public void NexusParserValidateCharBlock()
{
string filePath = utilityObj.xmlUtil.GetTextValue(
Constants.SimpleNexusCharBlockNode,
Constants.FilePathNode).TestDir();
NexusParser parser = new NexusParser();
IEnumerable <ISequenceAlignment> alignment = parser.Parse(filePath);
Assert.AreEqual(1, alignment.Count());
}
public static ir.File ParseFile(ICharStream input)
{
var lexer = new NexusLexer(input, Console.Out, Console.Error);
var tokenStream = new CommonTokenStream(lexer);
var parser = new NexusParser(tokenStream);
var ast = parser.file();
var visitor = new NexusGrammarVisitor();
var ir = (ir.File)visitor.Visit(ast);
return(ir);
}
public void NexusParserValidateCharBlock()
{
string filePath = Utility._xmlUtil.GetTextValue(
Constants.SimpleNexusCharBlockNode,
Constants.FilePathNode);
NexusParser parser = new NexusParser();
IList <ISequenceAlignment> alignment =
parser.Parse(filePath, true);
Assert.AreEqual(1, alignment.Count);
}
public void ValidateNexusParserProperties()
{
NexusParser parser = new NexusParser();
Assert.AreEqual(
utilityObj.xmlUtil.GetTextValue(Constants.NexusPropertyNode,
Constants.NexusDescriptionNode),
parser.Description);
Assert.AreEqual(
utilityObj.xmlUtil.GetTextValue(Constants.NexusPropertyNode,
Constants.NexusNameNode),
parser.Name);
Assert.AreEqual(null, parser.Alphabet);
}
/// <summary>
/// General method to invalidate Nexus parser
/// </summary>
/// <param name="nodeName">xml node name.</param>
/// <param name="method">Nexus Parse method parameters</param>
void InvalidateNexusParserTestCases(
string nodeName,
AdditionalParameters method)
{
try
{
string filePath = _utilityObj._xmlUtil.GetTextValue(
nodeName,
Constants.FilePathNode);
NexusParser parser = new NexusParser();
switch (method)
{
case AdditionalParameters.Parse:
parser.Parse(filePath, true);
break;
case AdditionalParameters.ParseOne:
parser.ParseOne(filePath, true);
break;
default:
break;
}
Assert.Fail();
}
catch (InvalidDataException)
{
ApplicationLog.WriteLine(
"Nexus Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Nexus Parser P2 : All the features validated successfully.");
}
catch (FormatException)
{
ApplicationLog.WriteLine(
"Nexus Parser P2 : All the features validated successfully.");
Console.WriteLine(
"Nexus Parser P2 : All the features validated successfully.");
}
}
public void ValidateNexusParserProperties()
{
NexusParser parser = new NexusParser(Encodings.Ncbi4NA);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.NexusPropertyNode,
Constants.NexusDescriptionNode),
parser.Description);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.NexusPropertyNode,
Constants.NexusNameNode),
parser.Name);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.NexusPropertyNode,
Constants.NexusFileTypesNode),
parser.FileTypes);
Assert.AreEqual(null, parser.Alphabet);
Assert.AreEqual(
Utility._xmlUtil.GetTextValue(Constants.NexusPropertyNode,
Constants.NexusEncodingNode),
parser.Encoding.ToString());
}
/// <summary>
/// Parsers the Nexus 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, AdditionalParameters addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(nodeName, Constants.FilePathNode).TestDir();
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine($"Nexus Parser BVT: Reading the File from location '{filePath}'");
// Get the rangelist after parsing.
