SimpleProfile implements Profile<S, C> { @Override public C getCompoundAt(int listIndex, int alignmentIndex) { return getAlignedSequence(listIndex).getCompoundAt(alignmentIndex); } protected  SimpleProfile(AlignedSequence<S, C> query, AlignedSequence<S, C> target);  SimpleProfile(S sequence); protected  SimpleProfile(S query, S target, List<Step> sx, int xb, int xa, List<Step> sy, int yb, int ya); protected  SimpleProfile(Profile<S, C> query, Profile<S, C> target, List<Step> sx, List<Step> sy);  SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences); @Override AlignedSequence<S, C> getAlignedSequence(int listIndex); @Override AlignedSequence<S, C> getAlignedSequence(S sequence); @Override List<AlignedSequence<S, C>> getAlignedSequences(); @Override List<AlignedSequence<S, C>> getAlignedSequences(int... listIndices); @Override List<AlignedSequence<S, C>> getAlignedSequences(S... sequences); @Override C getCompoundAt(int listIndex, int alignmentIndex); @Override C getCompoundAt(S sequence, int alignmentIndex); @Override int[] getCompoundCountsAt(int alignmentIndex); @Override int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds); @Override List<C> getCompoundsAt(int alignmentIndex); @Override CompoundSet<C> getCompoundSet(); @Override float[] getCompoundWeightsAt(int alignmentIndex); @Override float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds); @Override int getIndexOf(C compound); @Override int[] getIndicesAt(int alignmentIndex); @Override int getLastIndexOf(C compound); @Override int getLength(); @Override List<S> getOriginalSequences(); @Override int getSize(); @Override ProfileView<S, C> getSubProfile(Location location); @Override boolean hasGap(int alignmentIndex); @Override boolean isCircular(); @Override String toString(int width); @Override String toString(StringFormat format); @Override String toString(); @Override Iterator<AlignedSequence<S, C>> iterator();  }
@Test public void testGetCompoundAtIntInt() { assertEquals(global.getCompoundAt(1, 4).getShortName(), "D"); assertEquals(global.getCompoundAt(2, 3).getShortName(), "-"); assertEquals(local.getCompoundAt(1, 1).getShortName(), "R"); assertEquals(local.getCompoundAt(2, 2).getShortName(), "-"); assertEquals(single.getCompoundAt(1, 3).getShortName(), "N"); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds() { global.getCompoundAt(0, 4); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds2() { global.getCompoundAt(3, 4); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds3() { global.getCompoundAt(1, 0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds4() { global.getCompoundAt(2, 6); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds5() { local.getCompoundAt(0, 2); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds6() { local.getCompoundAt(3, 2); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds7() { local.getCompoundAt(1, 0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds8() { local.getCompoundAt(2, 4); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtIntIntOutOfBounds9() { single.getCompoundAt(1, 0); }
@Test public void testGetCompoundAtSInt() { assertEquals(global.getCompoundAt(query, 2).getShortName(), "R"); assertEquals(global.getCompoundAt(target, 5).getShortName(), "G"); assertNull(global.getCompoundAt(new ProteinSequence("AR"), 3)); assertEquals(local.getCompoundAt(query, 2).getShortName(), "N"); assertEquals(local.getCompoundAt(target, 3).getShortName(), "D"); assertNull(local.getCompoundAt(new ProteinSequence("AR"), 3)); assertEquals(single.getCompoundAt(query, 2).getShortName(), "R"); assertNull(single.getCompoundAt(target, 3)); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtSIntOutOfBounds() { global.getCompoundAt(query, 0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtSIntOutOfBounds2() { global.getCompoundAt(target, 6); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtSIntOutOfBounds3() { local.getCompoundAt(target, 0); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtSIntOutOfBounds4() { local.getCompoundAt(query, 4); }
@Test(expected=IndexOutOfBoundsException.class) public void testGetCompoundAtSIntOutOfBounds5() { single.getCompoundAt(query, 0); }