public void SetUp()
{
alphabet = new TestAlphabetClass();
alphabet2 = new TestAlphabetClass();
sym1 = new Symbol('a', "Ade", "Adenine");
sym2 = new Symbol('u', "Ura", "Uracil");
sym3 = new SymbolMeta('-', "GAP", "Gap");
}
public void TestAdd()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
Assert.AreEqual(0, sym.SymbolNumber);
//sym.remove(new Symbol('a', "adenine"));
sym.Add(new Symbol('a', "Ade", "Adenine"));
sym.Add(new Symbol('u', "Ura", "Adenine"));
Assert.AreEqual(2, sym.SymbolNumber);
Assert.AreEqual("Adenine", sym[0].Name);
Assert.AreEqual("Adenine", sym[1].Name);
}
/** Tests the replacement of symbols within the symbol set */
public void TestReplace()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
Symbol sym1 = new Symbol('a', "Ade", "Adenine");
Symbol sym2 = new Symbol('u', "Ura", "Uracil");
Symbol sym3 = new Symbol('t', "Thy", "Thymine");
sym.Add(sym1);
sym.Add(sym2);
Assert.AreEqual(2, sym.SymbolNumber);
sym.Replace(sym2, sym3);
Assert.AreEqual(2, sym.SymbolNumber);
Assert.AreEqual(sym3, sym[1]);
}
/** Tests the removal of symbols from the symbol set */
public void TestRemove()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
Symbol sym1 = new Symbol('a', "Ade", "Adenine");
Symbol sym2 = new Symbol('u', "Ura", "Uracil");
sym.Remove(sym1);
sym.Add(sym1);
sym.Add(sym2);
Assert.AreEqual(2, sym.SymbolNumber);
sym.Remove(sym1);
Assert.AreEqual(1, sym.SymbolNumber);
Assert.AreEqual(sym2, sym[0]);
}
/** Tests the comparision with a meta symbol */
public void TestEquals()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
Symbol sym2 = new Symbol('a', "Ade", "Adenine");
Symbol sym3 = new Symbol('u', "Ura", "Uracil");
Assert.AreEqual(true, sym.Equals(sym2));
Assert.AreEqual(true, sym2.Equals(sym));
sym.Add(sym2);
Assert.AreEqual(true, sym.Equals(sym2));
Assert.AreEqual(true, sym2.Equals(sym));
Assert.AreEqual(false, sym.Equals(sym3));
Assert.AreEqual(false, sym3.Equals(sym));
sym.Add(sym3);
Assert.AreEqual(true, sym.Equals(sym));
Assert.AreEqual(true, sym.Equals(sym2));
Assert.AreEqual(true, sym.Equals(sym3));
}
/// <summary>
/// Parses the motif description and generates a symbol array that describes
/// the motif. Alternatives are described by MetaSymbols.
/// </summary>
/// <param name="alphabet">Alphabet of the motif. </param>
/// <param name="motif">Motif description.</param>
/// <returns>Returns a symbol array.</returns>
public static List<Symbol> Symbols
(Alphabet alphabet, String motif)
{
List<Symbol> mySymbols = new List<Symbol>();
SymbolMeta alternative = null;
for (int i = 0; i < motif.Length; i++)
{
char letter = motif[i];
if (letter == '[')
{
if (alternative != null)
throw new ArgumentException
("'[' within alternative is not permitted");
alternative = new SymbolMeta('#', "ALT", "Alternative");
}
else
if (letter == ']')
{
if (alternative == null)
throw new ArgumentException
("Opening bracket for ']' is missing!");
mySymbols.Add(alternative);
alternative = null;
}
else
if (alternative != null)
alternative.Add(alphabet[letter]);
else
mySymbols.Add(alphabet[letter]);
}
if (alternative != null)
throw new ArgumentException
("']' is missing");
return mySymbols;
}
/** Tests the letter representation of the symbol set */
public void TestLetters()
{
SymbolMeta sym = new SymbolMeta('X', "XXX", "Unknown");
sym.Add(new Symbol('a', "Ade", "Adenine"));
sym.Add(new Symbol('u', "Ura", "Adenine"));
Assert.AreEqual("au", sym.Letters);
}
