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//
// 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
//
#ifndef NCL_NXSREADER_H
#define NCL_NXSREADER_H
#include "ncl/nxsdefs.h"
#include "ncl/nxsstring.h"
#include "ncl/nxsexception.h"
#include "ncl/nxstoken.h"
class NxsBlock;
class NxsBlockFactory;
class NxsTaxaBlockFactory;
class NxsAssumptionsBlockAPI;
class NxsCharactersBlockAPI;
class NxsTaxaBlockAPI;
class NxsTreesBlockAPI;
typedef std::list<NxsBlock *> BlockReaderList;
typedef std::map<std::string, BlockReaderList> BlockTypeToBlockList;
/*!
This is the class that orchestrates the reading of a NEXUS data file, and so is the central class to NCL.
NxsReader does not call delete on any of the blocks that are added to it via the Add method.
In the "classic" (v2.0) NCL API:
-# An NxsReader is created.
-# pointers to instances of NxsBlocks that are expected to be needed should be added to `blockList' using the
NxsReader::Add() member function.
-# NxsReader::Execute() 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 NxsBlock::Read() method is called.
-# NxsReader::PostBlockReadingHook(NxsBlock) is called after a block is successfully read. This allows one to gather
the parsed data from the NxsBlock. If another block of the same type is encountered, then NxsBlock::Reset()
will be called and the same NxsBlock instance will be used to read the next block.
.
Versions of NCL after 2.0.04 also support a "factory API" augments the former behavior:
-# An NxsReader is created.
-# In addition to NxsBlocks added using the Add method, you can register instances of a NxsBlockFactory using
the NxsReader::AddFactory() method.
-# In the NxsReader::Execute() method, if an appropriate block is not found in the `blockList` then the
the factories are asked to create a block for the current block name. The first non-NULL block pointer
returned is used.
-# PostBlockReadingHook is still called, but blocks created by a factory will not be "recycled" later in the
NxsReader::Execute(), so it is not necessary to pull all of the data out of them.
-#If a block created by a factory is skipped or has an error, then the factory will be notified using
NxsBlockFactory::BlockError(NxsBlock *) or NxsBlockFactory::BlockSkipped(NxsBlock *). In the event of
skipping or an error, NxsReader will never refer to that instance of the factory-created block again.
Hence the base class behavior of BlockError() and BlockSkipped() is to delete the instance.
-# Every time a NxsBlock successfully reads a NEXUS block, the NxsBlock is added to container of "used" blocks.
When a block is Reset() it is removed from this container. NxsReader::GetUsedBlocks() can be called at any
point to get a copy of this container (which maps a block type name to a list of NxsBlock*). This container
thus stores the state of the parsed NEXUS file. If no blocks were recycled (if all of the blocks came from
factories rather than blocks added using NxsReader::Add() method), then the GetUsedBlocks will contain binary
representation of every block parsed.
.
Important: The use of the factories that are supplied with NCL can trigger casts of pointers. This can be unsafe if
you create NxsBlocks that do not have the expected inheritance. For example, if you create a class to
read Taxa blocks, but do NOT derive this class from NxsTaxaBlockAPI then the casts will be unsafe. If you
do this, and you wish to use the factory API then you must write your own factories.
See NCL_TOP/examples/normalizer examples for an example of the factory API (using the MultiFormatReader). In those
examples the PublicNexusReader::PublicNexusReader() constructor is the function that installs the templates for
a clone factory.
\section NexusErrors Errors in NEXUS files
When an illegal construct is found, a NxsException is raised. This exception is caught within NxsReader::Execute
and NxsReader::NexusError is called. This allows subclasses of NxsReader to handle exceptional circumstances by
overriding one function. Whenever you are using a NxsReader instance that is NOT a subclass of ExceptionRaisingNxsReader
this is still the behavior (thus any code that was written to the v2.0 API will still have this behavior).
ExceptionRaisingNxsReader implements NexusError by raising another NxsException. This results in the exception
being propagated to the caller. The newer NxsReader classes (including PublicNexusReader and MultiFormatReader)
are derived from ExceptionRaisingNxsReader. So their Execute methods will also raise NxsExceptions. Deriving a subclass
of these classes and overriding NexusError would prevent this behavior.
The advantage of ExceptionRaisingNxsReader is that one is no longer required to subclass NxsReader to handle errors.
