93 startDiagonal(Seed<TPosition, ChainedSeed> const &seed)  in startDiagonal()
100 endDiagonal(Seed<TPosition, ChainedSeed> const &seed)  in endDiagonal()
108 leftDim0(Seed<TPosition, ChainedSeed> const &seed)  in leftDim0()
116 rightDim0(Seed<TPosition, ChainedSeed> const & seed)  in rightDim0()
124 leftDim1(Seed<TPosition, ChainedSeed> const &seed)  in leftDim1()
131 rightDim1(Seed<TPosition, ChainedSeed> const & seed)  in rightDim1()
139 length(Seed<TPosition, ChainedSeed> const & seed)  in length()
149 setLeftDim0(Seed<TPosition, ChainedSeed> &seed,   in setLeftDim0()
162 setRightDim0(Seed<TPosition,ChainedSeed> & seed,   in setRightDim0()
172 setLeftDim1(Seed<TPosition, ChainedSeed> &seed,   in setLeftDim1()
185 setRightDim1(Seed<TPosition,ChainedSeed> & seed,   in setRightDim1()
204 _getDiagSet(Seed<TPosition,ChainedSeed> const & seed){  in _getDiagSet()
211 _getDiagSet(Seed<TPosition,ChainedSeed> & seed){  in _getDiagSet()
230 appendDiag(Seed<TPosition,ChainedSeed> & seed,   in appendDiag()
231 		   Triple<TPosition, TPosition, TPosition> diag)  in appendDiag()
239 _getFirstDiag(Seed<TPosition,ChainedSeed> & seed){  in _getFirstDiag()
246 _getFirstDiag(Seed<TPosition,ChainedSeed> const & seed){  in _getFirstDiag()
253 _getLastDiag(Seed<TPosition,ChainedSeed> & seed){  in _getLastDiag()
260 _getLastDiag(Seed<TPosition,ChainedSeed> const & seed){  in _getLastDiag()
273 _mergeTwoSeeds(Seed<TPosition, ChainedSeed> &firstSeed,  in _mergeTwoSeeds()
324 _mergeTwoSeeds(Seed<TPosition, ChainedSeed> &firstSeed,   in _mergeTwoSeeds()
385 _mergeTwoSeedsScore(Seed<TPosition, ChainedSeed> &firstSeed,  in _mergeTwoSeedsScore()
456 _mergeTwoSeedsScore(Seed<TPosition, ChainedSeed> &firstSeed,  in _mergeTwoSeedsScore()
529 _setExtendedSeedDimensions(Seed<TPosition, ChainedSeed> & seed,  in _setExtendedSeedDimensions()
583 getAlignment(Seed<TPosition,ChainedSeed> &seed,  in getAlignment()
730 scoreSeed(Seed<TPosition, ChainedSeed> &seed, String<TText> &query, String<TText> &database, Score<…  in scoreSeed()