, including all inherited members.
| Add(NxsBlock *newBlock) | NxsReader | [virtual] |
| AddBlockToUsedBlockList(const std::string &, NxsBlock *, NxsToken *) | NxsReader | [protected] |
| AddFactory(NxsBlockFactory *) | PublicNexusReader | [protected, virtual] |
| AddReadAssumptionsBlock(NxsAssumptionsBlock *block) | PublicNexusReader | [inline] |
| AddReadBlock(const NxsString &blockID, NxsBlock *block) | NxsReader | [inline, virtual] |
| AddReadCharactersBlock(NxsCharactersBlock *block) | PublicNexusReader | [inline] |
| AddReadDataBlock(NxsDataBlock *block) | PublicNexusReader | [inline] |
| AddReadDistancesBlock(NxsDistancesBlock *block) | PublicNexusReader | [inline] |
| AddReadTaxaBlock(NxsTaxaBlock *block) | PublicNexusReader | [inline] |
| AddReadTreesBlock(NxsTreesBlock *block) | PublicNexusReader | [inline] |
| AddReadUnalignedBlock(NxsUnalignedBlock *block) | PublicNexusReader | [inline] |
| AddReadUnknownBlock(NxsStoreTokensBlockReader *block) | PublicNexusReader | [inline] |
| AMBIGUOUS_CONTENT_WARNING enum value | NxsReader | |
| AssignBlockPriority(NxsBlock *b, int priorityLevel) | NxsReader | |
| BlockIsASingeltonReader(NxsBlock *) const | NxsReader | [protected] |
| BlockListEmpty() | NxsReader | |
| BlockReadHook(const NxsString &currBlockName, NxsBlock *currBlock, NxsToken *token=NULL) | NxsReader | [protected] |
| ClearContent() | PublicNexusReader | [inline, virtual] |
| ClearUsedBlockList() | PublicNexusReader | [virtual] |
| conversionOutputRecord | PublicNexusReader | |
| CoreExecutionTasks(NxsToken &token, bool notifyStartStop=true) | NxsReader | [protected] |
| CreateBlockFromFactories(const std::string &currBlockName, NxsToken &token, NxsBlockFactory **sourceOfBlock=NULL) | NxsReader | |
| cullIdenticalTaxaBlocks(bool v=true) | NxsReader | [inline] |
| DataFormatType enum name | MultiFormatReader | |
| DebugReportBlock(NxsBlock &nexusBlock) | NxsReader | [virtual] |
| DeleteBlocksFromFactories() | PublicNexusReader | [inline, virtual] |
| DemoteBlocks(int priorityLevel=-1) | NxsReader | |
| DEPRECATED_WARNING enum value | NxsReader | |
| Detach(NxsBlock *newBlock) | NxsReader | |
| EnteringBlock(NxsString blockName) | NxsReader | [virtual] |
| ExceptionRaisingNxsReader(NxsReader::WarningHandlingMode mode=NxsReader::WARNINGS_TO_STDERR) | ExceptionRaisingNxsReader | [inline] |
| Execute(NxsToken &token, bool notifyStartStop=true) | PublicNexusReader | [virtual] |
| ExecuteBlock(NxsToken &token, const NxsString &currBlockName, NxsBlock *currBlock, NxsBlockFactory *sourceOfBlock) | NxsReader | [protected] |
| ExecuteStarting() | NxsReader | [virtual] |
| ExecuteStopping() | NxsReader | [virtual] |
| ExitingBlock(NxsString blockName) | NxsReader | [virtual] |
| FATAL_WARNING enum value | NxsReader | |
| FindBlockByTitle(const BlockReaderList &chosenBlockList, const char *title, unsigned *nMatches) | NxsReader | [protected] |
| FindBlockOfTypeByTitle(const std::string &btype, const char *title, unsigned *nMatches) | NxsReader | [protected] |
| formatNameToCode(const std::string &) | MultiFormatReader | [static] |
| GetAllTitlesForBlock(const NxsBlock *b) const | NxsReader | |
| GetAssumptionsBlock(const NxsTaxaBlock *taxa, unsigned index) const | PublicNexusReader | |
| GetAssumptionsBlockTemplate() | PublicNexusReader | [inline] |
| GetBlockPriority(NxsBlock *b) const | NxsReader | |
| GetBlocksFromLastExecuteInOrder() | NxsReader | [inline] |
| GetCharactersBlock(const NxsTaxaBlock *taxa, unsigned index) const | PublicNexusReader | |