\section signalsection Signal Handling in NCL:
Traditionally, the user of an application can send an SIGINT to cause it to stop. NCL has very limited support
for handling signals, and this support is turned off by default.
If you want NCL to raise an NxsSignalCanceledParseException if a signal is encountered during a parse then call:
NxsReader::setNCLCatchesSignals(true);
before calling Execute on your NxsReader instance. Note that only the slowly-parsed blocks (TREES and CHARACTERS) and
the NxsReader currently check to see if a signal has been caught. So the NxsSignalCanceledParseException will often
have a generic message indicating that the signal was caught during the parse.
The NCL signal handler is only installed during NxsReader::Execute calls!
Note: that if you want your program to exit on SIGINT, you can leave the signal handling turned off. If you do turn
NCL's signal handling on, then after you do your apps clean up you'll have to exit by something like this:
signal(SIGINT, SIG_DFL);
kill(getpid(), SIGINT);
\see http://www.cons.org/cracauer/sigint.html
*/
class NxsReader
{
static void installNCLSignalHandler();
static void uninstallNCLSignalHandler();
public:
/** Enum of arguments for ExceptionRaisingNxsReader ctor */
enum WarningHandlingMode
{
IGNORE_WARNINGS, /**< warnings that are not error-generating are ignored silently */
WARNINGS_TO_STDERR, /**< warnings that are not error-generating are written to standard error stream */
WARNINGS_TO_STDOUT, /**< warnings that are not error-generating are written to standard output stream */
WARNINGS_ARE_ERRORS /**< warnings that are not error-generating by some other mechanism are still converted to NxsException objects */
};
/** Enum different levels of warnings. See NxsReader::SetWarningOutputLevel*/
enum NxsWarnLevel
{ //TODO: we need another warning level for status messages.
UNCOMMON_SYNTAX_WARNING = 0, /**< Legal but uncommon syntax that could indicate a typo */
SKIPPING_CONTENT_WARNING = 1, /**< Content is being skipped by NCL */
OVERWRITING_CONTENT_WARNING = 2, /**< New content is replacing old information (eg. CharSets with the same name as a previously defined CharSet)*/
DEPRECATED_WARNING = 3, /**< Use of a deprecated feature */
AMBIGUOUS_CONTENT_WARNING = 4, /**< commands that could have multiple plausible interpretations */
ILLEGAL_CONTENT_WARNING = 5, /**< content that violates NEXUS rules, but is still parseable (eg. CharPartitions that only have some of the characters)*/
PROBABLY_INCORRECT_CONTENT_WARNING = 6, /**< Severe Warning that is generated when the file contains characters that should almost certainly be removed */
FATAL_WARNING = 7, /**< a higher warning level then any of the warning generated by NCL. Primarily used in constructs such as (FATAL_WARNING - 1) to mean only the most severe warnings.*/
SUPPRESS_WARNINGS_LEVEL = 8 /**< if the NxsReader's warning level is set to this, then warnings will be suppressed */
};
/*! If true then NCL will call a handler function if signals are encountered during NxsReader::Execute
(signal handling is off by default).
\sa The section on signal handling \ref signalsection
*/
static void setNCLCatchesSignals(bool);
/*! \returns true if NCL will call a handler function if signals are encountered during NxsReader::Execute
(signal handling is off by default).
\sa The section on signal handling \ref signalsection
*/
static bool getNCLCatchesSignals();
/*! Usually used internally when signal catching is enabled. If the number of sigints has changed, since the last
call, then NCL has detected a signal.
\sa The section on signal handling \ref signalsection
*/
static unsigned getNumSignalIntsCaught();
/*! Used internally. If NCL is handling SIGINTs then this will be incremented with every SIGINT.
