/// <summary> Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence
/// the atom will be added to a Monomer of type UNKNOWN in the specified Strand.
///
/// </summary>
/// <param name="oAtom"> The atom to add
/// </param>
/// <param name="oStrand">The strand the atom belongs to
/// </param>
public virtual void addAtom(IAtom oAtom, IStrand oStrand)
{
int atomCount = base.AtomCount;
// Add atom to AtomContainer
base.addAtom(oAtom);
if (atomCount != base.AtomCount && oStrand != null)
{
// Maybe better to throw nullpointer exception here, so user realises that
// Strand == null and Atom only gets added to this BioPolymer, but not to a Strand.
oStrand.addAtom(oAtom);
if (!strands.ContainsValue(oStrand.StrandName))
{
strands[oStrand.StrandName] = oStrand;
}
}
/* notifyChanged() is called by addAtom in
* AtomContainer */
}
/// <summary> Adds the atom to a specified Strand and a specified Monomer.
///
/// </summary>
/// <param name="oAtom">
/// </param>
/// <param name="oMonomer">
/// </param>
/// <param name="oStrand">
/// </param>
public virtual void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
{
int atomCount = base.AtomCount;
// Add atom to AtomContainer
base.addAtom(oAtom);
if (atomCount != base.AtomCount && oStrand != null)
{
oStrand.addAtom(oAtom, oMonomer); // Same problem as above: better to throw nullpointer exception?
if (!strands.ContainsKey(oStrand.StrandName))
{
strands[oStrand.StrandName] = oStrand;
}
}
/* The reasoning above is:
* All Monomers have to belong to a Strand and all atoms belonging to strands have to belong to a Monomer =>
* ? oMonomer != null and oStrand != null, oAtom is added to BioPolymer and to oMonomer in oStrand
* ? oMonomer == null and oStrand != null, oAtom is added to BioPolymer and default Monomer in oStrand
* ? oMonomer != null and oStrand == null, oAtom is added to BioPolymer, but not to a Monomer or Strand (especially good to maybe throw exception in this case)
* ? oMonomer == null and oStrand == null, oAtom is added to BioPolymer, but not to a Monomer or Strand
* */
}
/// <summary> Adds the atom to a specified Strand and a specified Monomer.
///
/// </summary>
/// <param name="oAtom">
/// </param>
/// <param name="oMonomer">
/// </param>
/// <param name="oStrand">
/// </param>
public virtual void addAtom(IAtom oAtom, IMonomer oMonomer, IStrand oStrand)
{
int atomCount = base.AtomCount;
// Add atom to AtomContainer
base.addAtom(oAtom);
if (atomCount != base.AtomCount && oStrand != null)
{
oStrand.addAtom(oAtom, oMonomer); // Same problem as above: better to throw nullpointer exception?
if (!strands.ContainsKey(oStrand.StrandName))
{
strands[oStrand.StrandName] = oStrand;
}
}
/* The reasoning above is:
* All Monomers have to belong to a Strand and all atoms belonging to strands have to belong to a Monomer =>
* ? oMonomer != null and oStrand != null, oAtom is added to BioPolymer and to oMonomer in oStrand
* ? oMonomer == null and oStrand != null, oAtom is added to BioPolymer and default Monomer in oStrand
* ? oMonomer != null and oStrand == null, oAtom is added to BioPolymer, but not to a Monomer or Strand (especially good to maybe throw exception in this case)
* ? oMonomer == null and oStrand == null, oAtom is added to BioPolymer, but not to a Monomer or Strand
* */
}
/// <summary> Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified. Hence
/// the atom will be added to a Monomer of type UNKNOWN in the specified Strand.
///
/// </summary>
/// <param name="oAtom"> The atom to add
/// </param>
/// <param name="oStrand">The strand the atom belongs to
/// </param>
public virtual void addAtom(IAtom oAtom, IStrand oStrand)
{
int atomCount = base.AtomCount;
// Add atom to AtomContainer
base.addAtom(oAtom);
if (atomCount != base.AtomCount && oStrand != null)
{
// Maybe better to throw nullpointer exception here, so user realises that
// Strand == null and Atom only gets added to this BioPolymer, but not to a Strand.
oStrand.addAtom(oAtom);
if (!strands.ContainsValue(oStrand.StrandName))
{
strands[oStrand.StrandName] = oStrand;
}
}
/* notifyChanged() is called by addAtom in
AtomContainer */
}