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Removed commented out code
Signed-off-by: maclean <gilleain.torrance@gmail.com>
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egonw committed Sep 18, 2011
1 parent c1a69a4 commit 16efbc0
Showing 1 changed file with 0 additions and 113 deletions.
Expand Up @@ -230,25 +230,6 @@ public void setBonds(IBond[] bonds)
this.bondCount = bonds.length;
}

/**
* Sets the array of electronContainers of this AtomContainer.
*
*@param electronContainers The array of electronContainers to be assigned to
* this AtomContainer
*@see #getElectronContainers
*/
// public void setElectronContainers(IElectronContainer[] electronContainers)
// {
// this.electronContainers = electronContainers;
// for (int f = 0; f < electronContainers.length; f++)
// {
// electronContainers[f].addListener(this);
// }
// setElectronContainerCount(electronContainers.length);
// notifyChanged();
// }


/**
* Sets the atom at position <code>number</code> in [0,..].
*
Expand Down Expand Up @@ -312,48 +293,6 @@ public ISingleElectron getSingleElectron(int number)
return singleElectrons[number];
}

/**
* Sets the ElectronContainer at position <code>number</code> in [0,..].
*
* @param number The position of the ElectronContainer to be set.
* @param electronContainer The ElectronContainer to be stored at position <code>number</code>
* @see #getElectronContainer(int)
*/
// public void setElectronContainer(int number, IElectronContainer electronContainer)
// {
// electronContainer.addListener(this);
// electronContainers[number] = electronContainer;
// notifyChanged();
// }


/**
* Sets the number of electronContainers in this container.
*
* @param electronContainerCount The number of electronContainers in this
* container
* @see #getElectronContainerCount
*/
// public void setElectronContainerCount(int electronContainerCount)
// {
// this.electronContainerCount = electronContainerCount;
// notifyChanged();
// }


/**
* Sets the number of atoms in this container.
*
*@param atomCount The number of atoms in this container
*@see #getAtomCount
*/
// public void setAtomCount(int atomCount)
// {
// this.atomCount = atomCount;
// notifyChanged();
// }


/**
* Returns an Iterable for looping over all atoms in this container.
*
Expand Down Expand Up @@ -997,19 +936,6 @@ public void add(IAtomContainer atomContainer)
}
}

/**
* Adds the <code>ElectronContainer</code>s found in atomContainer to this
* container.
*
*@param atomContainer AtomContainer with the new ElectronContainers
*/
// public void addElectronContainers(IAtomContainer atomContainer)
// {
//
// notifyChanged();
// }


/**
* Adds an atom to this container.
*
Expand Down Expand Up @@ -1563,48 +1489,9 @@ public Object clone() throws CloneNotSupportedException {
}
clone.addSingleElectron(newSe);
}
// for (int f = 0; f < getElectronContainerCount(); f++) {
// electronContainer = this.getElectronContainer(f);
// newEC = getBuilder().newElectronContainer();
// if (electronContainer instanceof IBond) {
// IBond bond = (IBond) electronContainer;
// newEC = (IElectronContainer)bond.clone();
// newAtoms = new IAtom[bond.getAtomCount()];
// for (int g = 0; g < bond.getAtomCount(); g++) {
// newAtoms[g] = clone.getAtom(getAtomNumber(bond.getAtom(g)));
// }
// ((IBond) newEC).setAtoms(newAtoms);
// } else if (electronContainer instanceof ILonePair) {
// IAtom atom = ((ILonePair) electronContainer).getAtom();
// newEC = (ILonePair)electronContainer.clone();
// ((ILonePair) newEC).setAtom(clone.getAtom(getAtomNumber(atom)));
// } else if (electronContainer instanceof ISingleElectron) {
// IAtom atom = ((ISingleElectron) electronContainer).getAtom();
// newEC = (ISingleElectron)electronContainer.clone();
// ((ISingleElectron) newEC).setAtom(clone.getAtom(getAtomNumber(atom)));
// } else {
// //logger.debug("Expecting EC, got: " + electronContainer.getClass().getName());
// newEC = (IElectronContainer) electronContainer.clone();
// }
// clone.addElectronContainer(newEC);
// }
return clone;
}

/**
* Grows the ElectronContainer array by a given size.
*
*@see #growArraySize
*/
// protected void growElectronContainerArray()
// {
// growArraySize = (electronContainers.length < growArraySize) ? growArraySize : electronContainers.length;
// IElectronContainer[] newelectronContainers = new IElectronContainer[electronContainers.length + growArraySize];
// System.arraycopy(electronContainers, 0, newelectronContainers, 0, electronContainers.length);
// electronContainers = newelectronContainers;
// }


/**
* Grows the atom array by a given size.
*
Expand Down

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