/** {@inheritDoc} */ @Override public Collection<String> getMonomerNames() { logger.debug("Getting monomer names"); return super.getMonomerNames(); }
@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; } }
@Override public IBioPolymer clone() throws CloneNotSupportedException { BioPolymer clone = (BioPolymer) super.clone(); clone.strands.clear(); for (Iterator<String> strands = clone.getStrandNames().iterator(); strands.hasNext();) { Strand strand = (Strand) clone.getStrand(strands.next().toString()).clone(); for (Iterator<String> iter = strand.getMonomerNames().iterator(); iter.hasNext();) { IMonomer monomer = strand.getMonomer(iter.next().toString()); Iterator<IAtom> atoms = monomer.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom((IAtom) atoms.next(), monomer, strand); } } } return clone; } }
@Override public IBioPolymer clone() throws CloneNotSupportedException { BioPolymer clone = (BioPolymer) super.clone(); clone.strands.clear(); for (Iterator<String> strands = clone.getStrandNames().iterator(); strands.hasNext();) { Strand strand = (Strand) clone.getStrand(strands.next().toString()).clone(); for (Iterator<String> iter = strand.getMonomerNames().iterator(); iter.hasNext();) { IMonomer monomer = strand.getMonomer(iter.next().toString()); Iterator<IAtom> atoms = monomer.atoms().iterator(); while (atoms.hasNext()) { clone.addAtom((IAtom) atoms.next(), monomer, strand); } } } return clone; } }