public void ClustalWParse()
{
string filepath = @"testdata\ClustalW\AlignmentData.aln";
Assert.IsTrue(File.Exists(filepath));
IList <Dictionary <string, string> > expectedOutput = new List <Dictionary <string, string> >();
Dictionary <string, string> expectedAlignment = new Dictionary <string, string>();
expectedAlignment["CYS1_DICDI"] = "-----MKVILLFVLAVFTVFVSS---------------RGIPPEEQ------------SQ"
+ "FLEFQDKFNKKY-SHEEYLERFEIFKSNLGKIEELNLIAINHKADTKFGVNKFADLSSDE"
+ "FKNYYLNNKEAIFTDDLPVADYLDDEFINSIPTAFDWRTRG-AVTPVKNQGQCGSCWSFS"
+ "TTGNVEGQHFISQNKLVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNG"
+ "GIQTESSYPYTAETGTQCNFNSANIGAKISNFTMIP-KNETVMAGYIVSTGPLAIAADAV"
+ "E-WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNMPYWIVKNSWGADWGEQG"
+ "YIYLRRGKNTCGVSNFVSTSII--";
expectedAlignment["ALEU_HORVU"] = "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALR"
+ "FARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN----RKGLPYRLGINRFSDMSWEE"
+ "FQATRL-GAAQTCSATLAGNHLMRDA--AALPETKDWREDG-IVSPVKNQAHCGSCWTFS"
+ "TTGALEAAYTQATGKNISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNG"
+ "GIDTEESYPYKGVNGV-CHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVI"
+ "DGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGV-----PYWLIKNSWGADWGDNG"
+ "YFKMEMGKNMCAIATCASYPVVAA";
expectedAlignment["CATH_HUMAN"] = "------MWATLPLLCAGAWLLGV--------PVCGAAELSVNSLEK------------FH"
+ "FKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN----NGNHTFKMALNQFSDMSFAE"
+ "IKHKYLWSEPQNCSAT--KSNYLRGT--GPYPPSVDWRKKGNFVSPVKNQGACGSCWTFS"
+ "TTGALESAIAIATGKMLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNK"
+ "GIMGEDTYPYQGKDGY-CKFQPGKAIGFVKDVANITIYDEEAMVEAVALYNPVSFAFEVT"
+ "QDFMMYRTGIYSSTSCHKTPDKVNHAVLAVGYGEKNGI-----PYWIVKNSWGPQWGMNG"
+ "YFLIERGKNMCGLAACASYPIPLV";
expectedOutput.Add(expectedAlignment);
IList <ISequenceAlignment> actualOutput = null;
ISequenceAlignmentParser parser = new ClustalWParser();
using (StreamReader reader = File.OpenText(filepath))
{
actualOutput = parser.Parse(reader);
}
CompareOutput(actualOutput, expectedOutput);
}
/// <summary>
/// Parsers the ClustalW file for different test cases based
/// on Additional parameter
/// </summary>
/// <param name="nodeName">Xml Node name</param>
/// <param name="addParam">Additional parameter</param>
private void ParserGeneralTestCases(string nodeName,
AdditionalParameters addParam)
{
// Gets the Filename
string filePath = utilityObj.xmlUtil.GetTextValue(
nodeName, Constants.FilePathNode);
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine(string.Format(null,
"ClustalW Parser BVT: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
var parserObj = new ClustalWParser();
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:
using (var strRdrObj = new StreamReader(filePath))
{
sequenceAlignmentList = parserObj.Parse(strRdrObj);
}
break;
case AdditionalParameters.ParseOneTextReader:
using (var strRdrObj = new StreamReader(filePath))
{
sequenceAlignment = parserObj.ParseOne(strRdrObj);
}
break;
default:
break;
}
// Gets all the expected values from xml.
IList <Dictionary <string, string> > expectedAlignmentList =
new List <Dictionary <string, string> >();
var expectedAlignmentObj =
new Dictionary <string, string>();
XElement expectedAlignmentNodes = utilityObj.xmlUtil.GetNode(
nodeName, Constants.ExpectedAlignmentNode);
IEnumerable <XNode> nodes = expectedAlignmentNodes.Nodes();
//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 AdditionalParameters.ParseOne:
case AdditionalParameters.ParseOneTextReader:
sequenceAlignmentList = new List <ISequenceAlignment>();
sequenceAlignmentList.Add(sequenceAlignment);
break;
default:
break;
}
expectedAlignmentList.Add(expectedAlignmentObj);
Assert.IsTrue(CompareOutput(sequenceAlignmentList, expectedAlignmentList));
ApplicationLog.WriteLine(
"ClustalW Parser BVT: Successfully validated all the Alignment Sequences");
}
/// <summary>
/// Parsers the ClustalW 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);
Assert.IsFalse(string.IsNullOrEmpty(filePath));
ApplicationLog.WriteLine(string.Format((IFormatProvider)null,
"ClustalW Parser BVT: Reading the File from location '{0}'", filePath));
Console.WriteLine(string.Format((IFormatProvider)null,
"ClustalW Parser BVT: Reading the File from location '{0}'", filePath));
// Get the rangelist after parsing.
ClustalWParser parserObj = new ClustalWParser();
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:
using (StreamReader strRdrObj = new StreamReader(filePath))
{
sequenceAlignmentList = parserObj.Parse(strRdrObj);
}
break;
case AdditionalParameters.ParseOneTextReader:
using (StreamReader strRdrObj = new StreamReader(filePath))
{
sequenceAlignment = parserObj.ParseOne(strRdrObj);
}
break;
case AdditionalParameters.ParseOneTextReaderReadOnly:
using (StreamReader strRdrObj = new StreamReader(filePath))
{
sequenceAlignment = parserObj.ParseOne(strRdrObj, false);
}
break;
case AdditionalParameters.ParseTextReaderReadOnly:
using (StreamReader strRdrObj = new StreamReader(filePath))
{
sequenceAlignmentList = parserObj.Parse(strRdrObj, false);
}
break;
case AdditionalParameters.ParseReadOnly:
sequenceAlignmentList = parserObj.Parse(filePath,
false);
break;
case AdditionalParameters.ParseOneReadOnly:
sequenceAlignment = parserObj.ParseOne(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 = _utilityObj._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(
"ClustalW Parser BVT: Successfully validated all the Alignment Sequences");
Console.WriteLine(
"ClustalW Parser BVT: Successfully validated all the Alignment Sequences");
}