public void CheckIsGapFalseTest() { IAlphabet alphabet = Alphabets.DNA; bool actual = alphabet.CheckIsGap('A'); Assert.AreEqual(false, actual); }
public void CheckIsGapTrueTest() { IAlphabet alphabet = Alphabets.DNA; bool actual = alphabet.CheckIsGap('-'); Assert.AreEqual(true, actual); }
/// <summary> /// Checks if the provided item is a gap character or not /// </summary> /// <param name="alphabet">Alphabet to test against.</param> /// <param name="item">Item to be checked</param> /// <returns>True if the specified item is a gap</returns> public static bool CheckIsGap(this IAlphabet alphabet, char item) { if (alphabet == null) { throw new ArgumentNullException("alphabet", "Alphabet must be supplied."); } return(alphabet.CheckIsGap((byte)item)); }
static void Main(string[] args) { var parser = SequenceParsers.FindParserByFileName(Filename); if (parser == null) { Console.WriteLine("No parser found."); return; } List <ISequence> allSequences = parser .Parse() .ToList(); IAlphabet alphabet = allSequences[0].Alphabet; long totalColums = allSequences.Min(s => s.Count); //byte[] data = new byte[allSequences.Count]; for (int column = 0; column < totalColums; column++) { // for (int row = 0; row < allSequences.Count; row++) // data[row] = allSequences[row][column]; //ISequence newSequence = new Sequence(alphabet, data); ISequence newSequence = new Sequence(AmbiguousRnaAlphabet.Instance, allSequences .Select(s => s[column]).ToArray()); SequenceStatistics stats = new SequenceStatistics(newSequence); var TopCount = alphabet .Where(symbol => !alphabet.CheckIsGap(symbol)) .Select(symbol => new { Symbol = (char)symbol, Count = stats.GetCount(symbol), Frequency = stats.GetFraction(symbol) }) .Where(tc => tc.Count > 0) .OrderByDescending(c => c.Count) .FirstOrDefault(); if (TopCount != null) { Console.WriteLine("{0}: {1} = {2} of {3}", column, TopCount.Symbol, TopCount.Count, totalColums); } } }
public void CheckIsGapNullSequence() { IAlphabet alphabet = null; alphabet.CheckIsGap('A'); }
public void CheckIsGapNullSequence() { IAlphabet alphabet = null; Assert.Throws <ArgumentNullException>(() => alphabet.CheckIsGap('A')); }