public void TestDiscardProteinResiduesPerformance(string fastaFile, int iterations)
{
var dataFile = FileRefs.GetTestFile(fastaFile);
for (var x = 0; x < 2; x++)
{
var discardProteinResidues = x != 0;
var startTime = DateTime.UtcNow;
var proteinsRead = 0;
for (var i = 0; i < iterations; i++)
{
using var reader = new ProteinFileReader.FastaFileReader(dataFile.FullName)
{
DiscardProteinResidues = discardProteinResidues
};
while (reader.ReadNextProteinEntry())
{
proteinsRead++;
}
}
var endTime = DateTime.UtcNow;
Console.WriteLine("Elapsed time for {0} iterations with DiscardProteinResidues={1,-5} is {2:F1} seconds; {3:N0} total proteins read",
iterations, discardProteinResidues, endTime.Subtract(startTime).TotalSeconds, proteinsRead);
}
}
// ReSharper restore StringLiteralTypo
public void CheckProteinDescription(string fastaFile, string proteinNames, string proteinDescriptions, char delimiter)
{
var dataFile = FileRefs.GetTestFile(fastaFile);
var reader = new ProteinFileReader.FastaFileReader(dataFile.FullName);
ValidationLogic.CheckProteinDescription(reader, proteinNames, proteinDescriptions, delimiter);
}
// ReSharper restore StringLiteralTypo
public void CheckProteinNames(string fastaFile, string expectedFirstProteinNames, string expectedLastProteinNames)
{
var dataFile = FileRefs.GetTestFile(fastaFile);
var reader = new ProteinFileReader.FastaFileReader(dataFile.FullName);
ValidationLogic.CheckProteinNamesOrSequences(reader, expectedFirstProteinNames, expectedLastProteinNames);
}
public void CheckProteinStats(string fastaFile, int proteinCountExpected, int totalResidueCountExpected)
{
var dataFile = FileRefs.GetTestFile(fastaFile);
var reader = new ProteinFileReader.FastaFileReader(dataFile.FullName);
ValidationLogic.CheckProteinStats(reader, proteinCountExpected, totalResidueCountExpected);
}
public void TestPercentFileProcessed(string fastaFile, int progressIntervalProteins, double expectedAverageProgressPercentInterval)
{
var dataFile = FileRefs.GetTestFile(fastaFile);
var reader = new ProteinFileReader.FastaFileReader(dataFile.FullName);
var proteinsRead = 0;
var lastProgress = 0f;
var progressPercentIntervals = new List <double>();
if (progressIntervalProteins < 1)
{
progressIntervalProteins = 1;
}
while (reader.ReadNextProteinEntry())
{
proteinsRead++;
if (proteinsRead % progressIntervalProteins > 0)
{
continue;
}
var percentComplete = reader.PercentFileProcessed();
Console.WriteLine("{0:F1}% read", percentComplete);
var progressInterval = percentComplete - lastProgress;
progressPercentIntervals.Add(progressInterval);
lastProgress = percentComplete;
}
Console.WriteLine("{0:F1}% read at finish", reader.PercentFileProcessed());
Console.WriteLine();
var averageInterval = progressPercentIntervals.Average();
Console.WriteLine("Average progress interval: {0:F2}%", averageInterval);
if (expectedAverageProgressPercentInterval > 0)
{
Assert.AreEqual(expectedAverageProgressPercentInterval, averageInterval, 0.01);
}
}
public void TestDiscardProteinResidues(string fastaFile)
{
var dataFile = FileRefs.GetTestFile(fastaFile);
var proteinsRead = 0;
using var reader = new ProteinFileReader.FastaFileReader(dataFile.FullName)
{
DiscardProteinResidues = true
};
while (reader.ReadNextProteinEntry())
{
proteinsRead++;
Assert.IsEmpty(reader.ProteinSequence, "Protein sequence is not empty for {0}", reader.ProteinName);
}
Console.WriteLine("Read {0} proteins from {1}", proteinsRead, dataFile.FullName);
}