SimpleSequencePair extends SimpleProfile<S, C> implements SequencePair<S, C> { @Override public int getIndexInTargetAt(int alignmentIndex) { return getAlignedSequence(2).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 testGetIndexInTargetAt() { assertEquals(global.getIndexInTargetAt(1), 1); assertEquals(global.getIndexInTargetAt(2), 1); assertEquals(global.getIndexInTargetAt(3), 1); assertEquals(global.getIndexInTargetAt(4), 2); assertEquals(global.getIndexInTargetAt(5), 3); assertEquals(local.getIndexInTargetAt(1), 1); assertEquals(local.getIndexInTargetAt(2), 1); assertEquals(local.getIndexInTargetAt(3), 2); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInTargetAtOutOfBounds() { global.getIndexInTargetAt(0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInTargetAtOutOfBounds2() { global.getIndexInTargetAt(6); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInTargetAtOutOfBounds3() { local.getIndexInTargetAt(0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetIndexInTargetAtOutOfBounds4() { local.getIndexInTargetAt(4); }