\sa The section on signal handling \ref signalsection
*/
static void setNumSignalsIntsCaught(unsigned);
NxsReader();
virtual ~NxsReader();
// functions to add and remove Block reader objects or factories for block readers.
virtual void Add(NxsBlock *newBlock);
void Detach(NxsBlock *newBlock);
virtual void AddFactory(NxsBlockFactory *);
void RemoveFactory(NxsBlockFactory *);
// trigger for NEXUS parsing.
virtual void Execute(NxsToken& token, bool notifyStartStop = true);
// shortcuts for calling execute...
void ReadFilepath(const char *filename);
void ReadFilestream(std::istream & inf);
void ReadStringAsNexusContent(const std::string & s);
virtual void DebugReportBlock(NxsBlock &nexusBlock);
const char *NCLNameAndVersion();
const char *NCLCopyrightNotice();
const char *NCLHomePageURL();
// hooks for subclasses to specialize the behavior
virtual void ExecuteStarting();
virtual void ExecuteStopping();
virtual bool EnteringBlock(NxsString blockName);
virtual void ExitingBlock(NxsString blockName);
virtual void OutputComment(const NxsString &comment);
virtual void SkippingDisabledBlock(NxsString blockName);
virtual void SkippingBlock(NxsString blockName);
/*! This hook is called by the block readers when they encounter content
that is interpretable but is questionable (or even illegal according
to the NEXUS standard).
The default NexusWarn behavior is to generate a NexusException for any
warnLevel >= PROBABLY_INCORRECT_CONTENT_WARNING
and to ignore all other warnings.
*/
virtual void NexusWarn(const std::string &s, NxsWarnLevel warnLevel, file_pos pos, long line, long col)
{
if (warnLevel >= PROBABLY_INCORRECT_CONTENT_WARNING)
{
NxsString e(s.c_str());
throw NxsException(e, pos, line, col);
}
}
/*! Used internally as a more convenient way of calling NexusWarn */
void NexusWarnToken(const std::string &m, NxsWarnLevel warnLevel, const ProcessedNxsToken &token)
{
NexusWarn(m , warnLevel, token.GetFilePosition(), token.GetLineNumber(), token.GetColumnNumber());
}
/*! Used internally as a more convenient way of calling NexusWarn */
void NexusWarnToken(const std::string &m, NxsWarnLevel warnLevel, const NxsToken &token)
{
NexusWarn(m , warnLevel, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
}
/*! Called when a erron is detected */
virtual void NexusError(NxsString msg, file_pos pos, long line, long col);
virtual void ClearUsedBlockList();
NxsBlock *CreateBlockFromFactories(const std::string & currBlockName, NxsToken &token, NxsBlockFactory **sourceOfBlock = NULL);
BlockReaderList GetUsedBlocksInOrder();
BlockReaderList GetBlocksFromLastExecuteInOrder();
BlockTypeToBlockList GetUsedBlocks();
std::set<NxsBlock*> GetSetOfAllUsedBlocks();
NxsTaxaBlockAPI *GetLastStoredTaxaBlock();
NxsCharactersBlockAPI *GetLastStoredCharactersBlock();
NxsTreesBlockAPI *GetLastStoredTreesBlock();
NxsTaxaBlockAPI *GetTaxaBlockByTitle(const char *title, unsigned *nMatches);
NxsCharactersBlockAPI *GetCharBlockByTitle(const char *title, unsigned *nMatches);
NxsTreesBlockAPI *GetTreesBlockByTitle(const char *title, unsigned *nMatches);
NxsTaxaBlockFactory *GetTaxaBlockFactory();
//NxsCharactersBlockFactory *GetCharBlockFactory();
//NxsTreesBlockFactory *GetTreesBlockFactory();
void SetTaxaBlockFactory(NxsTaxaBlockFactory *);
//void SetCharBlockFactory(NxsCharactersBlockFactory *);
//void SetTreesBlockFactory(NxsTreesBlockFactory *);
virtual void DeleteBlocksFromFactories();
unsigned RemoveBlockFromUsedBlockList(NxsBlock *);
/*! throws away references to all blocks that that have been read. If the block
was registered with the reader, then "Reset" is called on the block.
If the block came from a factory then the reference to the block is
removed from the reader (resulting in a memory leak if the client
code does not delete the block).
This can be called if the client would like to store the information
from the NEXUS file, and get rid of the blocks to save memory (but
still maintain things like factories that were registered with the
NxsReader and tweaks to the default settings).
*/
virtual void ClearContent();
/*!
This function is useful after ClearContext() has been called.
Instances of blocks that have been read can be registered with reader
so that future NEXUS files can be parsed with the context of those blocks.