NexusParser parserObj = new NexusParser();
IEnumerable <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case AdditionalParameters.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
sequenceAlignment = sequenceAlignmentList.First();
break;
case AdditionalParameters.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case AdditionalParameters.ParseTextReader:
using (var strRdrObj = File.OpenRead(filePath))
{
sequenceAlignmentList = parserObj.Parse(strRdrObj);
sequenceAlignment = sequenceAlignmentList.First();
}
break;
case AdditionalParameters.ParseOneTextReader:
using (var strRdrObj = File.OpenRead(filePath))
{
sequenceAlignment = parserObj.ParseOne(strRdrObj);
}
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
sequenceAlignmentList = new List <ISequenceAlignment> {
sequenceAlignment
};
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList.ToList(), expectedAlignmentList));
ApplicationLog.WriteLine("Nexus Parser BVT: Successfully validated all the Alignment Sequences");
}
public void NexusParse()
{
string filepath = @"TestUtils\Nexus\primate-mtDNA-interleaved.nex";
Assert.IsTrue(File.Exists(filepath));
IList <Dictionary <string, string> > expectedOutput = new List <Dictionary <string, string> >();
Dictionary <string, string> expectedAlignment = new Dictionary <string, string>();
expectedAlignment["Lemur_catta"] = "AAGCTTCATAGGAGCAACCATTCTAATAATCGCACATGGCCTTACATCATCCATATTATT"
+ "CTGTCTAGCCAACTCTAACTACGAACGAATCCATAGCCGTACAATACTACTAGCACGAGG"
+ "GATCCAAACCATTCTCCCTCTTATAGCCACCTGATGACTACTCGCCAGCCTAACTAACCT"
+ "AGCCCTACCCACCTCTATCAATTTAATTGGCGAACTATTCGTCACTATAGCATCCTTCTC"
+ "ATGATCAAACATTACAATTATCTTAATAGGCTTAAATATGCTCATCACCGCTCTCTATTC"
+ "CCTCTATATATTAACTACTACACAACGAGGAAAACTCACATATCATTCGCACAACCTAAA"
+ "CCCATCCTTTACACGAGAAAACACCCTTATATCCATACACATACTCCCCCTTCTCCTATT"
+ "TACCTTAAACCCCAAAATTATTCTAGGACCCACGTACTGTAAATATAGTTTAAA-AAAAC"
+ "ACTAGATTGTGAATCCAGAAATAGAAGCTCAAAC-CTTCTTATTTACCGAGAAAGTAATG"
+ "TATGAACTGCTAACTCTGCACTCCGTATATAAAAATACGGCTATCTCAACTTTTAAAGGA"
+ "TAGAAGTAATCCATTGGCCTTAGGAGCCAAAAA-ATTGGTGCAACTCCAAATAAAAGTAA"
+ "TAAATCTATTATCCTCTTTCACCCTTGTCACACTGATTATCCTAACTTTACCTATCATTA"
+ "TAAACGTTACAAACATATACAAAAACTACCCCTATGCACCATACGTAAAATCTTCTATTG"
+ "CATGTGCCTTCATCACTAGCCTCATCCCAACTATATTATTTATCTCCTCAGGACAAGAAA"
