| // Copyright (C) 1999-2003 Paul O. Lewis | |
| // | |
| // This file is part of NCL (Nexus Class Library) version 2.0. | |
| // | |
| // NCL is free software; you can redistribute it and/or modify | |
| // it under the terms of the GNU General Public License as published by | |
| // the Free Software Foundation; either version 2 of the License, or | |
| // (at your option) any later version. | |
| // | |
| // NCL is distributed in the hope that it will be useful, | |
| // but WITHOUT ANY WARRANTY; without even the implied warranty of | |
| // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | |
| // GNU General Public License for more details. | |
| // | |
| // You should have received a copy of the GNU General Public License | |
| // along with NCL; if not, write to the Free Software Foundation, Inc., | |
| // 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA | |
| // | |
| /*---------------------------------------------------------------------------------------------------------------------- | |
| | This is the class that orchestrates the reading of a NEXUS data file. An object of this class should be created, | |
| | and objects of any block classes that are expected to be needed should be added to `blockList' using the Add | |
| | member function. The Execute member function is then called, which reads the data file until encountering a block | |
| | name, at which point the correct block is looked up in `blockList' and that object's Read method called. | |
| */ | |
| class NxsReader | |
| { | |
| public: | |
| enum NxsTolerateFlags /* Flags used with data member tolerate used to allow some flexibility with respect to the NEXUS format */ | |
| { | |
| allowMissingInEquate = 0x0001, /* if set, equate symbols are allowed for missing data symbol */ | |
| allowPunctuationInNames = 0x0002 /* if set, some punctuation is allowed within tokens representing labels for taxa, characters, and sets */ | |
| }; | |
| NxsReader(); | |
| virtual ~NxsReader(); | |
| bool BlockListEmpty(); | |
| unsigned PositionInBlockList(NxsBlock *b); | |
| void Add(NxsBlock *newBlock); | |
| void Detach(NxsBlock *newBlock); | |
| void Reassign(NxsBlock *oldb, NxsBlock *newb); | |
| void Execute(NxsToken& token, bool notifyStartStop = true); | |
| virtual void DebugReportBlock(NxsBlock &nexusBlock); | |
| const char *NCLNameAndVersion(); | |
| const char *NCLCopyrightNotice(); | |
| const char *NCLHomePageURL(); | |
| virtual void ExecuteStarting(); | |
| virtual void ExecuteStopping(); | |
| virtual bool EnteringBlock(NxsString blockName); | |
| virtual void ExitingBlock(NxsString blockName); | |
| virtual void OutputComment(const NxsString &comment); | |
| virtual void NexusError(NxsString msg, file_pos pos, long line, long col); | |
| virtual void SkippingDisabledBlock(NxsString blockName); | |
| virtual void SkippingBlock(NxsString blockName); | |
| protected: | |
| NxsBlock *blockList; /* pointer to first block in list of blocks */ | |
| NxsBlock *currBlock; /* pointer to current block in list of blocks */ | |
| }; | |
| typedef NxsBlock NexusBlock; | |
| typedef NxsReader Nexus; | |