private void Cleanup()
{
_traversalStack.Clear();
_visitedNodes.Clear();
#if DEBUG
// Reset reentrancy test flag.
Interlocked.Exchange(ref _reentranceFlag, 0);
#endif
}
/// <summary>
/// Resolves conflicts either by bending bonds or stretching bonds in the
/// shortest path between an overlapping pair. Bending and stretch are tried
/// for each pair and the best resolution is used.
/// </summary>
/// <param name="pairs">pairs</param>
private void BendOrStretch(IEnumerable <AtomPair> pairs)
{
// without checking which bonds have been bent/stretch already we
// could end up repeating a lot of repeated work to no avail
var bendVisit = new Dictionary <IBond, AtomPair>();
var stretchVisit = new Dictionary <IBond, AtomPair>();
var bendStack = new IntStack(atoms.Length);
var stretchStack = new IntStack(atoms.Length);
foreach (var pair in pairs)
{
double score = congestion.Score();
// each attempt will be more aggressive/distorting
for (pair.attempt = 1; pair.attempt <= 3; pair.attempt++)
{
bendStack.Clear();
stretchStack.Clear();
// attempt both bending and stretching storing the
// best result in the provided buffer
var bendScore = Bend(pair, bendStack, buffer1, bendVisit);
var stretchScore = Stretch(pair, stretchStack, buffer2, stretchVisit);
// bending is better than stretching
if (bendScore < stretchScore && bendScore < score)
{
RestoreCoords(bendStack, buffer1);
congestion.Update(bendStack.xs, bendStack.len);
break;
}
// stretching is better than bending
else if (bendScore > stretchScore && stretchScore < score)
{
RestoreCoords(stretchStack, buffer2);
congestion.Update(stretchStack.xs, stretchStack.len);
break;
}
}
}
}