+ "CAATCATTTCCAACTGACATTGAATAACAATCCAAACCCTAAAACTATCTATTAGCTT";
expectedAlignment["Homo_sapiens"] = "AAGCTTCACCGGCGCAGTCATTCTCATAATCGCCCACGGGCTTACATCCTCATTACTATT"
+ "CTGCCTAGCAAACTCAAACTACGAACGCACTCACAGTCGCATCATAATCCTCTCTCAAGG"
+ "ACTTCAAACTCTACTCCCACTAATAGCTTTTTGATGACTTCTAGCAAGCCTCGCTAACCT"
+ "CGCCTTACCCCCCACTATTAACCTACTGGGAGAACTCTCTGTGCTAGTAACCACGTTCTC"
+ "CTGATCAAATATCACTCTCCTACTTACAGGACTCAACATACTAGTCACAGCCCTATACTC"
+ "CCTCTACATATTTACCACAACACAATGGGGCTCACTCACCCACCACATTAACAACATAAA"
+ "ACCCTCATTCACACGAGAAAACACCCTCATGTTCATACACCTATCCCCCATTCTCCTCCT"
+ "ATCCCTCAACCCCGACATCATTACCGGGTTTTCCTCTTGTAAATATAGTTTAACCAAAAC"
+ "ATCAGATTGTGAATCTGACAACAGAGGCTTA-CGACCCCTTATTTACCGAGAAAGCT-CA"
+ "CAAGAACTGCTAACTCATGCCCCCATGTCTAACAACATGGCTTTCTCAACTTTTAAAGGA"
+ "TAACAGCTATCCATTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA"
+ "TAACCATGCACACTACTATAACCACCCTAACCCTGACTTCCCTAATTCCCCCCATCCTTA"
+ "CCACCCTCGTTAACCCTAACAAAAAAAACTCATACCCCCATTATGTAAAATCCATTGTCG"
+ "CATCCACCTTTATTATCAGTCTCTTCCCCACAACAATATTCATGTGCCTAGACCAAGAAG"
+ "TTATTATCTCGAACTGACACTGAGCCACAACCCAAACAACCCAGCTCTCCCTAAGCTT";
expectedAlignment["Pan"] = "AAGCTTCACCGGCGCAATTATCCTCATAATCGCCCACGGACTTACATCCTCATTATTATT"
+ "CTGCCTAGCAAACTCAAATTATGAACGCACCCACAGTCGCATCATAATTCTCTCCCAAGG"
+ "ACTTCAAACTCTACTCCCACTAATAGCCTTTTGATGACTCCTAGCAAGCCTCGCTAACCT"
+ "CGCCCTACCCCCTACCATTAATCTCCTAGGGGAACTCTCCGTGCTAGTAACCTCATTCTC"
+ "CTGATCAAATACCACTCTCCTACTCACAGGATTCAACATACTAATCACAGCCCTGTACTC"
+ "CCTCTACATGTTTACCACAACACAATGAGGCTCACTCACCCACCACATTAATAACATAAA"
+ "GCCCTCATTCACACGAGAAAATACTCTCATATTTTTACACCTATCCCCCATCCTCCTTCT"
+ "ATCCCTCAATCCTGATATCATCACTGGATTCACCTCCTGTAAATATAGTTTAACCAAAAC"
+ "ATCAGATTGTGAATCTGACAACAGAGGCTCA-CGACCCCTTATTTACCGAGAAAGCT-TA"
+ "TAAGAACTGCTAATTCATATCCCCATGCCTGACAACATGGCTTTCTCAACTTTTAAAGGA"
+ "TAACAGCCATCCGTTGGTCTTAGGCCCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA"
+ "TAACCATGTATACTACCATAACCACCTTAACCCTAACTCCCTTAATTCTCCCCATCCTCA"
+ "CCACCCTCATTAACCCTAACAAAAAAAACTCATATCCCCATTATGTGAAATCCATTATCG"
+ "CGTCCACCTTTATCATTAGCCTTTTCCCCACAACAATATTCATATGCCTAGACCAAGAAG"
+ "CTATTATCTCAAACTGGCACTGAGCAACAACCCAAACAACCCAGCTCTCCCTAAGCTT";
expectedAlignment["Gorilla"] = "AAGCTTCACCGGCGCAGTTGTTCTTATAATTGCCCACGGACTTACATCATCATTATTATT"
+ "CTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATTCTCTCTCAAGG"
