser = new NewickParser())
{
parser.Parse(filePath);
string name = parser.Name;
string fileTypes = parser.FileTypes;
string description = parser.Description;
Assert.AreEqual(Constants.ParserName, name);
Assert.AreEqual(Constants.ParserFileTypes, fileTypes);
Assert.AreEqual(Constants.ParserDescription, description);
}
ApplicationLog.WriteLine(
"Phylogenetic Tree Parser P1: Validated all properties in Parser class.");
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Phylogenetic Tree Parser P1: Validated all properties in Parser class.");
}
public void TestNamesOnInternalNodes()
{
string filename = @"TestUtils\\positives.newick".TestDir();
var parser = new NewickParser();
var tree = parser.Parse(filename);
Assert.AreEqual(3, tree.Root.Children.Count);
}
public static void LoadTree(int treeIndex)
{
if (treeIndex >= 0 && treeIndex < TreeFiles.Length)
{
CurrentTreeFileName = TreeFiles[treeIndex].name;
CurrentTreeIndex = treeIndex;
Node.clearMaxDepth();
CurrentTree = NewickParser.Parse(NEWICK_RELATIVE_DIRECTORY_PATH + "/" + TreeFiles[treeIndex].name);
if (CurrentTree != null)
{
DBQueries.ExtractMetaInformation(CurrentTree, CurrentTreeFileName + ".db");
}
}
}
/// <summary>
/// General method to invalidate Newick Parser.
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Newick Parse method parameters</param>
/// </summary>
void PhylogeneticTreeParserGeneralTests(
string nodeName,
AdditionalParameters method)
{
try
{
string filePath = _utilityObj.xmlUtil.GetTextValue(
nodeName,
Constants.FilePathNode);
switch (method)
{
case AdditionalParameters.TextReader:
using (StreamReader reader = File.OpenText(filePath))
{
using (NewickParser nwParserObj = new NewickParser())
{
nwParserObj.Parse(reader);
}
}
break;
case AdditionalParameters.StringBuilder:
using (StreamReader reader = File.OpenText(filePath))
{
StringBuilder strBuilderObj =
new StringBuilder(reader.ReadToEnd());
using (NewickParser nwParserObj = new NewickParser())
{
nwParserObj.Parse(strBuilderObj);
}
}
break;
default:
break;
}
Assert.Fail();
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"GFF Parser P2 : All the features validated successfully.");
Console.WriteLine(
"GFF Parser P2 : All the features validated successfully.");
}
}
public void PhylogeneticTreeP2ParserInvalidateParseBuilder()
{
try
{
using (NewickParser nwParserObj = new NewickParser())
{
nwParserObj.Parse(null as StringBuilder);
}
Assert.Fail();
}
catch (ArgumentNullException)
{
ApplicationLog.WriteLine(
"GFF Parser P2 : All the features validated successfully.");
}
}
public void PhylogeneticTreeP1ParserValidateAllProperties()
{
NewickParser parser = new NewickParser();
{
string name = parser.Name;
string fileTypes = parser.SupportedFileTypes;
string description = parser.Description;
Assert.AreEqual(Constants.ParserName, name);
Assert.AreEqual(Constants.ParserFileTypes, fileTypes);
Assert.AreEqual(Constants.ParserDescription, description.Replace("\r\n", "\n"));
}
ApplicationLog.WriteLine(
"Phylogenetic Tree Parser P1: Validated all properties in Parser class.");
}
public void NewickFileTest()
{
// parse
Perf.Start("Parsing...");
string filepath = @"TestData\PhylogeneticTree\tree.txt";
NewickParser parser = new NewickParser();
Tree phylogeneticTree = parser.Parse(filepath);
Perf.End();
string outpath = @"TestData\PhylogeneticTree\out.txt";
Perf.Start("Formatting...");
NewickFormatter formatter = new NewickFormatter();
formatter.Format(phylogeneticTree, outpath);
Perf.End();
Assert.AreEqual(true, FileCompare(filepath, outpath));
}
public void NewickStringTest()
{
StringBuilder input = new StringBuilder("(A:0.1,B:0.2,(C:0.3,D:0.4):0.5);");
// parse
Perf.Start("Parsing...");
using (NewickParser parser = new NewickParser())
{
Tree phylogeneticTree = parser.Parse(input);
Perf.End();
Perf.Start("Formatting...");
NewickFormatter formatter = new NewickFormatter();
string output = formatter.FormatString(phylogeneticTree);
Perf.End();
Assert.AreEqual(input.ToString(), output);
}
}
public void PhylogeneticTreeBvtParserValidateNewickExtended()
