PublicNexusReader

AddFactory AddReadAssumptionsBlock AddReadCharactersBlock AddReadDataBlock AddReadDistancesBlock AddReadTaxaBlock AddReadTreesBlock AddReadUnalignedBlock AddReadUnknownBlock ClearContent ClearUsedBlockList conversionOutputRecord DeleteBlocksFromFactories Execute GetAssumptionsBlock GetAssumptionsBlockTemplate GetCharactersBlock GetCharactersBlockTemplate GetDataBlockTemplate GetDistancesBlock GetDistancesBlockTemplate GetNumAssumptionsBlocks GetNumAssumptionsBlocks GetNumAssumptionsBlocks GetNumCharactersBlocks GetNumDistancesBlocks GetNumTaxaBlocks GetNumTreesBlocks GetNumUnalignedBlocks GetNumUnknownBlocks GetTaxaBlock GetTaxaBlockTemplate GetTreesBlock GetTreesBlockTemplate GetUnalignedBlock GetUnalignedBlockTemplate GetUnknownBlock GetUnknownBlockTemplate NEXUS_ASSUMPTIONS_BLOCK_BIT NEXUS_CHARACTERS_BLOCK_BIT NEXUS_DISTANCES_BLOCK_BIT NEXUS_SETS_BLOCK_BIT NEXUS_TREES_BLOCK_BIT NEXUS_UNALIGNED_BLOCK_BIT NEXUS_UNKNOWN_BLOCK_BIT NexusBlocksToRead parseFileOrThrow PostExecuteHook PublicNexusReader RegisterTaxa

PublicNexusReader::PublicNexusReader ( const int  blocksToRead = -1, NxsReader::WarningHandlingMode  warnModeArg = NxsReader::WARNINGS_TO_STDERR   ) Creates a new PublicNexusReader. Creates a reader for the specified blocks. blocksToRead -1 indicates that every block type should be read. alternatively, the caller can OR-together bits of the NexusBlocksToRead enum to indicate which blocks should be processed. mode should be a facet of the NxsReader::WarningHandlingMode enum that indicates where warning messages should be directed. The first argument is integer with bits that is composed of bits from PublicNexusReader::NexusBlocksToRead, indicating which of the public blocks should be read. Either compose the argument by ORing together bits (such as NEXUS_TREES_BLOCK_BIT|NEXUS_TAXA_BLOCK_BIT) or simply pass in -1 to read all public blocks. The "standard" NCL NxsBlock (NxsCharactersBlock, NxsTaxaBlock...) instances will be created as initial clone block templates in the contained NxsCloneBlockFactory. These instances can be altered by using getting pointers to them using the GetAssumptionsBlockTemplate(), GetTaxaBlockTemplate()... methods. Parameters: blocksToRead  integer with bits that is composed of bits from PublicNexusReader::NexusBlocksToRead, indicating which of the public blocks should be read warnModeArg  warning mode (passed to ExceptionRaisingNxsReader::ExceptionRaisingNxsReader() Definition at line 246 of file nxspublicblocks.cpp.