, including all inherited members.
| AddNewCodonPosPartition(const std::string &label, const NxsPartition &inds, bool isDefault) | NxsCharactersBlock | [virtual] |
| AddNewExSet(const std::string &label, const NxsUnsignedSet &inds) | NxsCharactersBlock | [virtual] |
| AddNewIndexSet(const std::string &label, const NxsUnsignedSet &inds) | NxsCharactersBlock | [virtual] |
| AddNewPartition(const std::string &label, const NxsPartition &inds) | NxsCharactersBlock | [virtual] |
| ApplyExset(NxsUnsignedSet &exset) | NxsCharactersBlock | [virtual] |
| ApplyIncludeset(NxsUnsignedSet &inset) | NxsCharactersBlock | |
| AugmentedSymbolsToMixed() | NxsCharactersBlock | |
| CharLabelToNumber(NxsString s) NCL_COULD_BE_CONST | NxsCharactersBlock | [inline, virtual] |
| CharLabelToNumber(const std::string &s) const | NxsCharactersBlock | [virtual] |
| CloneBlock(NxsBlockMapper &memo) const | NxsBlock | [virtual] |
| codon enum value | NxsCharactersBlock | |
| CodonPosPartitionToPosList(const NxsPartition &codonPos, std::list< int > *charIndices) | NxsCharactersBlock | [static] |
| Consume(NxsCharactersBlock &other) | NxsCharactersBlock | |
| continuous enum value | NxsCharactersBlock | |
| DataTypesEnum enum name | NxsCharactersBlock | |
| DebugShowMatrix(std::ostream &out, bool use_matchchar, const char *marginText=NULL) const | NxsCharactersBlock | [virtual] |
| DemandEquals(NxsToken &token, const char *contextString) const | NxsBlock | [inline, protected] |
| DemandIsAtEquals(NxsToken &token, const char *contextString) const | NxsBlock | [protected] |
| DemandPositiveInt(NxsToken &token, const char *contextString) const | NxsBlock | [protected] |
| Disable() | NxsBlock | |
| dna enum value | NxsCharactersBlock | |
| Enable() | NxsBlock | |
| ExcludeCharacter(unsigned i) | NxsCharactersBlock | |
| GenerateNxsException(NxsToken &token, const char *message=NULL) const | NxsBlock | [protected] |
| GenerateUnexpectedTokenNxsException(NxsToken &token, const char *expected=NULL) const | NxsBlock | [protected] |
| GetAllDatatypeMappers() const | NxsCharactersBlock | [inline, virtual] |
| GetAllowAugmentingOfSequenceSymbols() const | NxsCharactersBlock | [inline] |
| GetBlockIDCommandString() const | NxsBlock | [inline] |
| GetCharLabel(unsigned i) const | NxsCharactersBlock | [inline] |
| GetContinuousValues(unsigned taxIndex, unsigned charIndex, const std::string key) NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetDataType() const | NxsCharactersBlock | [inline] |
| GetDatatypeMapForMixedType() const | NxsCharactersBlock | [inline] |
| GetDatatypeName() const | NxsCharactersBlock | [inline] |
| GetDefaultCodonPosPartitionName() const | NxsCharactersBlock | [inline, virtual] |
| GetDiscreteMatrixRow(unsigned taxonIndex) const | NxsCharactersBlock | |
| GetExcludedIndexSet() const | NxsCharactersBlock | [inline] |
| GetGapModeSetting() const | NxsCharactersBlock | [inline, virtual] |
| GetGapSymbol() const | NxsCharactersBlock | [inline] |
| GetID() const | NxsBlock | |
| GetImpliedBlocks() | NxsCharactersBlock | [inline, virtual] |
| GetImpliedBlocksConst() const | NxsBlock | [virtual] |
| GetIndicesForLabel(const std::string &label, NxsUnsignedSet *inds) const | NxsCharactersBlock | [virtual] |
| GetIndicesFromSetOrAsNumber(const std::string &label, NxsUnsignedSet *inds, const NxsUnsignedSetMap &itemSets, const unsigned maxInd, const char *itemType) | NxsLabelToIndicesMapper | [protected, static] |
| GetIndicesFromSets(const std::string &label, NxsUnsignedSet *inds, const NxsUnsignedSetMap &itemSets) | NxsLabelToIndicesMapper | [protected, static] |