+ "ACTCCAAACCCTACTCCCACTAATAGCCCTTTGATGACTTCTGGCAAGCCTCGCCAACCT"
+ "CGCCTTACCCCCCACCATTAACCTACTAGGAGAGCTCTCCGTACTAGTAACCACATTCTC"
+ "CTGATCAAACACCACCCTTTTACTTACAGGATCTAACATACTAATTACAGCCCTGTACTC"
+ "CCTTTATATATTTACCACAACACAATGAGGCCCACTCACACACCACATCACCAACATAAA"
+ "ACCCTCATTTACACGAGAAAACATCCTCATATTCATGCACCTATCCCCCATCCTCCTCCT"
+ "ATCCCTCAACCCCGATATTATCACCGGGTTCACCTCCTGTAAATATAGTTTAACCAAAAC"
+ "ATCAGATTGTGAATCTGATAACAGAGGCTCA-CAACCCCTTATTTACCGAGAAAGCT-CG"
+ "TAAGAGCTGCTAACTCATACCCCCGTGCTTGACAACATGGCTTTCTCAACTTTTAAAGGA"
+ "TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA"
+ "TAACTATGTACGCTACCATAACCACCTTAGCCCTAACTTCCTTAATTCCCCCTATCCTTA"
+ "CCACCTTCATCAATCCTAACAAAAAAAGCTCATACCCCCATTACGTAAAATCTATCGTCG"
+ "CATCCACCTTTATCATCAGCCTCTTCCCCACAACAATATTTCTATGCCTAGACCAAGAAG"
+ "CTATTATCTCAAGCTGACACTGAGCAACAACCCAAACAATTCAACTCTCCCTAAGCTT";
expectedAlignment["Orangutan"] = "AAGCTTCACCGGCGCAACCACCCTCATGATTGCCCATGGACTCACATCCTCCCTACTGTT"
+ "CTGCCTAGCAAACTCAAACTACGAACGAACCCACAGCCGCATCATAATCCTCTCTCAAGG"
+ "CCTTCAAACTCTACTCCCCCTAATAGCCCTCTGATGACTTCTAGCAAGCCTCACTAACCT"
+ "TGCCCTACCACCCACCATCAACCTTCTAGGAGAACTCTCCGTACTAATAGCCATATTCTC"
+ "TTGATCTAACATCACCATCCTACTAACAGGACTCAACATACTAATCACAACCCTATACTC"
+ "TCTCTATATATTCACCACAACACAACGAGGTACACCCACACACCACATCAACAACATAAA"
+ "ACCTTCTTTCACACGCGAAAATACCCTCATGCTCATACACCTATCCCCCATCCTCCTCTT"
+ "ATCCCTCAACCCCAGCATCATCGCTGGGTTCGCCTACTGTAAATATAGTTTAACCAAAAC"
+ "ATTAGATTGTGAATCTAATAATAGGGCCCCA-CAACCCCTTATTTACCGAGAAAGCT-CA"
+ "CAAGAACTGCTAACTCTCACT-CCATGTGTGACAACATGGCTTTCTCAGCTTTTAAAGGA"
+ "TAACAGCTATCCCTTGGTCTTAGGATCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA"
+ "CAGCCATGTTTACCACCATAACTGCCCTCACCTTAACTTCCCTAATCCCCCCCATTACCG"
+ "CTACCCTCATTAACCCCAACAAAAAAAACCCATACCCCCACTATGTAAAAACGGCCATCG"
+ "CATCCGCCTTTACTATCAGCCTTATCCCAACAACAATATTTATCTGCCTAGGACAAGAAA"
+ "CCATCGTCACAAACTGATGCTGAACAACCACCCAGACACTACAACTCTCACTAAGCTT";
expectedAlignment["Hylobates"] = "AAGCTTTACAGGTGCAACCGTCCTCATAATCGCCCACGGACTAACCTCTTCCCTGCTATT"
+ "CTGCCTTGCAAACTCAAACTACGAACGAACTCACAGCCGCATCATAATCCTATCTCGAGG"
+ "GCTCCAAGCCTTACTCCCACTGATAGCCTTCTGATGACTCGCAGCAAGCCTCGCTAACCT"
+ "CGCCCTACCCCCCACTATTAACCTCCTAGGTGAACTCTTCGTACTAATGGCCTCCTTCTC"
+ "CTGGGCAAACACTACTATTACACTCACCGGGCTCAACGTACTAATCACGGCCCTATACTC"
+ "CCTTTACATATTTATCATAACACAACGAGGCACACTTACACACCACATTAAAAACATAAA"
