SimpleSequencePair extends SimpleProfile<S, C> implements SequencePair<S, C> { @Override public C getCompoundInQueryAt(int alignmentIndex) { return getAlignedSequence(1).getCompoundAt(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 testGetCompoundInQueryAt() { assertEquals(global.getCompoundInQueryAt(1).getShortName(), "A"); assertEquals(global.getCompoundInQueryAt(2).getShortName(), "R"); assertEquals(global.getCompoundInQueryAt(3).getShortName(), "N"); assertEquals(global.getCompoundInQueryAt(4).getShortName(), "D"); assertEquals(global.getCompoundInQueryAt(5).getShortName(), "-"); assertEquals(local.getCompoundInQueryAt(1).getShortName(), "R"); assertEquals(local.getCompoundInQueryAt(2).getShortName(), "N"); assertEquals(local.getCompoundInQueryAt(3).getShortName(), "D"); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundInQueryAtOutOfBounds() { global.getCompoundInQueryAt(0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundInQueryAtOutOfBounds2() { global.getCompoundInQueryAt(6); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundInQueryAtOutOfBounds3() { local.getCompoundInQueryAt(0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundInQueryAtOutOfBounds4() { local.getCompoundInQueryAt(4); }