| AlignmentManager(const SequenceSet *sSet, const AlignmentSet *aSet) | AlignmentManager | |
| AlignmentManager(const SequenceSet *sSet, const AlignmentSet *aSet, const UpdateAlignList &updates) | AlignmentManager | |
| alignmentSet | AlignmentManager | private |
| blaster | AlignmentManager | |
| BlockAlignAllUpdates(void) | AlignmentManager | |
| blockAligner | AlignmentManager | |
| BlockAlignUpdate(BlockMultipleAlignment *single) | AlignmentManager | |
| CalculateRowScoresWithThreader(double weightPSSM) | AlignmentManager | |
| CreateMultipleFromPairwiseWithIBM(const PairwiseAlignmentList &alignments) | AlignmentManager | |
| dependentsVisible | AlignmentManager | mutableprivate |
| ExtendAllUpdates(void) | AlignmentManager | |
| ExtendUpdate(BlockMultipleAlignment *single) | AlignmentManager | |
| GetAlignmentColor(const Sequence *sequence, unsigned int seqIndex, StyleSettings::eColorScheme colorScheme) const | AlignmentManager | |
| GetAlignmentSetDependentSequences(std::vector< const Sequence * > *sequences) const | AlignmentManager | |
| GetAlignmentSetDependentVisibilities(std::vector< bool > *visibilities) const | AlignmentManager | |
| GetCurrentMultipleAlignment(void) const | AlignmentManager | |
| GetStructureProteins(std::vector< const Sequence * > *chains) const | AlignmentManager | |
| GetUpdateSequences(std::list< const Sequence * > *updateSequences) const | AlignmentManager | |
| Init(void) | AlignmentManager | private |
| IsAligned(const Sequence *sequence, unsigned int seqIndex) const | AlignmentManager | |
| IsInAlignment(const Sequence *sequence) const | AlignmentManager | |
| MergeUpdates(const UpdateMap &updates, bool mergeToNeighbor) | AlignmentManager | |
| NewAlignments(const SequenceSet *sSet, const AlignmentSet *aSet) | AlignmentManager | private |
| NewMultipleWithRows(const std::vector< bool > &visibilities) | AlignmentManager | |
| NUpdates(void) const | AlignmentManager | |
| originalMultiple | AlignmentManager | private |
| originalRowOrder | AlignmentManager | private |
| PairwiseAlignmentList typedef | AlignmentManager | |
| PurgeSequence(const MoleculeIdentifier *identifier) | AlignmentManager | |
| RealignAllDependentStructures(bool highlightedOnly) const | AlignmentManager | |
| RealignDependentSequences(BlockMultipleAlignment *multiple, const std::vector< unsigned int > &dependentsToRealign) | AlignmentManager | |
| ReplaceUpdatesInASN(ncbi::objects::CCdd::TPending &newUpdates) const | AlignmentManager | |
| SavePairwiseFromMultiple(const BlockMultipleAlignment *multiple, const std::vector< unsigned int > &rowOrder) | AlignmentManager | |
| SelectionChangedCallback(const std::vector< bool > &original, std::vector< bool > &itemsEnabled) | ShowHideCallbackObject | inlinevirtual |
| sequenceSet | AlignmentManager | private |
| sequenceViewer | AlignmentManager | private |
| ShowHideCallbackFunction(const std::vector< bool > &itemsEnabled) | AlignmentManager | virtual |
| ShowSequenceViewer(bool showNow) const | AlignmentManager | |
| ShowUpdateWindow(void) const | AlignmentManager | |
| ThreadAllUpdates(const ThreaderOptions &options) | AlignmentManager | |
| threader | AlignmentManager | |
| ThreadUpdate(const ThreaderOptions &options, BlockMultipleAlignment *single) | AlignmentManager | |
| UpdateAlignList typedef | AlignmentManager | |
| UpdateMap typedef | AlignmentManager | |
| updateViewer | AlignmentManager | private |
| ~AlignmentManager(void) | AlignmentManager | virtual |
| ~ShowHideCallbackObject(void) | ShowHideCallbackObject | inlinevirtual |