+ "ACCCTCACTCACACGAGAAAACATATTAATACTTATGCACCTCTTCCCCCTCCTCCTCCT"
+ "AACCCTCAACCCTAACATCATTACTGGCTTTACTCCCTGTAAACATAGTTTAATCAAAAC"
+ "ATTAGATTGTGAATCTAACAATAGAGGCTCG-AAACCTCTTGCTTACCGAGAAAGCC-CA"
+ "CAAGAACTGCTAACTCACTATCCCATGTATGACAACATGGCTTTCTCAACTTTTAAAGGA"
+ "TAACAGCTATCCATTGGTCTTAGGACCCAAAAATTTTGGTGCAACTCCAAATAAAAGTAA"
+ "TAGCAATGTACACCACCATAGCCATTCTAACGCTAACCTCCCTAATTCCCCCCATTACAG"
+ "CCACCCTTATTAACCCCAATAAAAAGAACTTATACCCGCACTACGTAAAAATGACCATTG"
+ "CCTCTACCTTTATAATCAGCCTATTTCCCACAATAATATTCATGTGCACAGACCAAGAAA"
+ "CCATTATTTCAAACTGACACTGAACTGCAACCCAAACGCTAGAACTCTCCCTAAGCTT";
expectedAlignment["Macaca_fuscata"] = "AAGCTTTTCCGGCGCAACCATCCTTATGATCGCTCACGGACTCACCTCTTCCATATATTT"
+ "CTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGAGG"
+ "ACTTCAAATCCTACTTCCACTAACAGCCTTTTGATGATTAACAGCAAGCCTTACTAACCT"
+ "TGCCCTACCCCCCACTATCAATCTACTAGGTGAACTCTTTGTAATCGCAACCTCATTCTC"
+ "CTGATCCCATATCACCATTATGCTAACAGGACTTAACATATTAATTACGGCCCTCTACTC"
+ "TCTCCACATATTCACTACAACACAACGAGGAACACTCACACATCACATAATCAACATAAA"
+ "GCCCCCCTTCACACGAGAAAACACATTAATATTCATACACCTCGCTCCAATTATCCTTCT"
+ "ATCCCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAGATATAGTTTAACTAAAAC"
+ "ACTAGATTGTGAATCTAACCATAGAGACTCA-CCACCTCTTATTTACCGAGAAAACT-CG"
+ "CAAGGACTGCTAACCCATGTACCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA"
+ "TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAA"
+ "TAATCATGCACACCCCCATCATTATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTG"
+ "CCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAA"
+ "TATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAA"
+ "CAACCATTTGGAGCTGACATTGAATAATGACCCAAACACTAGACCTAACGCTAAGCTT";
expectedAlignment["M._mulatta"] = "AAGCTTTTCTGGCGCAACCATCCTCATGATTGCTCACGGACTCACCTCTTCCATATATTT"
+ "CTGCCTAGCCAATTCAAACTATGAACGCACTCACAACCGTACCATACTACTGTCCCGGGG"
+ "ACTTCAAATCCTACTTCCACTAACAGCTTTCTGATGATTAACAGCAAGCCTTACTAACCT"
+ "TGCCCTACCCCCCACTATCAACCTACTAGGTGAACTCTTTGTAATCGCGACCTCATTCTC"
+ "CTGGTCCCATATCACCATTATATTAACAGGATTTAACATACTAATTACGGCCCTCTACTC"
+ "CCTCCACATATTCACCACAACACAACGAGGAGCACTCACACATCACATAATCAACATAAA"
+ "ACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATCATCCTCCT"
+ "ATCTCTCAACCCCAACATCATCCTGGGGTTTACTTCCTGTAGATATAGTTTAACTAAAAC"
+ "ATTAGATTGTGAATCTAACCATAGAGACTTA-CCACCTCTTATTTACCGAGAAAACT-CG"