For example one might want to reregister a NxsTaxaBlock before reading
a trees file, then you could call:
reader->AddReadBlock("TAXA", taxaB);
NOTE: if you are using a PublicNexusReader, or MultiFormatReader
you should almost certainly call the type-specific forms such as
reader->AddReadTaxaBlock(taxaB);
*/
virtual void AddReadBlock(const NxsString &blockID, NxsBlock *block)
{
this->BlockReadHook(blockID, block);
}
/*! Call cullIdenticalTaxaBlocks(true) before reading a file if you want
the reader to discard a TaxaBlock that is identical to a previous
taxa block. Use of this assumes that the reader of taxa blocks is
a NxsTaxaBlockAPI instance.
\warning: this function should only be called if you have registered
a NxsTaxaBlockFactory. The culling of blocks WILL CALL DELETE
on them.
*/
void cullIdenticalTaxaBlocks(bool v=true)
{
this->destroyRepeatedTaxaBlocks = v;
}
std::vector<std::string> GetAllTitlesForBlock(const NxsBlock *b) const;
/*! Passing true to this method is a hacky way to enable all status messages while still filtering
NexusWarn messages.
*/
void SetAlwaysReportStatusMessages(bool v) {
this->alwaysReportStatusMessages = v;
}
/*! The reader's currentWarningLevel is set here.
By default this field is set to UNCOMMON_SYNTAX_WARNING.
By setting it to any other facet of NxsWarnLevel you can reduce the
number of warnings sent to std::cerr.
The warning level is checked in ExceptionRaisingNxsReader::NexusWarn
and NxsReader::statusMessage.
If the level of the message is greater or equal to the readers level
then the message will be sent to std::cerr
By calling SetWarningOutputLevel(SUPPRESS_WARNINGS_LEVEL) you can
make the reader ignore warnings.
\note if alwaysReportStatusMessages then NxsReader::statusMessage
will report all messages
*/
void SetWarningOutputLevel(NxsWarnLevel lev) {
currentWarningLevel = lev;
}
NxsWarnLevel GetWarningOutputLevel() const {
return currentWarningLevel;
}
/*! Messages about the status processing a file (such as "Executing...")
are sent here. If the reader's currentWarningLevel is set to the lowest
level (UNCOMMON_SYNTAX_WARNING) then these messages will show up in stderr.
*/
virtual void statusMessage(const std::string & m) const;
/*! \deprecated This function is almost never needed.
\returns if true no blocks have registered as readers (does not indicate
whether content has been read, nor does it indicate if any
factories have been added).
*/
bool BlockListEmpty();
unsigned PositionInBlockList(NxsBlock *b);
void Reassign(NxsBlock *oldb, NxsBlock *newb);
/*! The block `b` will be given a priority level of `priorityLevel`
By default all blocks have priority level of 0. Lowering a blocks
priority level below 0, means that a Get....ByTitle() function
will not return the block if it finds a matching block that has
a higher priority
If you are re-using blocks (if you are not using the v2.1 API) be
aware that if a block has a low (negative) priority, but is then
used to read content then its priority will be bumped back up to 0.
The block priority affects calls Get...ByTitle() functions and
Find...ByTitle() functions.
This function is mainly used to "demote" NxsTaxaBlock instances so that they
will not clash with a TAXA block found in the file. \ref TaxaBlockClashes
*/
void AssignBlockPriority(NxsBlock *b, int priorityLevel);
/*! Returns the block priority for a block (or 0 if the block instance is unknown) */
int GetBlockPriority(NxsBlock *b) const;
/*! Lowers the priority of all read blocks to `priorityLevel` */
void DemoteBlocks(int priorityLevel=-1);
protected:
/*! A convenience function to allow one to quickly get a list of block reader
that were generated (or used) in reading a filepath */
static BlockReaderList parseFileWithReader(NxsReader & reader, const char *filepath, bool parsePrivateBlocks=true, bool storeTokenInfo=true);
static bool nclCatchesSignals; // default False;
typedef void (*SignalHandlerFuncPtr) (int);
static SignalHandlerFuncPtr prevSignalCatcher; // the signal handler that was installed before NCL's signal handler
static unsigned numSigIntsCaught;
