/** {@inheritDoc} */ @Override public void addAtom(IAtom oAtom, IMonomer oMonomer) { logger.debug("Adding atom to monomer: ", oAtom, oMonomer); super.addAtom(oAtom, oMonomer); }
/** * * Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the * atom gets added to a Monomer of type UNKNOWN in a Strand of type UNKNOWN. * * @param oAtom The atom to add * */ @Override public void addAtom(IAtom oAtom) { addAtom(oAtom, getMonomer("")); }
/** {@inheritDoc} */ @Override public void addAtom(IAtom atom) { logger.debug("Adding atom: ", atom); super.addAtom(atom); }
/** * * Adds the atom oAtom without specifying a Monomer or a Strand. Therefore the * atom gets added to a Monomer of type UNKNOWN in a Strand of type UNKNOWN. * * @param oAtom The atom to add * */ @Override public void addAtom(IAtom oAtom) { addAtom(oAtom, getMonomer("")); }
/** * Adds the atom oAtom to a specified Monomer. Additionally, it keeps * record of the iCode. * * @param oAtom The atom to add * @param oMonomer The monomer the atom belongs to */ @Override public void addAtom(IAtom oAtom, IMonomer oMonomer) { super.addAtom(oAtom, oMonomer); if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName())) sequentialListOfMonomers.add(oMonomer.getMonomerName()); }
/** * Adds the atom oAtom to a specified Monomer. Additionally, it keeps * record of the iCode. * * @param oAtom The atom to add * @param oMonomer The monomer the atom belongs to */ @Override public void addAtom(IAtom oAtom, IMonomer oMonomer) { super.addAtom(oAtom, oMonomer); if (!sequentialListOfMonomers.contains(oMonomer.getMonomerName())) sequentialListOfMonomers.add(oMonomer.getMonomerName()); }
@Override public IStrand clone() throws CloneNotSupportedException { Strand clone = (Strand) super.clone(); clone.monomers.clear(); for (Iterator<String> iter = clone.getMonomerNames().iterator(); iter.hasNext();) { Monomer monomerClone = (Monomer) (clone.getMonomer(iter.next().toString()).clone()); Iterator<IAtom> atoms = monomerClone.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom(atoms.next(), monomerClone); } } return clone; } }
@Override public IStrand clone() throws CloneNotSupportedException { Strand clone = (Strand) super.clone(); clone.monomers.clear(); for (Iterator<String> iter = clone.getMonomerNames().iterator(); iter.hasNext();) { Monomer monomerClone = (Monomer) (clone.getMonomer(iter.next().toString()).clone()); Iterator<IAtom> atoms = monomerClone.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom(atoms.next(), monomerClone); } } return clone; } }