@Test public void testSet_int_Object() { ConformerContainer container = new ConformerContainer(confs); int location = 5; container.set(location, container.get(location + 1)); Assert.assertEquals(location, container.indexOf(container.get(location + 1))); }
@Override public boolean hasNext() { boolean slurpedConformers = false; if (lastMol != null) container = new ConformerContainer(lastMol); if (!nextIsKnown) { while (imdlr.hasNext()) { slurpedConformers = true; IAtomContainer mol = (IAtomContainer) imdlr.next(); if (container.size() == 0) container.add(mol); else { if (container.getTitle().equals(mol.getTitle())) container.add(mol); else { lastMol = mol; hasNext = true; break; } } } hasNext = container.size() > 0 && slurpedConformers; } if (!hasNext) container = null; nextIsKnown = true; return hasNext; }
/** * Remove the specified conformer. * * @param o The conformer to remove (should be castable to IAtomContainer) * @return true if the specified conformer was present and removed, false if not found */ @Override public boolean remove(Object o) { IAtomContainer atomContainer = (IAtomContainer) o; // we should never have a null conformer if (atomContainer == null) return false; int index = indexOf(atomContainer); if (index >= 0) { remove(index); return true; } return false; }
@Override public IAtomContainer set(int i, IAtomContainer atomContainer) { if (!title.equals(atomContainer.getTitle())) throw new IllegalArgumentException( "The input molecules does not have the same title as the other conformers"); Point3d[] tmp = getCoordinateList(atomContainer); IAtomContainer oldAtomContainer = get(i); coordinates.set(i, tmp); return oldAtomContainer; }
@Test public void testContains_Object() { ConformerContainer container = new ConformerContainer(confs); Assert.assertEquals(nconfs, container.size()); Assert.assertTrue(container.contains(container.get(3))); }
@Test public void testRemove_int() { ConformerContainer container = new ConformerContainer(confs); container.clear(); Assert.assertEquals(0, container.size()); for (int i = 0; i < nconfs; i++) container.add(confs[i]); Assert.assertEquals(nconfs, container.size()); container.remove(0); Assert.assertEquals(nconfs - 1, container.size()); }
@Test public void testLastIndexOf_Object() { ConformerContainer container = new ConformerContainer(confs); Assert.assertEquals(nconfs, container.size()); int x = container.lastIndexOf(container.get(3)); Assert.assertEquals(3, container.lastIndexOf(container.get(3))); }
@Test(expected = IndexOutOfBoundsException.class) public void testGet2() { ConformerContainer container = new ConformerContainer(confs); for (int i = 0; i < container.size() + 1; i++) container.get(i); }
@Test public void testAdd_Object() { ConformerContainer container = new ConformerContainer(); Assert.assertNotNull(container); for (IAtomContainer conf : confs) container.add(conf); Assert.assertEquals(nconfs, container.size()); }
@Test public void testIndexOf_IAtomContainer() { ConformerContainer container = new ConformerContainer(confs); IAtomContainer ac = container.get(2); int index = container.indexOf(ac); Assert.assertEquals(2, index); }
@Test public void testSize() { ConformerContainer container = new ConformerContainer(confs); Assert.assertEquals(nconfs, container.size()); }
@Test public void testContains() { ConformerContainer container = new ConformerContainer(confs); IAtomContainer o = container.get(0); Assert.assertTrue(container.contains(o)); }
@Test public void testClear() { ConformerContainer container = new ConformerContainer(confs); Assert.assertEquals(nconfs, container.size()); container.clear(); Assert.assertEquals(0, container.size()); }
@Test(expected = UnsupportedOperationException.class) public void testRemoveAll_Collection() { ConformerContainer container = new ConformerContainer(confs); Assert.assertNotNull(container); Assert.assertEquals(nconfs, container.size()); container.removeAll(container); Assert.assertEquals(0, container.size()); }
@Test(expected = UnsupportedOperationException.class) public void testContainsAll_Collection() { ConformerContainer container = new ConformerContainer(confs); Assert.assertNotNull(container); Assert.assertEquals(nconfs, container.size()); Assert.assertTrue(container.containsAll(container)); }
@Test public void testAdd_int_Object() { ConformerContainer container = new ConformerContainer(confs); container.add(5, confs[5]); }
/** * Removes the conformer at the specified position. * * @param i The position in the list to remove * @return The conformer that was at the specified position */ @Override public IAtomContainer remove(int i) { IAtomContainer oldAtomContainer = get(i); coordinates.remove(i); return oldAtomContainer; }
@Test(expected = IndexOutOfBoundsException.class) public void testGet_int() { ConformerContainer container = new ConformerContainer(confs); container.get(100); }
@Test public void testGetTitle() { ConformerContainer container = new ConformerContainer(confs); Assert.assertEquals("myMolecule", container.getTitle()); }
@Test public void testIndexOf_Object() { ConformerContainer container = new ConformerContainer(confs); Assert.assertNotNull(container); int counter = 0; for (IAtomContainer conf : confs) { Assert.assertEquals(counter, container.indexOf(conf)); counter++; } }