| GetCharactersBlockTemplate() | PublicNexusReader | [inline] |
| GetCharBlockByTitle(const char *title, unsigned *nMatches) | NxsReader | |
| GetDataBlockTemplate() | PublicNexusReader | [inline] |
| GetDistancesBlock(const NxsTaxaBlock *taxa, unsigned index) const | PublicNexusReader | |
| GetDistancesBlockTemplate() | PublicNexusReader | [inline] |
| getFormatNames() | MultiFormatReader | [static] |
| GetLastStoredBlockByID(const std::string &key) | NxsReader | [protected] |
| GetLastStoredCharactersBlock() | NxsReader | |
| GetLastStoredTaxaBlock() | NxsReader | |
| GetLastStoredTreesBlock() | NxsReader | |
| getNCLCatchesSignals() | NxsReader | [static] |
| GetNumAssumptionsBlocks(const NxsTaxaBlock *taxa) const | PublicNexusReader | |
| GetNumAssumptionsBlocks(const NxsCharactersBlock *chars) const | PublicNexusReader | |
| GetNumAssumptionsBlocks(const NxsTreesBlock *trees) const | PublicNexusReader | |
| GetNumCharactersBlocks(const NxsTaxaBlock *taxa) const | PublicNexusReader | |
| GetNumDistancesBlocks(const NxsTaxaBlock *taxa) const | PublicNexusReader | |
| getNumSignalIntsCaught() | NxsReader | [static] |
| GetNumTaxaBlocks() const | PublicNexusReader | |
| GetNumTreesBlocks(const NxsTaxaBlock *taxa) const | PublicNexusReader | |
| GetNumUnalignedBlocks(const NxsTaxaBlock *taxa) const | PublicNexusReader | |
| GetNumUnknownBlocks() const | PublicNexusReader | |
| GetOriginalTaxaBlock(const NxsTaxaBlockAPI *) const | NxsReader | [protected] |
| GetSetOfAllUsedBlocks() | NxsReader | |
| GetTaxaBlock(unsigned index) const | PublicNexusReader | |
| GetTaxaBlockByTitle(const char *title, unsigned *nMatches) | NxsReader | |
| GetTaxaBlockFactory() | NxsReader | [inline] |
| GetTaxaBlockTemplate() | PublicNexusReader | [inline] |
| GetTreesBlock(const NxsTaxaBlock *taxa, unsigned index) const | PublicNexusReader | |
| GetTreesBlockByTitle(const char *title, unsigned *nMatches) | NxsReader | |
| GetTreesBlockTemplate() | PublicNexusReader | [inline] |
| GetUnalignedBlock(const NxsTaxaBlock *taxa, unsigned index) const | PublicNexusReader | |
| GetUnalignedBlockTemplate() | PublicNexusReader | [inline] |
| GetUnknownBlock(unsigned index) const | PublicNexusReader | |
| GetUnknownBlockTemplate() const | PublicNexusReader | [inline] |
| GetUsedBlocks() | NxsReader | [inline] |
| GetUsedBlocksInOrder() | NxsReader | [inline] |
| IGNORE_WARNINGS enum value | NxsReader | |
| ILLEGAL_CONTENT_WARNING enum value | NxsReader | |
| IsRepeatedTaxaBlock(const NxsTaxaBlockAPI *) const | NxsReader | [inline, protected] |
| MultiFormatReader(const int blocksToRead=-1, NxsReader::WarningHandlingMode mode=NxsReader::WARNINGS_TO_STDERR) | MultiFormatReader | [inline] |
| NCLCopyrightNotice() | NxsReader | |
| NCLHomePageURL() | NxsReader | |
| NCLNameAndVersion() | NxsReader | |
| NewBlockTitleCheckHook(const std::string &blockname, NxsBlock *p, NxsToken *token) | NxsReader | [protected] |
| NEXUS_ASSUMPTIONS_BLOCK_BIT enum value | PublicNexusReader | |
| NEXUS_CHARACTERS_BLOCK_BIT enum value | PublicNexusReader | |
| NEXUS_DISTANCES_BLOCK_BIT enum value | PublicNexusReader | |
| NEXUS_SETS_BLOCK_BIT enum value | PublicNexusReader | |
| NEXUS_TREES_BLOCK_BIT enum value | PublicNexusReader | |
| NEXUS_UNALIGNED_BLOCK_BIT enum value | PublicNexusReader | |
| NEXUS_UNKNOWN_BLOCK_BIT enum value | PublicNexusReader | |
| NexusBlocksToRead enum name | PublicNexusReader | |
