{
String s = String.valueOf((char) i);
String ss = Rna.getRNASecStrucState(s);
-
+
/*
* valid SS chars are a-z, A-Z, and various brackets;
* anything else is returned as a space
assertEquals(" ", ss);
}
}
-
+
/*
* a string is processed character by character
*/
}
}
+ @Test(groups = { "Functional" })
+ public void testIsCanonicalPair()
+ {
+ String bases = "acgtuACGTU";
+ for (int i = 0; i < bases.length(); i++)
+ {
+ for (int j = 0; j < bases.length(); j++)
+ {
+ char first = bases.charAt(i);
+ char second = bases.charAt(j);
+ boolean result = Rna.isCanonicalPair(first, second);
+ String pair = new String(new char[] { first, second })
+ .toUpperCase();
+ if (pair.equals("AT") || pair.equals("TA") || pair.equals("AU")
+ || pair.equals("UA") || pair.equals("GC")
+ || pair.equals("CG"))
+ {
+ assertTrue(pair + " should be valid", result);
+ }
+ else
+ {
+ assertFalse(pair + " should be invalid", result);
+ }
+ }
+ }
+ }
+
/**
* Tests for isOpeningParenthesis with char or String argument
*/
public void testIsRnaSecondaryStructureSymbol()
{
assertFalse(Rna.isRnaSecondaryStructureSymbol(null));
-
+
/*
* only A-Z, a-z, ()[]{}<> are valid symbols
*/