private void distinguishAndPropogateGroup(int groupIndex, Chain chain, string group3,
int seqcode, int firstAtomIndex, int maxAtomIndex)
{
// System.out.println("distinguish & propogate group:" +
// " group3:" + group3 +
// " seqcode:" + Group.getSeqcodeString(seqcode) +
// " firstAtomIndex:" + firstAtomIndex +
// " maxAtomIndex:" + maxAtomIndex);
int distinguishingBits = 0;
// clear previous specialAtomIndexes
for (int i = JmolConstants.ATOMID_MAX; --i >= 0; )
specialAtomIndexes[i] = Int32.MinValue;
if (specialAtomIDs != null)
{
for (int i = maxAtomIndex; --i >= firstAtomIndex; )
{
int specialAtomID = specialAtomIDs[i];
if (specialAtomID > 0)
{
if (specialAtomID < JmolConstants.ATOMID_DISTINGUISHING_ATOM_MAX)
distinguishingBits |= 1 << specialAtomID;
specialAtomIndexes[specialAtomID] = i;
}
}
}
int lastAtomIndex = maxAtomIndex - 1;
if (lastAtomIndex < firstAtomIndex)
throw new System.NullReferenceException();
Group group = null;
// System.out.println("distinguishingBits=" + distinguishingBits);
if ((distinguishingBits & JmolConstants.ATOMID_PROTEIN_MASK) == JmolConstants.ATOMID_PROTEIN_MASK)
{
// System.out.println("may be an AminoMonomer");
group = AminoMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (distinguishingBits == JmolConstants.ATOMID_ALPHA_ONLY_MASK)
{
// System.out.println("AlphaMonomer.validateAndAllocate");
group = AlphaMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (((distinguishingBits & JmolConstants.ATOMID_NUCLEIC_MASK) == JmolConstants.ATOMID_NUCLEIC_MASK))
{
group = NucleicMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
else if (distinguishingBits == JmolConstants.ATOMID_PHOSPHORUS_ONLY_MASK)
{
// System.out.println("PhosphorusMonomer.validateAndAllocate");
group = PhosphorusMonomer.validateAndAllocate(chain, group3, seqcode, firstAtomIndex, lastAtomIndex, specialAtomIndexes, atoms);
}
if (group == null)
group = new Group(chain, group3, seqcode, firstAtomIndex, lastAtomIndex);
chain.addGroup(group);
groups[groupIndex] = group;
////////////////////////////////////////////////////////////////
for (int i = maxAtomIndex; --i >= firstAtomIndex; )
atoms[i].Group = group;
}
public static Monomer[] getNucleicMonomers(Group[] groups, int firstGroupIndex)
{
NucleicMonomer previous = null;
int count = 0;
for (int i = firstGroupIndex; i < groups.Length; ++i, ++count)
{
Group group = groups[i];
if (!(group is NucleicMonomer))
break;
NucleicMonomer current = (NucleicMonomer) group;
if (current.polymer != null)
break;
if (!current.isConnectedAfter(previous))
break;
previous = current;
}
if (count == 0)
return null;
Monomer[] monomers = new Monomer[count];
for (int j = 0; j < count; ++j)
monomers[j] = (NucleicMonomer) groups[firstGroupIndex + j];
return monomers;
}
public void addGroup(Group group)
{
if (groupCount == groups.Length)
groups = (Group[]) Util.doubleLength(groups);
groups[groupCount++] = group;
}
public static Polymer allocatePolymer(Group[] groups, int firstGroupIndex)
{
// System.out.println("allocatePolymer()");
Monomer[] monomers;
monomers = getAminoMonomers(groups, firstGroupIndex);
if (monomers != null)
{
// System.out.println("an AminoPolymer");
return new AminoPolymer(monomers);
}
monomers = getAlphaMonomers(groups, firstGroupIndex);
if (monomers != null)
{
// System.out.println("an AlphaPolymer");
return new AlphaPolymer(monomers);
}
monomers = getNucleicMonomers(groups, firstGroupIndex);
if (monomers != null)
{
// System.out.println("a NucleicPolymer");
return new NucleicPolymer(monomers);
}
monomers = getPhosphorusMonomers(groups, firstGroupIndex);
if (monomers != null)
{
// System.out.println("an AlphaPolymer");
return new PhosphorusPolymer(monomers);
}
System.Console.Out.WriteLine("Polymer.allocatePolymer() ... why am I here?");
throw new System.NullReferenceException();
}
public int getSelectedGroupIndex(Group group)
{
int selectedGroupIndex = 0;
for (int i = 0; i < groupCount; ++i)
{
if (bsSelectedGroups.Get(i))
{
if (groups[i] == group)
return selectedGroupIndex;
++selectedGroupIndex;
}
}
return - 1;
}