+ "CGAGGACTGCTAACCCATGTATCCGTACCTAAAATTACGGTTTTCTCAACTTTTAAAGGA"
+ "TAACAGCTATCCATTGACCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAA"
+ "TAATCATGCACACCCCTATCATAATAACAACCCTTATCTCCCTAACTCTCCCAATTTTTG"
+ "CCACCCTCATCAACCCTTACAAAAAACGTCCATACCCAGATTACGTAAAAACAACCGTAA"
+ "TATATGCTTTCATCATCAGCCTCCCCTCAACAACTTTATTCATCTTCTCAAACCAAGAAA"
+ "CAACCATTTGAAGCTGACATTGAATAATAACCCAAACACTAGACCTAACACTAAGCTT";
expectedAlignment["M._fascicularis"] = "AAGCTTCTCCGGCGCAACCACCCTTATAATCGCCCACGGGCTCACCTCTTCCATGTATTT"
+ "CTGCTTGGCCAATTCAAACTATGAGCGCACTCATAACCGTACCATACTACTATCCCGAGG"
+ "ACTTCAAATTCTACTTCCATTGACAGCCTTCTGATGACTCACAGCAAGCCTTACTAACCT"
+ "TGCCCTACCCCCCACTATTAATCTACTAGGCGAACTCTTTGTAATCACAACTTCATTTTC"
+ "CTGATCCCATATCACCATTGTGTTAACGGGCCTTAATATACTAATCACAGCCCTCTACTC"
+ "TCTCCACATGTTCATTACAGTACAACGAGGAACACTCACACACCACATAATCAATATAAA"
+ "ACCCCCCTTCACACGAGAAAACATATTAATATTCATACACCTCGCTCCAATTATCCTTCT"
+ "ATCTCTCAACCCCAACATCATCCTGGGGTTTACCTCCTGTAAATATAGTTTAACTAAAAC"
+ "ATTAGATTGTGAATCTAACTATAGAGGCCTA-CCACTTCTTATTTACCGAGAAAACT-CG"
+ "CAAGGACTGCTAATCCATGCCTCCGTACTTAAAACTACGGTTTCCTCAACTTTTAAAGGA"
+ "TAACAGCTATCCATTGACCTTAGGAGTCAAAAACATTGGTGCAACTCCAAATAAAAGTAA"
+ "TAATCATGCACACCCCCATCATAATAACAACCCTCATCTCCCTGACCCTTCCAATTTTTG"
+ "CCACCCTCACCAACCCCTATAAAAAACGTTCATACCCAGACTACGTAAAAACAACCGTAA"
+ "TATATGCTTTTATTACCAGTCTCCCCTCAACAACCCTATTCATCCTCTCAAACCAAGAAA"
+ "CAACCATTTGGAGTTGACATTGAATAACAACCCAAACATTAGACCTAACACTAAGCTT";
expectedAlignment["M._sylvanus"] = "AAGCTTCTCCGGTGCAACTATCCTTATAGTTGCCCATGGACTCACCTCTTCCATATACTT"
+ "CTGCTTGGCCAACTCAAACTACGAACGCACCCACAGCCGCATCATACTACTATCCCGAGG"
+ "ACTCCAAATCCTACTCCCACTAACAGCCTTCTGATGATTCACAGCAAGCCTTACTAATCT"
+ "TGCTCTACCCTCCACTATTAATCTACTGGGCGAACTCTTCGTAATCGCAACCTCATTTTC"
+ "CTGATCCCACATCACCATCATACTAACAGGACTGAACATACTAATTACAGCCCTCTACTC"
+ "TCTTCACATATTCACCACAACACAACGAGGAGCGCTCACACACCACATAATTAACATAAA"
+ "ACCACCTTTCACACGAGAAAACATATTAATACTCATACACCTCGCTCCAATTATTCTTCT"
+ "ATCTCTTAACCCCAACATCATTCTAGGATTTACTTCCTGTAAATATAGTTTAATTAAAAC"
+ "ATTAGACTGTGAATCTAACTATAGAAGCTTA-CCACTTCTTATTTACCGAGAAAACT-TG"
+ "CAAGGACCGCTAATCCACACCTCCGTACTTAAAACTACGGTTTTCTCAACTTTTAAAGGA"
+ "TAACAGCTATCCATTGGCCTTAGGAGTCAAAAATATTGGTGCAACTCCAAATAAAAGTAA"
+ "TAATCATGTATACCCCCATCATAATAACAACTCTCATCTCCCTAACTCTTCCAATTTTCG"
+ "CTACCCTTATCAACCCCAACAAAAAACACCTATATCCAAACTACGTAAAAACAGCCGTAA"
