public void TestIsRepeat()
{
// mononucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("AAAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("TAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAATAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAAAAT"));
// dinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATATAT"));
Assert.True(OverlapEvaluator.IsRepeat("ATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("AATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("ATATAATA"));
// trinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATG")); // 3x ATG
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGA")); // 3x ATG + A
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGAT")); // 3x ATG + AT
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGAG")); // 3x ATG + AG
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGTG")); // 3x ATG + TG
Assert.True(OverlapEvaluator.IsRepeat("AA"));
Assert.False(OverlapEvaluator.IsRepeat("ATC"));
Assert.False(OverlapEvaluator.IsRepeat("AT"));
Assert.False(OverlapEvaluator.IsRepeat("A"));
Assert.True(OverlapEvaluator.IsRepeat("ATA"));
}
public void TestIsRepeat()
{
// mononucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("AAAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("TAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAATAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAAAAT"));
// dinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATATAT"));
Assert.True(OverlapEvaluator.IsRepeat("ATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("AATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("ATATAATA"));
// trinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATG")); // 3x ATG
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGA")); // 3x ATG + A
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGAT")); // 3x ATG + AT
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGAG")); // 3x ATG + AG
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGTG")); // 3x ATG + TG
Assert.True(OverlapEvaluator.IsRepeat("TGATGATGATG")); // 3x ATG, starts with end of unit
Assert.True(OverlapEvaluator.IsRepeat("GATGATGATG")); // 3x ATG, starts with end of unit
Assert.True(OverlapEvaluator.IsRepeat("GATGATGATGA")); // 3x ATG, partials on either side
Assert.True(OverlapEvaluator.IsRepeat("AA"));
Assert.False(OverlapEvaluator.IsRepeat("ATC"));
Assert.False(OverlapEvaluator.IsRepeat("AT"));
Assert.False(OverlapEvaluator.IsRepeat("A"));
Assert.True(OverlapEvaluator.IsRepeat("ATA"));
Assert.True(OverlapEvaluator.IsRepeat("ATAT"));
Assert.False(OverlapEvaluator.IsRepeat("ATGCAATGCA")); // Unit too long
}