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

void NxsReader::Execute ( NxsToken &  token, bool  notifyStartStop = true   ) [virtual] Reads the NxsReader data file from the input stream provided by `token'. This function is responsible for reading through the name of a each block. Once it has read a block name, it searches for a block reader to handle reading the remainder of the block's contents. The block object's Read() method is responsible for reading the END or ENDBLOCK command as well as the trailing semicolon. Execute() handles reading comments that are outside of blocks, as well as the initial "#NEXUS" keyword. As discussed in Errors in NEXUS files exceptions raised during parsing result in calls to NexusError() If `notifyStartStop' is false then ExecuteStart and ExecuteStop functions will not to be called. The order of operations is: Read until next Begin command. Search through the registered block instances to find one that returns true from NxsBlock::CanReadBlockType() If none is found then CreateBlockFromFactories is called. If no appropriate block reader has been created, then SkippingBlock hook will be called (and the NxsReader will call ReadUntilEndblock to read until the END of the block before returning to step 1. If an appropriate block reader was found in steps 2 or 3 then ExecuteBlock() will be called. Parameters: token  the token object used to grab NxsReader tokens notifyStartStop  if true, ExecuteStarting and ExecuteStopping will be called Reimplemented in PublicNexusReader. Definition at line 608 of file nxsreader.cpp.