/// <summary>
/// General method to invalidate Phylip parser
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Phylip Parser method parameters</param>
void InvalidatePhylipParserTestCases(
string nodeName,
ParserTestAttributes method)
{
try
{
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName,
Constants.FilePathNode);
PhylipParser parser = new PhylipParser();
switch (method)
{
case ParserTestAttributes.Parse:
parser.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
parser.ParseOne(filePath);
break;
default:
break;
}
Assert.Fail();
}
catch (InvalidDataException)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Phylip Parser P2 : All the features validated successfully.");
}
}
/// <summary>
/// Parsers the Phylip file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
static void ParserGeneralTestCases(string nodeName,
ParserTestAttributes addParam)
{
// Gets the Filename
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
Assert.IsNotEmpty(filePath);
ApplicationLog.WriteLine(string.Format(
"Phylip Parser BVT: Reading the File from location '{0}'", filePath));
Console.WriteLine(string.Format(
"Phylip Parser BVT: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
PhylipParser parserObj = new PhylipParser();
IList <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case ParserTestAttributes.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case ParserTestAttributes.ParseTextReader:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath));
break;
case ParserTestAttributes.ParseOneTextReader:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath));
break;
case ParserTestAttributes.ParseOneTextReaderReadOnly:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath), false);
break;
case ParserTestAttributes.ParseTextReaderReadOnly:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath), false);
break;
case ParserTestAttributes.ParseReadOnly:
sequenceAlignmentList = parserObj.Parse(filePath,
false);
break;
case ParserTestAttributes.ParseOneReadOnly:
sequenceAlignment = parserObj.ParseOne(filePath,
false);
break;
case ParserTestAttributes.ParseEncoding:
PhylipParser parser =
new PhylipParser(Encodings.Ncbi4NA);
sequenceAlignmentList = parser.Parse(
new StreamReader(filePath), false);
break;
default:
break;
}
// Gets all the expected values from xml.
IList <Dictionary <string, string> > expectedAlignmentList =
new List <Dictionary <string, string> >();
Dictionary <string, string> expectedAlignmentObj =
new Dictionary <string, string>();
XmlNode expectedAlignmentNodes = Utility._xmlUtil.GetNode(
nodeName, Constants.ExpectedAlignmentNode);
XmlNodeList alignNodes = expectedAlignmentNodes.ChildNodes;
// Create a ISequenceAlignment List
switch (addParam)
{
case ParserTestAttributes.ParseOne:
case ParserTestAttributes.ParseOneTextReader:
case ParserTestAttributes.ParseOneTextReaderReadOnly:
case ParserTestAttributes.ParseOneReadOnly:
sequenceAlignmentList = new List <ISequenceAlignment>();
sequenceAlignmentList.Add(sequenceAlignment);
break;
default:
break;
}
foreach (XmlNode expectedAlignment in alignNodes)
{
expectedAlignmentObj[expectedAlignment.Name] =
expectedAlignment.InnerText;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList,
expectedAlignmentList));
ApplicationLog.WriteLine(
"Phylip Parser BVT: Successfully validated all the Alignment Sequences");
Console.WriteLine(
"Phylip Parser BVT: Successfully validated all the Alignment Sequences");
}
public void PhylipParseOne()
{
string filepath = @"TestUtils\Phylip\dna.phy";
Assert.IsTrue(File.Exists(filepath));
IList <Dictionary <string, string> > expectedOutput = new List <Dictionary <string, string> >();
Dictionary <string, string> expectedAlignment = new Dictionary <string, string>();
expectedAlignment["Cow"] = "ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA"
+ "CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC"
+ "ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA"
+ "GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT"
+ "TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA"
+ "GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC"
+ "TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT"
+ "CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA"
+ "CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC"
+ "CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC"
+ "GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA"
+ "AAATGATCTGCGTCAATATTA---------------------TAA";
expectedAlignment["Carp"] = "ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT"
+ "CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT"
+ "ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA"
+ "ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC"
+ "CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA"
+ "GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC"
+ "TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC"
+ "CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA"
+ "CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT"
+ "CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT"
+ "GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA"
+ "AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA";
expectedAlignment["Chicken"] = "ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC"
+ "GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC"
+ "CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA"
+ "GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC"
+ "CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC"
+ "GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC"
+ "TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT"
+ "CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC"
+ "CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT"
+ "CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC"
+ "GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA"
+ "GCCTGATCCTCACTA------------------CTGTCATCTTAA";
expectedAlignment["Human"] = "ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT"
+ "ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT"
+ "GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA"
+ "ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC"
+ "CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT"
+ "GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC"
+ "TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT"
+ "CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG"
+ "CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC"
+ "CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT"
+ "GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA"
+ "ATA---------------------GGGCCCGTATTTACCCTATAG";