| NexusError(NxsString msg, file_pos pos, long line, long col) | ExceptionRaisingNxsReader | [inline, virtual] |
| NexusWarn(const std::string &msg, NxsWarnLevel level, file_pos pos, long line, long col) | ExceptionRaisingNxsReader | [virtual] |
| NexusWarnToken(const std::string &m, NxsWarnLevel warnLevel, const ProcessedNxsToken &token) | NxsReader | [inline] |
| NexusWarnToken(const std::string &m, NxsWarnLevel warnLevel, const NxsToken &token) | NxsReader | [inline] |
| NxsReader() | NxsReader | |
| NxsWarnLevel enum name | NxsReader | |
| OutputComment(const NxsString &comment) | NxsReader | [virtual] |
| OVERWRITING_CONTENT_WARNING enum value | NxsReader | |
| parseFileOrThrow(const char *filepath, NxsReader::WarningHandlingMode mode=NxsReader::WARNINGS_TO_STDERR, bool parsePrivateBlocks=true, bool storeTokenInfo=true) | PublicNexusReader | [static] |
| parseFileWithReader(NxsReader &reader, const char *filepath, bool parsePrivateBlocks=true, bool storeTokenInfo=true) | NxsReader | [protected, static] |
| PositionInBlockList(NxsBlock *b) | NxsReader | |
| PostBlockReadingHook(NxsBlock &) | NxsReader | [protected, virtual] |
| PostExecuteHook() | PublicNexusReader | [protected] |
| PROBABLY_INCORRECT_CONTENT_WARNING enum value | NxsReader | |
| PublicNexusReader(const int blocksToRead=-1, NxsReader::WarningHandlingMode mode=NxsReader::WARNINGS_TO_STDERR) | PublicNexusReader | |
| readFastaFile(std::istream &inf, NxsCharactersBlock::DataTypesEnum dt) | MultiFormatReader | |
| ReadFilepath(const char *filepath, const char *formatName) | MultiFormatReader | |
| ReadFilepath(const char *filepath, DataFormatType format) | MultiFormatReader | |
| PublicNexusReader::ReadFilepath(const char *filename) | NxsReader | |
| ReadFilestream(std::istream &inf) | NxsReader | |
| ReadStream(std::istream &inp, const char *formatName) | MultiFormatReader | |
| ReadStream(std::istream &inp, DataFormatType format, const char *filepath=0L) | MultiFormatReader | |
| ReadStringAsNexusContent(const std::string &s) | NxsReader | |
| ReadUntilEndblock(NxsToken &token, const std::string &currBlockName) | NxsReader | [protected] |
| Reassign(NxsBlock *oldb, NxsBlock *newb) | NxsReader | |
| RegisterAltTitle(const NxsBlock *b, std::string t) | NxsReader | [protected] |
| RegisterTaxa(const std::vector< std::string > &tl) | PublicNexusReader | |
| RemoveBlockFromUsedBlockList(NxsBlock *) | NxsReader | |
| RemoveBlocksFromFactoriesFromUsedBlockLists() | NxsReader | [protected] |
| RemoveFactory(NxsBlockFactory *) | NxsReader | |
| SetAlwaysReportStatusMessages(bool v) | NxsReader | [inline] |
| setNCLCatchesSignals(bool) | NxsReader | [static] |
| setNumSignalsIntsCaught(unsigned) | NxsReader | [static] |
| SetTaxaBlockFactory(NxsTaxaBlockFactory *) | NxsReader | |
| SetWarningOutputLevel(NxsWarnLevel lev) | NxsReader | [inline] |
| SetWarningToErrorThreshold(int t) | ExceptionRaisingNxsReader | [inline] |
| SKIPPING_CONTENT_WARNING enum value | NxsReader | |
| SkippingBlock(NxsString blockName) | ExceptionRaisingNxsReader | [virtual] |
| SkippingDisabledBlock(NxsString blockName) | ExceptionRaisingNxsReader | [virtual] |
| statusMessage(const std::string &m) const | NxsReader | [virtual] |
| SUPPRESS_WARNINGS_LEVEL enum value | NxsReader | |
| UNCOMMON_SYNTAX_WARNING enum value | NxsReader | |
| WarningHandlingMode enum name | NxsReader | |
| WARNINGS_ARE_ERRORS enum value | NxsReader | |
| WARNINGS_TO_STDERR enum value | NxsReader | |
| WARNINGS_TO_STDOUT enum value | NxsReader | |
1.6.3
