PublicNexusReader Member List

This is the complete list of members for PublicNexusReader, 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 valueNxsReader
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]
conversionOutputRecordPublicNexusReader
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]
DebugReportBlock(NxsBlock &nexusBlock)NxsReader [virtual]
DeleteBlocksFromFactories()PublicNexusReader [inline, virtual]
DemoteBlocks(int priorityLevel=-1)NxsReader
DEPRECATED_WARNING enum valueNxsReader
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 valueNxsReader
FindBlockByTitle(const BlockReaderList &chosenBlockList, const char *title, unsigned *nMatches)NxsReader [protected]
FindBlockOfTypeByTitle(const std::string &btype, const char *title, unsigned *nMatches)NxsReader [protected]
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]
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 valueNxsReader
ILLEGAL_CONTENT_WARNING enum valueNxsReader
IsRepeatedTaxaBlock(const NxsTaxaBlockAPI *) const NxsReader [inline, protected]
NCLCopyrightNotice()NxsReader
NCLHomePageURL()NxsReader
NCLNameAndVersion()NxsReader
NewBlockTitleCheckHook(const std::string &blockname, NxsBlock *p, NxsToken *token)NxsReader [protected]
NEXUS_ASSUMPTIONS_BLOCK_BIT enum valuePublicNexusReader
NEXUS_CHARACTERS_BLOCK_BIT enum valuePublicNexusReader
NEXUS_DISTANCES_BLOCK_BIT enum valuePublicNexusReader
NEXUS_SETS_BLOCK_BIT enum valuePublicNexusReader
NEXUS_TREES_BLOCK_BIT enum valuePublicNexusReader
NEXUS_UNALIGNED_BLOCK_BIT enum valuePublicNexusReader
NEXUS_UNKNOWN_BLOCK_BIT enum valuePublicNexusReader
NexusBlocksToRead enum namePublicNexusReader
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 nameNxsReader
OutputComment(const NxsString &comment)NxsReader [virtual]
OVERWRITING_CONTENT_WARNING enum valueNxsReader
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 valueNxsReader
PublicNexusReader(const int blocksToRead=-1, NxsReader::WarningHandlingMode mode=NxsReader::WARNINGS_TO_STDERR)PublicNexusReader
ReadFilepath(const char *filename)NxsReader
ReadFilestream(std::istream &inf)NxsReader
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 valueNxsReader
SkippingBlock(NxsString blockName)ExceptionRaisingNxsReader [virtual]
SkippingDisabledBlock(NxsString blockName)ExceptionRaisingNxsReader [virtual]
statusMessage(const std::string &m) const NxsReader [virtual]
SUPPRESS_WARNINGS_LEVEL enum valueNxsReader
UNCOMMON_SYNTAX_WARNING enum valueNxsReader
WarningHandlingMode enum nameNxsReader
WARNINGS_ARE_ERRORS enum valueNxsReader
WARNINGS_TO_STDERR enum valueNxsReader
WARNINGS_TO_STDOUT enum valueNxsReader
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