| GetInternalRepresentation(unsigned i, unsigned j, unsigned k=0) NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetItems() const | NxsCharactersBlock | [inline] |
| GetMatchcharSymbol() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetMaximalStateSetOfColumn(const unsigned colIndex) const | NxsCharactersBlock | |
| GetMaxObsNumStates(bool countMissingStates=true, bool onlyActiveChars=false) NCL_COULD_BE_CONST | NxsCharactersBlock | [virtual] |
| GetMissingSymbol() const | NxsCharactersBlock | [inline] |
| GetNamedStateSetOfColumn(const unsigned colIndex) const | NxsCharactersBlock | |
| GetNChar() const | NxsCharactersBlock | [inline] |
| GetNCharTotal() const | NxsCharactersBlock | [inline, virtual] |
| GetNexus() const | NxsBlock | [inline] |
| GetNumActiveChar() NCL_COULD_BE_CONST | NxsCharactersBlock | |
| GetNumChar() const | NxsCharactersBlock | [inline] |
| GetNumEliminated() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetNumEquates() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetNumIncludedChars() const | NxsCharactersBlock | [inline] |
| GetNumMatrixCols() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetNumMatrixRows() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetNumObsStates(unsigned columnIndex, bool countMissingStates=true) NCL_COULD_BE_CONST | NxsCharactersBlock | [inline, virtual] |
| GetNumStates(unsigned i, unsigned j) NCL_COULD_BE_CONST | NxsCharactersBlock | |
| GetNumUserEquates() const | NxsCharactersBlock | [inline] |
| GetNxsTransformationManagerRef() const | NxsCharactersBlock | [inline, virtual] |
| GetObsStates(unsigned columnIndex, bool countMissingStates=true) const | NxsCharactersBlock | [inline] |
| GetOriginalDataType() const | NxsCharactersBlock | [inline] |
| GetSimpleContinuousValue(unsigned i, unsigned j) NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetState(unsigned i, unsigned j, unsigned k=0) const | NxsCharactersBlock | [inline] |
| GetStateLabel(unsigned charIndex, unsigned charStateIndex) const | NxsCharactersBlock | [inline] |
| GetStateLabel(unsigned charIndex, unsigned charStateIndex) | NxsCharactersBlock | [inline] |
| GetStatesFormat() const | NxsCharactersBlock | [inline] |
| GetSymbols() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| GetTaxaLinkStatus() const | NxsTaxaBlockSurrogate | [inline] |
| GetTaxonLabel(unsigned i) const | NxsCharactersBlock | [inline] |
| HandleBasicBlockCommands(NxsToken &token) | NxsBlock | [protected] |
| HandleBlockIDCommand(NxsToken &token) | NxsBlock | [virtual] |
| HandleCharlabels(NxsToken &token) | NxsCharactersBlock | [protected] |
| HandleCharstatelabels(NxsToken &token) | NxsCharactersBlock | [protected] |
| HandleDimensions(NxsToken &token, NxsString newtaxaLabel, NxsString ntaxLabel, NxsString ncharLabel) | NxsCharactersBlock | [protected] |
| HandleEliminate(NxsToken &token) | NxsCharactersBlock | [protected] |
| HandleEndblock(NxsToken &token) | NxsBlock | [virtual] |
| HandleFormat(NxsToken &token) | NxsCharactersBlock | [protected, virtual] |
| HandleLinkCommand(NxsToken &token) | NxsCharactersBlock | [inline, virtual] |
| HandleMatrix(NxsToken &token) | NxsCharactersBlock | [protected, virtual] |
| HandleNextTokenState(NxsToken &token, unsigned taxNum, unsigned charNum, NxsDiscreteStateRow &row, NxsDiscreteDatatypeMapper &, const NxsDiscreteStateRow *firstTaxonRow, const NxsString &nameStr) | NxsCharactersBlock | [protected] |
| HandleStatelabels(NxsToken &token) | NxsCharactersBlock | [protected] |
| HandleStdMatrix(NxsToken &token) | NxsCharactersBlock | [protected, virtual] |
