public void SetUp()
{
alpha = DnaAlphabet.Instance();
symbols = new SymbolArray(alpha, "actgactg");
this.indexer = new IndexerDirect(2);
accessor = new AccessorLinear(indexer, 4, symbols);
}
public void SetUp()
{
alpha = DnaAlphabet.Instance();
symbols = new SymbolArray(alpha, "tatgacgt");
this.indexer = new IndexerDirect(2);
accessor = new AccessorTransparent(indexer, 4, symbols);
}
public void SetUp()
{
alpha = DnaAlphabet.Instance();
symbols = new SymbolArray(alpha, "actgactg");
indexer = new IndexerDirect(2);
indexerReverse = new IndexerReverse(2,symbols.Length);
accessor = new AccessorCircular(this.indexer, 4, symbols);
}
/** Tests the construction of symbol arrays */
public void TestConstructor() {
Symbol[] symbols = {alpha['A'], alpha['G']};
SymbolArray symbolArray;
symbolArray = new SymbolArray(alpha, symbols);
Assert.AreEqual(2, symbolArray.Length);
Assert.AreEqual(alpha, symbolArray.Alphabet);
symbolArray = new SymbolArray(alpha, "AG");
Assert.AreEqual(2, symbolArray.Length);
Assert.AreEqual(alpha, symbolArray.Alphabet); //Query for alphabet type;
}
/** Tests the Getter for symbols */
public void TestSymbolAt()
{
SymbolArray symbolArray;
Symbol[] symbols = { alpha['A'], alpha['C'], null };
symbolArray = new SymbolArray(alpha, symbols);
Assert.AreEqual(alpha['A'], symbolArray.SymbolAt(0));
Assert.AreEqual(alpha['C'], symbolArray.SymbolAt(1));
Assert.AreEqual(null, symbolArray.SymbolAt(2));
symbolArray = new SymbolArray(alpha, "ACü");
Assert.AreEqual(alpha['A'], symbolArray.SymbolAt(0));
Assert.AreEqual(alpha['C'], symbolArray.SymbolAt(1));
Assert.AreEqual(alpha['N'], symbolArray.SymbolAt(2)); // default letter
}
public void TestInstance()
{
SymbolArray symbols = new SymbolArray(DnaAlphabet.Instance(), "ACTG");
Assert.AreEqual
(true, AccessorFactory.Instance
(AccessorFactory.LIN_DIR, 0, 0, 0, symbols) is AccessorLinear);
Assert.AreEqual
(true, AccessorFactory.Instance
(AccessorFactory.CIRC_DIR, 0, 0, 0, symbols) is AccessorCircular);
Assert.AreEqual
(true, AccessorFactory.Instance
(AccessorFactory.TRANS_DIR, 0, 0, 0, symbols) is AccessorTransparent);
Assert.AreEqual
(true, AccessorFactory.Instance
(AccessorFactory.LIN_REV_COMP, 0, 0, 0, symbols) is AccessorComplement);
}
public void SetUp()
{
alpha = DnaAlphabet.Instance();
symbols = new SymbolArray(alpha, "actg");
accessor = new AccessorComplement(symbols);
}