Uses of Class

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.