+ "TATATGCTTTCATTACCAGCCTCTCTTCAACAACTTTATATATATTCTTAAACCAAGAAA"
+ "CAATCATCTGAAGCTGGCACTGAATAATAACCCAAACACTAAGCCTAACATTAAGCTT";
expectedAlignment["Saimiri_sciureus"] = "AAGCTTCACCGGCGCAATGATCCTAATAATCGCTCACGGGTTTACTTCGTCTATGCTATT"
+ "CTGCCTAGCAAACTCAAATTACGAACGAATTCACAGCCGAACAATAACATTTACTCGAGG"
+ "GCTCCAAACACTATTCCCGCTTATAGGCCTCTGATGACTCCTAGCAAATCTCGCTAACCT"
+ "CGCCCTACCCACAGCTATTAATCTAGTAGGAGAATTACTCACAATCGTATCTTCCTTCTC"
+ "TTGATCCAACTTTACTATTATATTCACAGGACTTAATATACTAATTACAGCACTCTACTC"
+ "ACTTCATATGTATGCCTCTACACAGCGAGGTCCACTTACATACAGCACCAGCAATATAAA"
+ "ACCAATATTTACACGAGAAAATACGCTAATATTTATACATATAACACCAATCCTCCTCCT"
+ "TACCTTGAGCCCCAAGGTAATTATAGGACCCTCACCTTGTAATTATAGTTTAGCTAAAAC"
+ "ATTAGATTGTGAATCTAATAATAGAAGAATA-TAACTTCTTAATTACCGAGAAAGTG-CG"
+ "CAAGAACTGCTAATTCATGCTCCCAAGACTAACAACTTGGCTTCCTCAACTTTTAAAGGA"
+ "TAGTAGTTATCCATTGGTCTTAGGAGCCAAAAACATTGGTGCAACTCCAAATAAAAGTAA"
+ "TA---ATACACTTCTCCATCACTCTAATAACACTAATTAGCCTACTAGCGCCAATCCTAG"
+ "CTACCCTCATTAACCCTAACAAAAGCACACTATACCCGTACTACGTAAAACTAGCCATCA"
+ "TCTACGCCCTCATTACCAGTACCTTATCTATAATATTCTTTATCCTTACAGGCCAAGAAT"
+ "CAATAATTTCAAACTGACACTGAATAACTATCCAAACCATCAAACTATCCCTAAGCTT";
expectedAlignment["Tarsius_syrichta"] = "AAGTTTCATTGGAGCCACCACTCTTATAATTGCCCATGGCCTCACCTCCTCCCTATTATT"
+ "TTGCCTAGCAAATACAAACTACGAACGAGTCCACAGTCGAACAATAGCACTAGCCCGTGG"
+ "CCTTCAAACCCTATTACCTCTTGCAGCAACATGATGACTCCTCGCCAGCTTAACCAACCT"
+ "GGCCCTTCCCCCAACAATTAATTTAATCGGTGAACTGTCCGTAATAATAGCAGCATTTTC"
+ "ATGGTCACACCTAACTATTATCTTAGTAGGCCTTAACACCCTTATCACCGCCCTATATTC"
+ "CCTATATATACTAATCATAACTCAACGAGGAAAATACACATATCATATCAACAATATCAT"
+ "GCCCCCTTTCACCCGAGAAAATACATTAATAATCATACACCTATTTCCCTTAATCCTACT"
+ "ATCTACCAACCCCAAAGTAATTATAGGAACCATGTACTGTAAATATAGTTTAAACAAAAC"
+ "ATTAGATTGTGAGTCTAATAATAGAAGCCCAAAGATTTCTTATTTACCAAGAAAGTA-TG"
+ "CAAGAACTGCTAACTCATGCCTCCATATATAACAATGTGGCTTTCTT-ACTTTTAAAGGA"
+ "TAGAAGTAATCCATCGGTCTTAGGAACCGAAAA-ATTGGTGCAACTCCAAATAAAAGTAA"
+ "TAAATTTATTTTCATCCTCCATTTTACTATCACTTACACTCTTAATTACCCCATTTATTA"
+ "TTACAACAACTAAAAAATATGAAACACATGCATACCCTTACTACGTAAAAAACTCTATCG"
+ "CCTGCGCATTTATAACAAGCCTAGTCCCAATGCTCATATTTCTATACACAAATCAAGAAA"
+ "TAATCATTTCCAACTGACATTGAATAACGATTCATACTATCAAATTATGCCTAAGCTT";
expectedOutput.Add(expectedAlignment);
IList <ISequenceAlignment> actualOutput = null;