expectedAlignment["Loach"] = "ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT"
+ "CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT"
+ "GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA"
+ "ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA"
+ "CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG"
+ "GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC"
+ "TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC"
+ "CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA"
+ "CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC"
+ "CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT"
+ "GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA"
+ "AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA";
expectedAlignment["Mouse"] = "ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA"
+ "ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT"
+ "ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA"
+ "GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT"
+ "CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA"
+ "GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA"
+ "TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC"
+ "CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC"
+ "CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT"
+ "CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT"
+ "GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA"
+ "AACTGATCTGCTTCAATAATT---------------------TAA";
expectedAlignment["Rat"] = "ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT"
+ "ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT"
+ "ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA"
+ "GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC"
+ "CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA"
+ "GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC"
+ "TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT"
+ "CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG"
+ "CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC"
+ "CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC"
+ "GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA"
+ "AACTGATCAGCTTCTATAATT---------------------TAA";
expectedAlignment["Seal"] = "ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA"
+ "CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC"
+ "ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA"
+ "GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA"
+ "TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA"
+ "GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA"
+ "TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT"
+ "CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC"
+ "CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC"
+ "CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT"
+ "GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG"
+ "AAATGATCTACCTCAATGCTT---------------------TAA";
expectedAlignment["Whale"] = "ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC"
+ "CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC"
+ "ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA"
+ "GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA"
+ "TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA"
+ "GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC"
+ "TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC"
+ "CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC"
+ "CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC"
+ "CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC"
+ "GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA"
+ "AAATGATCTGTATCAATACTA---------------------TAA";
expectedAlignment["Frog"] = "ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA"
+ "CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC"
+ "ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG"
+ "ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC"
+ "CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC"
+ "GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT"
+ "TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT"
+ "CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC"
+ "CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT"
+ "CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC"
+ "GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA"
+ "AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA";
expectedOutput.Add(expectedAlignment);
List <ISequenceAlignment> actualOutput = new List <ISequenceAlignment>();
ISequenceAlignment actualAlignment = null;
ISequenceAlignmentParser parser = new PhylipParser();
using (StreamReader reader = File.OpenText(filepath))
{
actualAlignment = parser.ParseOne(reader);
}
actualOutput.Add(actualAlignment);
CompareOutput(actualOutput, expectedOutput);
}
/// <summary>
/// Parsers the Phylip file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
void ParserGeneralTestCases(string nodeName, ParserTestAttributes addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine($"Phylip Parser BVT: Reading the File from location '{filePath}'");
// Get the range list after parsing.
PhylipParser parserObj = new PhylipParser();
IEnumerable <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case ParserTestAttributes.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case ParserTestAttributes.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case ParserTestAttributes.ParseTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignmentList = parserObj.Parse(rdrObj).ToList();
}
break;
case ParserTestAttributes.ParseOneTextReader:
using (var rdrObj = File.OpenRead(filePath))
{
sequenceAlignment = parserObj.ParseOne(rdrObj);
}
break;
default:
break;
}
// Gets all the expected values from xml.
var expectedAlignmentList = new List <Dictionary <string, string> >();
var expectedAlignmentObj = new Dictionary <string, string>();
XElement expectedAlignmentNodes = utilityObj.xmlUtil.GetNode(nodeName, Constants.ExpectedAlignmentNode);
IList <XNode> nodes = expectedAlignmentNodes.Nodes().ToList();
//Get all the values from the elements in the node.
foreach (XElement node in nodes)
{
expectedAlignmentObj[node.Name.ToString()] = node.Value;
}
// Create a ISequenceAlignment List
switch (addParam)
{
case ParserTestAttributes.ParseOne:
case ParserTestAttributes.ParseOneTextReader:
sequenceAlignmentList = new List <ISequenceAlignment> {
sequenceAlignment
};
break;
default:
break;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList.ToList(), expectedAlignmentList));
ApplicationLog.WriteLine("Phylip Parser BVT: Successfully validated all the Alignment Sequences");
}