, including all inherited members.
| active | AlignerManager | [private] |
| aligner | AlignerManager | [private] |
| AlignerManager(IAligner *aligner) | AlignerManager | |
| alignPartition(Partition partition, int startType) | AlignerManager | |
| baseColumn | AlignerManager | [private] |
| baseRow | AlignerManager | [private] |
| bestScoreLastColumn | AlignerManager | [private] |
| bestScoreLastRow | AlignerManager | [private] |
| bestScoreList | AlignerManager | [private] |
| bestScoreLocation | AlignerManager | [private] |
| blockPruning | AlignerManager | [private] |
| blocksFile | AlignerManager | [private] |
| dispatchColumn(int j, const cell_t *buffer, int len) | AlignerManager | [virtual] |
| dispatchRow(int i, const cell_t *buffer, int len) | AlignerManager | [virtual] |
| dispatchScore(score_t score, int bx=-1, int by=-1) | AlignerManager | [virtual] |
| findBestCell(const cell_t *buffer, int len) | AlignerManager | [private] |
| findFullGap(int len, bool openGap, SeekableCellsReader *cellsReader) | AlignerManager | [private] |
| findGoalCell(const cell_t *buffer, cell_t *base, int len, CellsReader *cellsReader) | AlignerManager | [private] |
| firstColumnInitType | AlignerManager | [private] |
| firstColumnReader | AlignerManager | [private] |
| firstRowFile | AlignerManager | [private] |
| firstRowInitType | AlignerManager | [private] |
| firstRowReader | AlignerManager | [private] |
| foundCrosspoint | AlignerManager | [private] |
| gapExtension | AlignerManager | [private] |
| gapOpen | AlignerManager | [private] |
| getBestScoreLastColumn() const | AlignerManager | |
| getBestScoreLastRow() const | AlignerManager | |
| getFirstColumnInitType() | AlignerManager | [virtual] |
| getFirstRowInitType() | AlignerManager | [virtual] |
| getNextCrosspoint() const | AlignerManager | |
| getRecurrenceType() const | AlignerManager | [virtual] |
| getSpecialColumnInterval() const | AlignerManager | [virtual] |
| getSpecialRowInterval() const | AlignerManager | [virtual] |
| getSuperPartition() | AlignerManager | [virtual] |
| goalScore | AlignerManager | [private] |
| goalScoreLocation | AlignerManager | [private] |
| IManager() | IManager | [inline, protected] |
| isFoundCrosspoint() const | AlignerManager | |
| lastColumnPos | AlignerManager | [private] |
| lastColumnReader | AlignerManager | [private] |
| lastColumnWriter | AlignerManager | [private] |
| lastRowPos | AlignerManager | [private] |
| lastRowReader | AlignerManager | [private] |
| lastRowWriter | AlignerManager | [private] |
| match | AlignerManager | [private] |
| mismatch | AlignerManager | [private] |
| mustContinue() | AlignerManager | [virtual] |
| mustDispatchLastCell() | AlignerManager | [virtual] |
| mustDispatchLastColumn() | AlignerManager | [virtual] |
| mustDispatchLastRow() | AlignerManager | [virtual] |
| mustDispatchScores() | AlignerManager | [virtual] |
| mustDispatchSpecialColumns() | AlignerManager | [virtual] |
| mustDispatchSpecialRows() | AlignerManager | [virtual] |
| mustPruneBlocks() | AlignerManager | [virtual] |
| nextCrosspoint | AlignerManager | [private] |
| partition | AlignerManager | [private] |
| receiveFirstColumn(cell_t *buffer, int len) | AlignerManager | [virtual] |
| receiveFirstRow(cell_t *buffer, int len) | AlignerManager | [virtual] |
| recurrenceType | AlignerManager | [private] |
| score_params | AlignerManager | [private] |
| seq0_offset | AlignerManager | [private] |
| seq1_offset | AlignerManager | [private] |
| setBestScoreList(BestScoreList *bestScoreList, const int bestScoreLocation=AT_NOWHERE) | AlignerManager | |
| setBlockPruning(bool blockPruning) | AlignerManager | |
| setBlocksFile(BlocksFile *blocksFile) | AlignerManager | |
| setFirstColumnSource(SeekableCellsReader *firstColumnReader) | AlignerManager | [private] |
| setFirstRowSource(SeekableCellsReader *firstColumnReader) | AlignerManager | [private] |
| setGoalScore(int goalScore, const int goalScoreLocation=AT_NOWHERE) | AlignerManager | |
| setLastColumnDestination(CellsWriter *lastColumnWriter) | AlignerManager | [private] |
| setLastColumnReader(SeekableCellsReader *lastColumnReader) | AlignerManager | |
| setLastRowDestination(CellsWriter *lastRowWriter) | AlignerManager | [private] |
| setLastRowReader(SeekableCellsReader *lastRowReader) | AlignerManager | |
| setPenalties(const int match, const int mismatch, const int gapOpen, const int gapExtension) | AlignerManager | |
| setRecurrenceType(int recurrenceType) | AlignerManager | |
| setSequences(Sequence *seq0, Sequence *seq1, int i0, int j0, int i1, int j1, FILE *stats=NULL) | AlignerManager | |
| setSpecialRowInterval(const int specialRowInterval) | AlignerManager | |
| setSpecialRowsPartition(SpecialRowsPartition *specialRowsPartition) | AlignerManager | |
| setSuperPartition(Partition superPartition) | AlignerManager | |
| specialRowInterval | AlignerManager | [private] |
| specialRowsPartition | AlignerManager | [private] |
| startType | AlignerManager | [private] |
| stopAligner() | AlignerManager | [private] |
| superPartition | AlignerManager | [private] |
| unsetGoalScore() | AlignerManager | |
| unsetSequences() | AlignerManager | |
| unsetSuperPartition() | AlignerManager | |
| ~AlignerManager() | AlignerManager | [virtual] |
| ~IManager() | IManager | [inline, protected] |