ISequenceAlignmentParser parser = new NexusParser();
using (StreamReader reader = File.OpenText(filepath))
{
actualOutput = parser.Parse(reader);
}
CompareOutput(actualOutput, expectedOutput);
}
/// <summary>
/// Parsers the Nexus 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,
AdditionalParameters addParam)
{
// Gets the Filename
string filePath = Utility._xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
Assert.IsNotEmpty(filePath);
ApplicationLog.WriteLine(string.Format(
"Nexus Parser BVT: Reading the File from location '{0}'", filePath));
Console.WriteLine(string.Format(
"Nexus Parser BVT: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
NexusParser parserObj = new NexusParser();
IList <ISequenceAlignment> sequenceAlignmentList = null;
ISequenceAlignment sequenceAlignment = null;
// Gets the SequenceAlignment list based on the parameters.
switch (addParam)
{
case AdditionalParameters.Parse:
sequenceAlignmentList = parserObj.Parse(filePath);
break;
case AdditionalParameters.ParseOne:
sequenceAlignment = parserObj.ParseOne(filePath);
break;
case AdditionalParameters.ParseTextReader:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath));
break;
case AdditionalParameters.ParseOneTextReader:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath));
break;
case AdditionalParameters.ParseOneTextReaderReadOnly:
sequenceAlignment = parserObj.ParseOne(
new StreamReader(filePath), false);
break;
case AdditionalParameters.ParseTextReaderReadOnly:
sequenceAlignmentList = parserObj.Parse(
new StreamReader(filePath), false);
break;
case AdditionalParameters.ParseReadOnly:
sequenceAlignmentList = parserObj.Parse(filePath,
false);
break;
case AdditionalParameters.ParseOneReadOnly:
sequenceAlignment = parserObj.ParseOne(filePath,
false);
break;
case AdditionalParameters.ParseEncoding:
NexusParser parser = new NexusParser(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 AdditionalParameters.ParseOne:
case AdditionalParameters.ParseOneTextReader:
case AdditionalParameters.ParseOneTextReaderReadOnly:
case AdditionalParameters.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(
"Nexus Parser BVT: Successfully validated all the Alignment Sequences");
Console.WriteLine(
"Nexus Parser BVT: Successfully validated all the Alignment Sequences");
}
