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'));
}