| HandleTaxLabels(NxsToken &token) | NxsTaxaBlockSurrogate | [protected, virtual] |
| HandleTitleCommand(NxsToken &token) | NxsBlock | [virtual] |
| HandleTransposedMatrix(NxsToken &token) | NxsCharactersBlock | [protected, virtual] |
| HasCharLabels() const | NxsCharactersBlock | [inline] |
| ImplementsLinkAPI() const | NxsBlock | |
| IncludeCharacter(unsigned i) | NxsCharactersBlock | |
| IsActiveChar(unsigned j) const | NxsCharactersBlock | [inline] |
| IsActiveTaxon(unsigned i) const | NxsTaxaBlockSurrogate | [inline, virtual] |
| IsEliminated(unsigned charIndex) NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| IsEmpty() NCL_COULD_BE_CONST | NxsBlock | |
| IsEnabled() NCL_COULD_BE_CONST | NxsBlock | |
| IsExcluded(unsigned j) const | NxsCharactersBlock | [inline] |
| IsExcluded(unsigned j) | NxsCharactersBlock | [inline] |
| IsGapState(unsigned taxInd, unsigned charInd) NCL_COULD_BE_CONST | NxsCharactersBlock | |
| IsInSymbols(char ch) NCL_COULD_BE_CONST | NxsCharactersBlock | [protected] |
| IsInterleave() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| IsLabels() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| IsMissingState(unsigned i, unsigned j) NCL_COULD_BE_CONST | NxsCharactersBlock | |
| IsPolymorphic(unsigned i, unsigned j) NCL_COULD_BE_CONST | NxsCharactersBlock | |
| IsRespectCase() const | NxsCharactersBlock | [inline, virtual] |
| IsTokens() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| IsTranspose() NCL_COULD_BE_CONST | NxsCharactersBlock | [inline] |
| IsUserSupplied() NCL_COULD_BE_CONST | NxsBlock | |
| mixed enum value | NxsCharactersBlock | |
| NewProteinCharactersBlock(const NxsCharactersBlock *codonBlock, bool mapPartialAmbigToUnknown, bool gapToUnknown, const std::vector< NxsDiscreteStateCell > &aaIndices) | NxsCharactersBlock | [static] |
| nucleotide enum value | NxsCharactersBlock | |
| NxsBlock() | NxsBlock | |
| NxsCharactersBlock(NxsTaxaBlockAPI *tb, NxsAssumptionsBlockAPI *ab) | NxsCharactersBlock | |
| protein enum value | NxsCharactersBlock | |
| Read(NxsToken &token) | NxsCharactersBlock | [protected, virtual] |
| Report(std::ostream &out) NCL_COULD_BE_CONST | NxsCharactersBlock | [virtual] |
| Reset() | NxsCharactersBlock | [virtual] |
| ResetSymbols() | NxsCharactersBlock | [protected] |
| rna enum value | NxsCharactersBlock | |
| SetAllowAugmentingOfSequenceSymbols(bool v) | NxsCharactersBlock | [inline] |
| SetConvertAugmentedToMixed(bool v) | NxsCharactersBlock | [inline] |
| SetGapModeSetting(GapModeEnum m) | NxsCharactersBlock | [inline, virtual] |
| SetGapSymbol(char) | NxsCharactersBlock | [inline] |
| SetImplementsLinkAPI(bool v) | NxsBlock | |
| SetNexus(NxsReader *nxsptr) | NxsCharactersBlock | [inline, virtual] |
| SetSupportMixedDatatype(bool v) | NxsCharactersBlock | [inline] |
| ShowStateLabels(std::ostream &out, unsigned i, unsigned c, unsigned first_taxon) const | NxsCharactersBlock | |
| ShowStates(std::ostream &out, unsigned i, unsigned j) NCL_COULD_BE_CONST | NxsCharactersBlock | [protected] |
| SkippingCommand(NxsString commandName) | NxsBlock | [virtual] |
| TaxonIndHasData(const unsigned ind) const | NxsCharactersBlock | [inline] |
| TaxonLabelToNumber(NxsString s) const | NxsCharactersBlock | [inline, virtual] |
| WasRestrictionDataype() const | NxsCharactersBlock | [inline] |
| WriteAsNexus(std::ostream &out) const | NxsCharactersBlock | [virtual] |
| WriteLinkCommand(std::ostream &out) const | NxsCharactersBlock | [inline, virtual] |
| WriteStates(NxsDiscreteDatum &d, char *s, unsigned slen) NCL_COULD_BE_CONST | NxsCharactersBlock | [protected] |
| ~NxsBlock() | NxsBlock | [virtual] |
1.6.3
