public void TestConstructor () {
Sequence seq = new Sequence( AlphabetType.AA, "ArTGü" );
Assert.AreEqual( 5, seq.Length );
Assert.AreEqual( "AA", seq.Alphabet.Name );
Assert.AreEqual( "ARTGX", seq.Letters() );
seq = new Sequence( AlphabetType.RNA, "AcUGz" );
Assert.AreEqual( "acugn", seq.Letters() );
seq = new Sequence( AlphabetType.RNA, seq );
Assert.AreEqual( "acugn", seq.Letters() );
seq = new Sequence( AlphabetType.UNKNOWN, "actgactg" );
Assert.AreEqual( "actgactg", seq.Letters() );
Assert.AreEqual( AlphabetFactory.Instance( AlphabetType.DNA ), seq.Alphabet );
seq = new Sequence( AlphabetType.UNKNOWN, "AMCMKQQRTAYWY" );
Assert.AreEqual( "AMCMKQQRTAYWY", seq.Letters() );
Assert.AreEqual( AlphabetFactory.Instance( AlphabetType.PROTEIN ), seq.Alphabet );
Alphabet alpha = DnaAlphabet.Instance();
Symbol[] symbols = { alpha['A'], alpha['C'], alpha['T'] };
seq = new Sequence( alpha, symbols, false );
symbols[0] = alpha['G']; //shouldnt be able to change the symbol
Assert.AreEqual( "act", seq.Letters() );
}
/** Test of the string representation for sections */
public void TestLetters2 () {
Sequence seq = new Sequence( AlphabetType.AA, "ARTG", true );
Assert.AreEqual( "ARTG", seq.Letters( 1, 4 ) );
Assert.AreEqual( "ARTGA", seq.Letters( 1, 5 ) );
Assert.AreEqual( "RT", seq.Letters( 2, 3 ) );
Assert.AreEqual( "GAR", seq.Letters( 4, 6 ) );
}
/** Test of the string representation */
public void TestLetters () {
Sequence seq = new Sequence( AlphabetType.AA, "ARTGARTG" );
Assert.AreEqual( "ARTGARTG", seq.Letters() );
}
/// <summary>
/// The implementation ensures that
/// a match fails for a given position if there is no match. Otherwise the
/// matcher might return a match at a different position.
/// <see cref="QUT.Bio.BioPatML.Patterns.IPattern">IPattern Match(Sequence, int) method</see>
/// </summary>
/// <param name="sequence"> the sequence for matching</param>
/// <param name="position"> position used for matching</param>
/// <returns></returns>
public override Match Match(Sequence sequence, int position)
{
String charSequence = sequence.Letters(position, sequence.Length);
int startIndex = position - 1;
//String charSequence = sequence.Letters();
System.Text.RegularExpressions.Match myMatch;
if(!IsCaseSensitive)
myMatch = Regex.Match(charSequence, RegularEx, RegexOptions.IgnoreCase);
else
myMatch = Regex.Match(charSequence, RegularEx);
if (myMatch.Success)
{
//if ((myMatch.Index + (position - 1)) //Minus away the infront seq's position -1 for the start index 0
// != position - 1)
int foundIndex = myMatch.Index + startIndex;
if ((foundIndex) != position - 1)
//if((myMatch.Index) != position - 1)
{
//Increment = myMatch.Index + 1 - position;
Increment = foundIndex + 1 - position;
return (null);
}
Increment = 1;
Matched.Set(sequence, foundIndex + 1,
myMatch.Length, sequence.Strand, 1.0);
//GetMatch().Set(sequence, myMatch.Index + 1,
// myMatch.Length, sequence.Strand, 1.0);
return (Matched);
}
Increment = Math.Max(1, sequence.Length - position);
return null;
}