static bool prevSignalStored ;
void CoreExecutionTasks(NxsToken& token, bool notifyStartStop = true);
void AddBlockToUsedBlockList(const std::string &, NxsBlock *, NxsToken *);
bool BlockIsASingeltonReader(NxsBlock *) const ;
void BlockReadHook(const NxsString &currBlockName, NxsBlock *currBlock, NxsToken *token = NULL );
bool ExecuteBlock(NxsToken &token, const NxsString &currBlockName, NxsBlock *currBlock, NxsBlockFactory * sourceOfBlock);
NxsBlock *FindBlockOfTypeByTitle(const std::string &btype, const char *title, unsigned *nMatches);
NxsBlock *FindBlockByTitle(const BlockReaderList & chosenBlockList, const char *title, unsigned *nMatches);
BlockReaderList FindAllBlocksByTitle(const BlockReaderList & chosenBlockList, const char *title);
NxsBlock *GetLastStoredBlockByID(const std::string &key);
NxsTaxaBlockAPI *GetOriginalTaxaBlock(const NxsTaxaBlockAPI *) const;
bool IsRepeatedTaxaBlock(const NxsTaxaBlockAPI *) const;
void NewBlockTitleCheckHook(const std::string &blockname, NxsBlock *p, NxsToken *token);
bool ReadUntilEndblock(NxsToken &token, const std::string & currBlockName);
void RegisterAltTitle(const NxsBlock * b, std::string t);
std::set<NxsBlock *> RemoveBlocksFromFactoriesFromUsedBlockLists();
virtual void PostBlockReadingHook(NxsBlock &);
NxsBlock *blockList; /* pointer to first block in list of blocks */
NxsBlock *currBlock; /* pointer to current block in list of blocks */
typedef std::list<NxsBlockFactory *> BlockFactoryList;
NxsTaxaBlockFactory *taxaBlockFactory;
BlockFactoryList factories; /* list of pointers to factories capable of creating NxsBlock objects*/
bool destroyRepeatedTaxaBlocks;
NxsWarnLevel currentWarningLevel;
bool alwaysReportStatusMessages;
private:
BlockReaderList FindAllBlocksByTitleNoPrioritization(const BlockReaderList & chosenBlockList, const char *title);
BlockReaderList blocksInOrder;
std::map<NxsBlock *, int> blockPriorities;
BlockReaderList lastExecuteBlocksInOrder;
BlockTypeToBlockList blockTypeToBlockList;
typedef std::pair<unsigned, std::list<std::string> > NxsBlockTitleHistory;
typedef std::map<std::string, NxsBlockTitleHistory > NxsBlockTitleHistoryMap;
NxsBlockTitleHistoryMap blockTitleHistoryMap;
std::map<const NxsBlock *, std::list<std::string> > blockTitleAliases; // to deal with culling blocks and then using the titles of culled copies
};
typedef NxsBlock NexusBlock;
typedef NxsReader Nexus;
/*! A subclass of NxsReader that is used in much of NCL v2.1.
The NexusError function raises a NxsException so that all errors are treated
as parse-ending conditions that the caller of Execute must handle.
See \ref NexusErrors
*/
class ExceptionRaisingNxsReader : public NxsReader
{
public:
/*! The `warnMode` argument should be a facet of NxsReader::WarningHandlingMode
this arguments determines what happens to warnings which are NOT converted
to exceptions -- by default only content that is probably incorrect will
be converted to a NxsException -- see ::SetWarningToErrorThreshold().
*/
ExceptionRaisingNxsReader(NxsReader::WarningHandlingMode mode=NxsReader::WARNINGS_TO_STDERR)
:warnMode(mode),
warningToErrorThreshold(PROBABLY_INCORRECT_CONTENT_WARNING)
{}
/*! Raise a NxsException. */
void NexusError(NxsString msg, file_pos pos, long line, long col)
{
throw NxsException(msg, pos, line, col);
}
virtual void NexusWarn(const std::string & msg, NxsWarnLevel level, file_pos pos, long line, long col);
void SkippingBlock(NxsString blockName);
void SkippingDisabledBlock(NxsString blockName);
/*! Sets the threshold for converting a warning into an error. This
is useful for making the parser stricter.
Argument should be a facet of NxsReader::NxsWarnLevel.
Overrides the default setting of PROBABLY_INCORRECT_CONTENT_WARNING
*/
void SetWarningToErrorThreshold(int t)
{
warningToErrorThreshold = t;
}
virtual void ClearContent()
{
NxsReader::ClearContent();
}
private:
NxsReader::WarningHandlingMode warnMode;
int warningToErrorThreshold;
};
/*! A subclass of NxsReader that is used preserves the same output style as version 2.0, but
allows for more flexibility in the streams that are used for output.
