Uses of Class
CmpSpots.CmpPairSecondary.OptimizedPair

Uses of CmpPairSecondary.OptimizedPair in CmpSpots

Methods in CmpSpots with parameters of type CmpPairSecondary.OptimizedPair

private DbSpot	CmpPairSecondary.findBetterAltPairedSpot(CmpPairSecondary.OptimizedPair op) findBetterAltPairedSpot() - look for better matching landmark set for the p1 spot with a US or AP label in otherSample such that the dP for the new pair is better than the current dP.
private DbSpot	CmpPairSecondary.findOptNNspot(CmpPairSecondary.OptimizedPair op) findBetterAltPairedSpot() - look for better match kAlt in otherSample the dP for the new pair must be better than the old.
private void	CmpPairSecondary.rePairSpotsInAltLMset(CmpPairSecondary.OptimizedPair op) rePairSpotsInAltLMset() - move Gi spot in LM[k] to LM[kAlt] by adjusting pointers and also adjust pairing statistics.