public void FastaParserForManyFiles()
{
string path = @"TestUtils\FASTA";
Assert.IsTrue(Directory.Exists(path));
int count = 0;
FastaParser parser = new FastaParser();
FastaFormatter formatter = new FastaFormatter();
DirectoryInfo di = new DirectoryInfo(path);
foreach (FileInfo fi in di.GetFiles("*.fasta"))
{
using (StreamReader reader = File.OpenText(fi.FullName))
{
ApplicationLog.WriteLine("parsing file {0}...", fi.FullName);
foreach (Sequence seq in parser.Parse(reader))
{
ApplicationLog.Write(formatter.FormatString(seq));
count++;
}
}
ApplicationLog.WriteLine("parsing file {0}...", fi.FullName);
}
Assert.IsTrue(count >= 3);
((FastaParser)parser).Dispose();
}
private void WriteToLog(string ExceptionMessage)
{
// Let the calling process know there was an error
HasError = true;
ExceptionMessage += "\n\nAdditional information:\n\n" + Information;
ApplicationLog logger = new ApplicationLog(ExceptionMessage);
logger.Write();
}
public void FastAFormatterInvalidateClose()
{
try
{
FastAFormatter formatter = new FastAFormatter();
formatter.Close();
Assert.Fail();
}
catch (InvalidOperationException ex)
{
ApplicationLog.Write("Fasta P2 : InvalidOperationException caught successfully. " + ex.Message);
}
}
public void FastAFormatterInvalidateFormatString()
{
ISequence iSeq = null;
try
{
string formattedString = FastAFormatter.FormatString(iSeq);
Assert.Fail();
}
catch (ArgumentNullException ex)
{
ApplicationLog.Write("Fasta P2 : ArgumentNullException caught successfully. " + ex.Message);
}
}
public void ValidateWriteForValidLogFile()
{
string output = utilityObj.xmlUtil.GetTextValue(
Constants.ApplicationLogNode, Constants.ExpectedOutputNode);
//// Open the file for write.
String expectedOutput = ApplicationLog.Write(output);
Assert.IsTrue(ApplicationLog.Ready);
Assert.AreEqual(output, expectedOutput);
ApplicationLog.WriteLine(string.Concat(
"ApplicationLog BVT: Validation of Write method for File completed successfully."));
}
/// <summary>
/// Writes F matrix to application log. Used for test and debugging.
/// Only _FSource can be dumped.
/// _FScore, _M, _Ix, _Iy are not stored as part of memory optimization.
/// </summary>
protected void DumpF()
{
if (_FSource != null)
{
ApplicationLog.WriteLine(string.Empty);
ApplicationLog.WriteLine("_FSource");
for (int cell = 0; cell < _nCols * _nRows; cell++)
{
if (cell % _nCols == 0)
{
ApplicationLog.WriteLine(string.Empty);
}
ApplicationLog.Write("{0,4} ", _FSource[cell]);
}
}
}
public void InvalidateParseWithEmptyParam()
{
try
{
AggregateNumbers aggregateNos = new AggregateNumbers();
CommandLineArguments parser = new CommandLineArguments();
//add parameters
parser.Parameter(ArgumentType.Required, "bValue", ArgumentValueType.Bool, "bv", "bool");
parser.Parameter(ArgumentType.Required, "iValue", ArgumentValueType.Int, "iv", "int");
string[] args = { "-:true", "-iValue:5" };
parser.Parse(args, aggregateNos);
Assert.Fail();
}
catch (ArgumentSyntaxException ex)
{
ApplicationLog.Write("Successfully caught ArgumentSyntaxException : " + ex.Message);
}
}
public void InvalidateParseWithWrongParamName()
{
try
{
AggregateNumbers aggregateNos = new AggregateNumbers();
CommandLineArguments parser = new CommandLineArguments();
//add parameters
parser.Parameter(ArgumentType.Required, "bValue", ArgumentValueType.Bool, "bv", "bool");
parser.Parameter(ArgumentType.Required, "iValue", ArgumentValueType.Int, "iv", "int");
parser.Parameter(ArgumentType.Required, "bArrValues", ArgumentValueType.Bool, "bmv", "boolArrValues");
//pass char in integer array
string[] args = { "/wrongname:true", "/iValue:5", "/bArrValues:true", "false" };
parser.Parse(args, aggregateNos);
Assert.Fail();
}
catch (ArgumentParserException ex)
{
ApplicationLog.Write("Successfully caught ArgumentNotFoundException : " + ex.Message);
}
}
public void ValidateSequenceAlignersAll()
{
MUMmer mumobj = new MUMmer3();
Assert.AreEqual(mumobj.ToString(), SequenceAligners.MUMmer.ToString());
NeedlemanWunschAligner nwAlignerobj = new NeedlemanWunschAligner();
Assert.AreEqual(nwAlignerobj.ToString(), SequenceAligners.NeedlemanWunsch.ToString());
NUCmer nucobj = new NUCmer3();
Assert.AreEqual(nucobj.ToString(), SequenceAligners.NUCmer.ToString());
PairwiseOverlapAligner poAlignerobj = new PairwiseOverlapAligner();
Assert.AreEqual(poAlignerobj.ToString(), SequenceAligners.PairwiseOverlap.ToString());
SmithWatermanAligner swAlignerobj = new SmithWatermanAligner();
Assert.AreEqual(swAlignerobj.ToString(), SequenceAligners.SmithWaterman.ToString());
Assert.IsNotNull(SequenceAligners.All);
Console.Write("Successfully created all the objects in Sequence Aligners");
ApplicationLog.Write("Successfully created all the objects in Sequence Aligners");
}
