assertEquals(as.getAStr1(), as.getAStr2());
Mapping s1tos2 = as.getMappingFromS1(false);
- checkMapping(s1tos2,s1,s2);
+ checkMapping(s1tos2, s1, s2);
}
- public void checkMapping(Mapping s1tos2,SequenceI _s1,SequenceI _s2)
+ public void checkMapping(Mapping s1tos2, SequenceI _s1, SequenceI _s2)
{
System.out.println(s1tos2.getMap().toString());
for (int i = _s2.getStart(); i < _s2.getEnd(); i++)
{
- int p=s1tos2.getPosition(i);
- char s2c=_s2.getCharAt(i-_s2.getStart());
- char s1c=_s1.getCharAt(p-_s1.getStart());
- System.out.println("Position in s2: " + i +s2c
- + " maps to position in s1: " +p+s1c);
- assertEquals(s1c,s2c);
+ int p = s1tos2.getPosition(i);
+ char s2c = _s2.getCharAt(i - _s2.getStart());
+ char s1c = _s1.getCharAt(p - _s1.getStart());
+ System.out.println("Position in s2: " + i + s2c
+ + " maps to position in s1: " + p + s1c);
+ assertEquals(s1c, s2c);
}
}
+
@Test(groups = { "Functional" })
/**
* simple test that mapping from alignment corresponds identical positions.
assertEquals(as.getAStr1(), as.getAStr2().toUpperCase(Locale.ROOT));
Mapping s1tos2 = as.getMappingFromS1(false);
- assertEquals("ASdFA",as.getAStr2());
+ assertEquals("ASdFA", as.getAStr2());
// verify mapping is consistent between original all-caps sequences
- checkMapping(s1tos2,s1,s2);
+ checkMapping(s1tos2, s1, s2);
}
@Test(groups = { "Functional" })