SimpleSequencePair extends SimpleProfile<S, C> implements SequencePair<S, C> { @Override public int getIndexInQueryAt(int alignmentIndex) { return getAlignedSequence(1).getSequenceIndexAt(alignmentIndex); } SimpleSequencePair(AlignedSequence<S, C> query, AlignedSequence<S, C> target);  SimpleSequencePair(S query, S target, List<Step> sx, List<Step> sy);  SimpleSequencePair(S query, S target, List<Step> sx, int xb, int xa, List<Step> sy, int yb, int ya); @Override C getCompoundInQueryAt(int alignmentIndex); @Override C getCompoundInTargetAt(int alignmentIndex); @Override int getIndexInQueryAt(int alignmentIndex); @Override int getIndexInQueryForTargetAt(int targetIndex); @Override int getIndexInTargetAt(int alignmentIndex); @Override int getIndexInTargetForQueryAt(int queryIndex); @Override int getNumIdenticals(); @Override int getNumSimilars(); @Override AlignedSequence<S, C> getQuery(); @Override AlignedSequence<S, C> getTarget();  }
@Test public void testGetIndexInQueryAt() { assertEquals(global.getIndexInQueryAt(1), 1); assertEquals(global.getIndexInQueryAt(2), 2); assertEquals(global.getIndexInQueryAt(3), 3); assertEquals(global.getIndexInQueryAt(4), 4); assertEquals(global.getIndexInQueryAt(5), 4); assertEquals(local.getIndexInQueryAt(1), 2); assertEquals(local.getIndexInQueryAt(2), 3); assertEquals(local.getIndexInQueryAt(3), 4); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInQueryAtOutOfBounds() { global.getIndexInQueryAt(0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInQueryAtOutOfBounds2() { global.getIndexInQueryAt(6); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInQueryAtOutOfBounds3() { local.getIndexInQueryAt(0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInQueryAtOutOfBounds4() { local.getIndexInQueryAt(4); }