NxsReader

Add AddBlockToUsedBlockList AddFactory AddReadBlock AMBIGUOUS_CONTENT_WARNING AssignBlockPriority BlockIsASingeltonReader BlockListEmpty BlockReadHook ClearContent ClearUsedBlockList CoreExecutionTasks CreateBlockFromFactories cullIdenticalTaxaBlocks DebugReportBlock DeleteBlocksFromFactories DemoteBlocks DEPRECATED_WARNING Detach EnteringBlock Execute ExecuteBlock ExecuteStarting ExecuteStopping ExitingBlock FATAL_WARNING FindBlockByTitle FindBlockOfTypeByTitle GetAllTitlesForBlock GetBlockPriority GetBlocksFromLastExecuteInOrder GetCharBlockByTitle GetLastStoredBlockByID GetLastStoredCharactersBlock GetLastStoredTaxaBlock GetLastStoredTreesBlock getNCLCatchesSignals getNumSignalIntsCaught GetOriginalTaxaBlock GetSetOfAllUsedBlocks GetTaxaBlockByTitle GetTaxaBlockFactory GetTreesBlockByTitle GetUsedBlocks GetUsedBlocksInOrder IGNORE_WARNINGS ILLEGAL_CONTENT_WARNING IsRepeatedTaxaBlock NCLCopyrightNotice NCLHomePageURL NCLNameAndVersion NewBlockTitleCheckHook NexusError NexusWarn NexusWarnToken NexusWarnToken NxsReader NxsWarnLevel OutputComment OVERWRITING_CONTENT_WARNING parseFileWithReader PositionInBlockList PostBlockReadingHook PROBABLY_INCORRECT_CONTENT_WARNING ReadFilepath ReadFilestream ReadStringAsNexusContent ReadUntilEndblock Reassign RegisterAltTitle RemoveBlockFromUsedBlockList RemoveBlocksFromFactoriesFromUsedBlockLists RemoveFactory SetAlwaysReportStatusMessages setNCLCatchesSignals setNumSignalsIntsCaught SetTaxaBlockFactory SetWarningOutputLevel SKIPPING_CONTENT_WARNING SkippingBlock SkippingDisabledBlock statusMessage SUPPRESS_WARNINGS_LEVEL UNCOMMON_SYNTAX_WARNING WarningHandlingMode WARNINGS_ARE_ERRORS WARNINGS_TO_STDERR WARNINGS_TO_STDOUT

NxsTaxaBlockAPI * NxsReader::GetOriginalTaxaBlock ( const NxsTaxaBlockAPI *  testB  )  const [protected] Returns: a pointer to a previously process NxsTaxaBlock with the same taxon labels. The comparison of labels is case-insensitive and not affected by the ordering of taxa within the block. TAXA blocks are often repeated in sets of NEXUS files (because a bare TREES block constitutes an illegal NEXUS file, and because NCL spawns implied Taxa blocks if it reads just a Trees block). If NxsReader::cullIdenticalTaxaBlocks(true) has been called then NxsReader::GetOriginalTaxaBlock will be called as part of determining whether or not a taxa block should be deleted. Warning: : this is a hole in the const-correctness because the caller could (but shouldn't modify the Taxa block). Definition at line 792 of file nxsreader.cpp.