Messages from SkippingBlock, SkippingDisabledBlock, and Warnings are sent to the outstream
Warnings and Errors are written to the errstream
*/
class DefaultErrorReportNxsReader : public NxsReader
{
public:
static BlockReaderList parseFile(const char *filepath, std::ostream * stdOutstream, std::ostream * errOutstream, bool parsePrivateBlocks=true, bool storeTokenInfo=true);
/*! creates an instance that will write messages to the specified streams */
DefaultErrorReportNxsReader(std::ostream * stdOutstream, /*!< outputstream */
std::ostream * errOutstream) /*!< error stream */
:NxsReader(),
stdOut(stdOutstream),
errOut(errOutstream)
{
}
virtual ~DefaultErrorReportNxsReader() {}
/*! \returns true. silent */
virtual bool EnteringBlock(NxsString )
{
return true;
}
/*! writes a message to output */
void SkippingBlock(NxsString blockName)
{
if (stdOut != 0L)
{
*stdOut << "[!Skipping unknown block (" << blockName << ")...]\n";
stdOut->flush();
}
}
/*! writes a message to output */
void SkippingDisabledBlock(NxsString blockName)
{
if (stdOut != 0L)
{
*stdOut << "[!Skipping disabled block (" << blockName << ")...]\n";
stdOut->flush();
}
}
/*! writes a message to output and the error stream if the warnLevel >= currentWarningLevel
If the message is = PROBABLY_INCORRECT_CONTENT_WARNING (and the reader is not
ignoring warnings, a NxsException will be raised.
*/
void NexusWarn(const std::string & msg, /*!< description of the warning */
NxsWarnLevel warnLevel, /*!< severity of the warning*/
file_pos pos, long line, long col)
{
if (warnLevel < currentWarningLevel)
return;
if (warnLevel >= PROBABLY_INCORRECT_CONTENT_WARNING)
{
NxsString e(msg.c_str());
throw NxsException(e, pos, line, col);
}
if (errOut != 0)
{
*errOut << "\nWarning: ";
if (line > 0 || pos > 0)
*errOut << "at line " << line << ", column " << col << " (file position " << pos << "):\n";
*errOut << msg << std::endl;
}
else if (stdOut != 0L)
{
*stdOut << "\nWarning: ";
if (line > 0 || pos > 0)
*stdOut << "at line " << line << ", column " << col << " (file position " << pos << "):\n";
*stdOut << msg << std::endl;
}
}
/*! Raises a NxsException.
*/
void NexusError(NxsString msg, file_pos pos, long line, long col)
{
NexusWarn(msg, NxsReader::FATAL_WARNING, pos, line, col);
throw NxsException(msg, pos, line, col);
}
std::ostream * stdOut;
std::ostream * errOut;
};
/*!
Returns a map from all block ids that have been read to all instances that the NxsReader knows have been read and
have NOT been cleared.
NOTE: If the factory interface to NCL is not being used this may not be a complete list of all of the blocks that
have been read!!!
*/
inline BlockTypeToBlockList NxsReader::GetUsedBlocks()
{
return blockTypeToBlockList;
}
/*! Convenience function to get the factory for NxsTaxaBlocks */
inline bool NxsReader::IsRepeatedTaxaBlock(const NxsTaxaBlockAPI * testB) const
{
return (GetOriginalTaxaBlock(testB) != NULL);
}
/*! Returns a list of all blocks that the NxsReader knows have been read and have NOT been cleared.
If a block has been "implied" by another block then the implied block will appear before the
explicit block.
*/
inline BlockReaderList NxsReader::GetUsedBlocksInOrder()
{
return blocksInOrder;
}
/*! Similar to NxsReader::GetUsedBlocksInOrder, except this list of blocks is cleared at the beginning
of each NxsReader::Execute or (NxsReader::Read...) call. So the list returned list will
only reflect blocks from the last execution operation.
If a block has been "implied" by another block then the implied block will appear before the
explicit block.
*/
inline BlockReaderList NxsReader::GetBlocksFromLastExecuteInOrder()
{
return lastExecuteBlocksInOrder;
}
/*! Convenience function to get the factory for NxsTaxaBlocks */
inline NxsTaxaBlockFactory * NxsReader::GetTaxaBlockFactory()
{
return this->taxaBlockFactory;
}
#endif
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