This is the complete list of members for
AbstractAligner, including all inherited members.
| AbstractAligner() | AbstractAligner | |
| alignPartition(Partition partition)=0 | IAligner | [pure virtual] |
| clearStatistics()=0 | IAligner | [pure virtual] |
| createGrid(Partition partition) | AbstractAligner | [protected] |
| 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()=0 | IAligner | [pure virtual] |
| firstColumnTail | AbstractAligner | [private] |
| firstRowTail | AbstractAligner | [private] |
| forkCount | AbstractAligner | [private] |
| forkWeights | AbstractAligner | [private] |
| 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] |
| getParameters()=0 | IAligner | [pure virtual] |
| getProcessedCells()=0 | IAligner | [pure virtual] |
| getProgressString() const =0 | IAligner | [pure virtual] |
| getRecurrenceType() const | AbstractAligner | [protected] |
| getScoreParameters()=0 | IAligner | [pure virtual] |
| getSpecialColumnInterval() const | AbstractAligner | [protected] |
| getSpecialRowInterval() const | AbstractAligner | [protected] |
| getSuperPartition() | AbstractAligner | [protected] |
| grid | AbstractAligner | [private] |
| IAligner() | IAligner | [inline, protected] |
| initialize()=0 | IAligner | [pure virtual] |
| initializeBlockPruning(AbstractBlockPruning *blockPruner) | AbstractAligner | [protected] |
| manager | AbstractAligner | [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] |
| printFinalStatistics(FILE *file)=0 | IAligner | [pure virtual] |
| printInitialStatistics(FILE *file)=0 | IAligner | [pure virtual] |
| printStageStatistics(FILE *file)=0 | IAligner | [pure virtual] |
| printStatistics(FILE *file)=0 | IAligner | [pure virtual] |
| receiveFirstColumn(cell_t *buffer, int len) | AbstractAligner | [protected] |
| receiveFirstRow(cell_t *buffer, int len) | AbstractAligner | [protected] |
| 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] |
| unsetSequences()=0 | IAligner | [pure virtual] |
| ~AbstractAligner() | AbstractAligner | [virtual] |
| ~IAligner() | IAligner | [inline, protected] |
