, including all inherited members.
| AbstractAligner() | AbstractAligner | |
| AbstractBlockAligner(AbstractBlockProcessor *blockProcessor=NULL, BlockAlignerParameters *params=NULL) | AbstractBlockAligner | |
| alignBlock(int bx, int by, int i0, int j0, int i1, int j1)=0 | AbstractBlockAligner | [protected, pure virtual] |
| alignBlock(int bx, int by) | AbstractBlockAligner | [protected] |
| alignPartition(Partition partition) | AbstractBlockAligner | [virtual] |
| allocateStructures() | AbstractBlockAligner | [protected, virtual] |
| blockProcessor | AbstractBlockAligner | [private] |
| blockPruner | AbstractBlockAligner | [private] |
| clearStatistics() | AbstractBlockAligner | [virtual] |
| col | AbstractBlockAligner | [protected] |
| configureGrid(Partition partition) | AbstractBlockAligner | [private] |
| createGrid(Partition partition) | AbstractAligner | [protected] |
| deallocateStructures() | AbstractBlockAligner | [protected, virtual] |
| 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] |
| finalize() | AbstractBlockAligner | [virtual] |
| getCapabilities() | AbstractBlockAligner | [virtual] |
| getFirstColumnInitType() | AbstractAligner | [protected] |
| getFirstColumnTail() const | AbstractAligner | [protected] |
| getFirstRowInitType() | AbstractAligner | [protected] |
| getFirstRowTail() const | AbstractAligner | [protected] |
| getForkWeights() | AbstractAligner | [virtual] |
| getGrid() const | AbstractAligner | [protected, virtual] |
| getParameters() | AbstractBlockAligner | [virtual] |
| getProcessedCells() | AbstractBlockAligner | [virtual] |
| getProgressString() const | AbstractBlockAligner | [virtual] |
| getRecurrenceType() const | AbstractAligner | [protected] |
| getScoreParameters() | AbstractBlockAligner | [virtual] |
| getSpecialColumnInterval() const | AbstractAligner | [protected] |
| getSpecialRowInterval() const | AbstractAligner | [protected] |
| getSuperPartition() | AbstractAligner | [protected] |
| grid_scores | AbstractBlockAligner | [private] |
| IAligner() | IAligner | [inline, protected] |
| ignoreBlock(int bx, int by) | AbstractBlockAligner | [protected] |
| increaseBlockStat(const bool pruned) | AbstractBlockAligner | [protected, virtual] |
| initialize() | AbstractBlockAligner | [virtual] |
| initializeBlockPruning(AbstractBlockPruning *blockPruner) | AbstractAligner | [protected] |
| isBlockPruned(int bx, int by) const | AbstractBlockAligner | [protected] |
| isSpecialColumn(int by) | AbstractBlockAligner | [protected] |
| isSpecialRow(int by) | AbstractBlockAligner | [protected] |
| 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] |
| params | AbstractBlockAligner | [private] |
| preferredBlockSize | AbstractBlockAligner | [private] |
| preferredGridSize | AbstractBlockAligner | [private] |
| printFinalStatistics(FILE *file) | AbstractBlockAligner | [virtual] |
| printInitialStatistics(FILE *file) | AbstractBlockAligner | [virtual] |
| printStageStatistics(FILE *file) | AbstractBlockAligner | [virtual] |
| printStatistics(FILE *file) | AbstractBlockAligner | [virtual] |
| processBlock(int bx, int by, int i0, int j0, int i1, int j1) | AbstractBlockAligner | [protected] |
| pruningUpdate(int bx, int by, int score) | AbstractBlockAligner | [private] |
| receiveFirstColumn(cell_t *buffer, int len) | AbstractAligner | [protected] |
| receiveFirstRow(cell_t *buffer, int len) | AbstractAligner | [protected] |
| row | AbstractBlockAligner | [protected] |
| scheduleBlocks(int grid_width, int grid_height)=0 | AbstractBlockAligner | [protected, pure virtual] |
| score_params | AbstractBlockAligner | [private] |
| setForkCount(const int forkCount, const int *forkWeights=NULL) | AbstractAligner | [protected] |
| setManager(IManager *manager) | AbstractAligner | [virtual] |
| setPreferredSizes(int preferredBlockSize, int preferredGridSize) | AbstractBlockAligner | [protected] |
| setSequences(const char *seq0, const char *seq1, int seq0_len, int seq1_len) | AbstractBlockAligner | [virtual] |
| statMaxBlockHeight | AbstractBlockAligner | [private] |
| statMaxBlockWidth | AbstractBlockAligner | [private] |
| statMaxGridHeight | AbstractBlockAligner | [private] |
| statMaxGridWidth | AbstractBlockAligner | [private] |
| statMinBlockHeight | AbstractBlockAligner | [private] |
| statMinBlockWidth | AbstractBlockAligner | [private] |
| statMinGridHeight | AbstractBlockAligner | [private] |
| statMinGridWidth | AbstractBlockAligner | [private] |
| statPrunedBlocks | AbstractBlockAligner | [private] |
| statTotalBlocks | AbstractBlockAligner | [private] |
| unsetSequences() | AbstractBlockAligner | [virtual] |
| ~AbstractAligner() | AbstractAligner | [virtual] |
| ~AbstractBlockAligner() | AbstractBlockAligner | [virtual] |
| ~IAligner() | IAligner | [inline, protected] |
