, including all inherited members.
| AbstractAligner() | AbstractAligner | |
| AbstractDiagonalAligner() | AbstractDiagonalAligner | |
| alignPartition(Partition partition) | AbstractDiagonalAligner | [virtual] |
| clearPrunedBlocks(int b0, int b1)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| clearStatistics() | AbstractDiagonalAligner | [virtual] |
| configureGrid(Partition partition) | AbstractDiagonalAligner | [private] |
| createGrid(Partition partition) | AbstractAligner | [protected] |
| currentExternalDiagonal | AbstractDiagonalAligner | [private] |
| dispatchColumn(int j, const cell_t *buffer, int len) | AbstractAligner | [protected] |
| dispatchRow(int i, const cell_t *buffer, int len) | AbstractAligner | [protected] |
| dispatchScore(score_t score, int bx=-1, int by=-1) | AbstractAligner | [protected] |
| externalDiagonalCount | AbstractDiagonalAligner | [private] |
| finalize()=0 | IAligner | [pure virtual] |
| finalizeDiagonals()=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| finalizeIterations() | AbstractDiagonalAligner | [private] |
| flushBlockScores() | AbstractDiagonalAligner | [private] |
| flushLastCell() | AbstractDiagonalAligner | [private] |
| flushLastColumn() | AbstractDiagonalAligner | [private] |
| flushLastRow() | AbstractDiagonalAligner | [private] |
| flushSpecialRows() | AbstractDiagonalAligner | [private] |
| getBlockHeight()=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| getBlockScores()=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| getCapabilities()=0 | IAligner | [pure virtual] |
| getFirstColumnInitType() | AbstractAligner | [protected] |
| getFirstColumnTail() const | AbstractAligner | [protected] |
| getFirstRowInitType() | AbstractAligner | [protected] |
| getFirstRowTail() const | AbstractAligner | [protected] |
| getForkWeights() | AbstractAligner | [virtual] |
| getGrid() const | AbstractAligner | [protected, virtual] |
| getGridWidth(int width)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| getLastColumn(int i, int len)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| getLastRow(int j, int len)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| getParameters()=0 | IAligner | [pure virtual] |
| getPartition() const | AbstractDiagonalAligner | [protected] |
| getProcessedCells() | AbstractDiagonalAligner | [virtual] |
| getProgressString() const | AbstractDiagonalAligner | [virtual] |
| getRecurrenceType() const | AbstractAligner | [protected] |
| getScoreParameters()=0 | IAligner | [pure virtual] |
| getSpecialColumnInterval() const | AbstractAligner | [protected] |
| getSpecialRow(int j, int len)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| getSpecialRowInterval() const | AbstractAligner | [protected] |
| getSuperPartition() | AbstractAligner | [protected] |
| gridHeight | AbstractDiagonalAligner | [private] |
| gridWidth | AbstractDiagonalAligner | [private] |
| h_loadColumn | AbstractDiagonalAligner | [private] |
| hasMoreIterations() | AbstractDiagonalAligner | [private] |
| IAligner() | IAligner | [inline, protected] |
| initialize()=0 | IAligner | [pure virtual] |
| initializeBlockPruning(AbstractBlockPruning *blockPruner) | AbstractAligner | [protected] |
| initializeDiagonals()=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| isSpecialRow(int by) | AbstractDiagonalAligner | [private] |
| loadFirstColumn() | AbstractDiagonalAligner | [private] |
| loadFirstRow() | AbstractDiagonalAligner | [private] |
| matchLastColumn(const cell_t *buffer, const cell_t *base, int len, int goalScore) | AbstractAligner | [virtual] |
| mustContinue() | AbstractAligner | [protected] |
| mustDispatchLastCell() | AbstractAligner | [protected] |
| mustDispatchLastColumn() | AbstractAligner | [protected] |
| mustDispatchLastRow() | AbstractAligner | [protected] |
| mustDispatchScores() | AbstractAligner | [protected] |
| mustDispatchSpecialColumns() | AbstractAligner | [protected] |
| mustDispatchSpecialRows() | AbstractAligner | [protected] |
| mustPruneBlocks() | AbstractAligner | [protected] |
| partition | AbstractDiagonalAligner | [private] |
| prepareIterations() | AbstractDiagonalAligner | [private] |
| printFinalStatistics(FILE *file) | AbstractDiagonalAligner | [virtual] |
| printInitialStatistics(FILE *file) | AbstractDiagonalAligner | [virtual] |
| printStageStatistics(FILE *file) | AbstractDiagonalAligner | [virtual] |
| printStatistics(FILE *file) | AbstractDiagonalAligner | [virtual] |
| processDiagonal(int diagonal, int windowLeft, int windowRight)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| processNextIteration() | AbstractDiagonalAligner | [private] |
| pruneBlocks() | AbstractDiagonalAligner | [private] |
| pruner | AbstractDiagonalAligner | [private] |
| receiveFirstColumn(cell_t *buffer, int len) | AbstractAligner | [protected] |
| receiveFirstRow(cell_t *buffer, int len) | AbstractAligner | [protected] |
| setFirstColumn(const cell_t *cells, int i, int len)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| setFirstRow(const cell_t *cells, int j, int len)=0 | AbstractDiagonalAligner | [protected, pure virtual] |
| setForkCount(const int forkCount, const int *forkWeights=NULL) | AbstractAligner | [protected] |
| setManager(IManager *manager) | AbstractAligner | [virtual] |
| setSequences(const char *seq0, const char *seq1, int seq0_len, int seq1_len)=0 | IAligner | [pure virtual] |
| statMaxGridWidth | AbstractDiagonalAligner | [private] |
| statMinGridWidth | AbstractDiagonalAligner | [private] |
| statPrunedBlocksLeft | AbstractDiagonalAligner | [private] |
| statPrunedBlocksRight | AbstractDiagonalAligner | [private] |
| statTotalBlocks | AbstractDiagonalAligner | [private] |
| statTotalCells | AbstractDiagonalAligner | [private] |
| unsetSequences()=0 | IAligner | [pure virtual] |
| windowEnd | AbstractDiagonalAligner | [private] |
| windowStart | AbstractDiagonalAligner | [private] |
| ~AbstractAligner() | AbstractAligner | [virtual] |
| ~AbstractDiagonalAligner() | AbstractDiagonalAligner | [virtual] |
| ~IAligner() | IAligner | [inline, protected] |