{
NewickParser parser = new NewickParser();
{
using (var reader = File.OpenRead(@"TestUtils\NewickExtended.nhx".TestDir()))
{
Tree rootTree = parser.Parse(reader);
//Verify metadata at root
Assert.AreEqual("40", rootTree.Root.MetaData["N"]);
//Verify name at root
Assert.AreEqual("Euteleostomi", rootTree.Root.Name);
//now verify it also worked for a somewhat arbitrary internal node
var internalNode = rootTree.Root.Children.Keys.First().Children.Keys.First();
Assert.AreEqual("Tetrapoda", internalNode.Name);
Assert.AreEqual("0.00044378", internalNode.MetaData["PVAL"]);
Assert.AreEqual(8, internalNode.MetaData.Count);
}
}
}
/// <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;
using (NewickParser parser = new NewickParser())
{
Tree rootTree = null;
switch (formatParam)
{
case FormatterParameters.Object:
rootTree = GetFormattedObject(false);
break;
case FormatterParameters.ObjectSingleNode:
rootTree = GetFormattedObject(true);
break;
case FormatterParameters.ParseTextReader:
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 Formatter P1: File Exists in the Path '{0}'.",
filePath));
using (StreamReader reader = File.OpenText(filePath))
{
rootTree = parser.Parse(reader);
}
break;
case FormatterParameters.ParseStringBuilder:
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 Formatter P1: File Exists in the Path '{0}'.",
filePath));
using (StreamReader reader = File.OpenText(filePath))
{
StringBuilder strBuilderObj =
new StringBuilder(reader.ReadToEnd());
rootTree = parser.Parse(strBuilderObj);
}
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 Formatter P1: 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.TextWriter:
using (TextWriter writer = new StreamWriter(outputFilepath))
{
format.Format(rootTree, writer);
}
break;
case FormatterParameters.FormatString:
// Validate format String
string formatString = format.FormatString(rootTree);
string expectedFormatString = _utilityObj.xmlUtil.GetTextValue(nodeName,
Constants.FormatStringNode);
Assert.AreEqual(expectedFormatString, formatString);
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: Format string '{0}' is as expected.",
formatString));
Console.WriteLine(string.Format((IFormatProvider)null,
"Phylogenetic Tree Formatter P1: 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.
using (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 Formatter P1: 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 Formatter P1: 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 P1: The Node Names and Distance are as expected.");
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Phylogenetic Tree Parser P1: The Node Names and Distance are as expected.");
}
if (File.Exists(outputFilepath))
{
File.Delete(outputFilepath);
}
}
}
}
/// <summary>
/// Phylogenetic Tree Parsers General Tests
/// </summary>
/// <param name="nodeName">Xml node Name.</param>
/// <param name="addParam">Additional parameter</param>
void PhylogeneticTreeParserGeneralTests(string nodeName,
AdditionalParameters addParam)
{
// Gets the expected sequence from the Xml
string 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 P1: File Exists in the Path '{0}'.", filePath));
using (NewickParser parser = new NewickParser())
{
Tree rootTree = null;
switch (addParam)
{
case AdditionalParameters.TextReader:
using (StreamReader reader = File.OpenText(filePath))
{
rootTree = parser.Parse(reader);
}
break;
case AdditionalParameters.StringBuilder:
using (StreamReader reader = File.OpenText(filePath))
{
StringBuilder strBuilderObj = new StringBuilder(
reader.ReadToEnd());
rootTree = parser.Parse(strBuilderObj);
}
break;
default:
rootTree = parser.Parse(filePath);
break;
}
Node rootNode = rootTree.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 P1: 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 P1: The Node Names and Distance are as expected.");
// Logs to the NUnit GUI (Console.Out) window
Console.WriteLine(
"Phylogenetic Tree Parser P1: The Node Names and Distance are as expected.");
}
