C++ NxsToken::GetNextToken方法代码示例

/*----------------------------------------------------------------------------------------------------------------------
|	This function provides the ability to read everything following the block name (which is read by the NxsReader 
|	object) to the END or ENDBLOCK statement. Characters are read from the input stream `in'. Overrides the pure 
|	virtual function in the base class.
*/
void NxsEmptyBlock::Read(
  NxsToken &token)	/* the token used to read from `in'*/
	{
	isEmpty = false;

	// This should be the semicolon after the block name
	//
	token.GetNextToken();

	if (!token.Equals(";"))
		{
		errormsg = "Expecting ';' after ";
		errormsg += id;
		errormsg += " block name, but found ";
		errormsg += token.GetToken();
		errormsg += " instead";
		throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
		}

	for(;;)
		{
		token.GetNextToken();

		if (token.Equals("END"))
			{
			HandleEndblock(token);
			break;
			}

		else if(token.Equals("ENDBLOCK"))
			{
			HandleEndblock(token);
			break;
			}

		else
			{
			SkippingCommand(token.GetToken());

			do
				{
				token.GetNextToken();
				}
			while (!token.AtEOF() && !token.Equals(";"));

			if (token.AtEOF())
				{
				errormsg = "Unexpected end of file encountered";
				throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
				}
			}
		}
	}

/*!
	Called from HandleMatrix function to read in the next state. Returns true if next token encountered is a comma,
	false otherwise. A comma signals the end of data for the current taxon in an UNALIGNED block.
*/
bool NxsUnalignedBlock::HandleNextState(
  NxsToken & token,			/* is the token used to read from `in' */
  unsigned taxNum,				/* is the row in range [0..ntax) (used for error reporting only) */
  unsigned charNum,				/* is the column (used for error reporting only) */
  NxsDiscreteStateRow & row, const NxsString &nameStr)	/* is the container for storing new state */
	{
	token.SetLabileFlagBit(NxsToken::parentheticalToken);
	token.SetLabileFlagBit(NxsToken::curlyBracketedToken);
	token.SetLabileFlagBit(NxsToken::singleCharacterToken);

	token.GetNextToken();

	if (token.Equals(",") || token.Equals(";"))
		return false;
	const NxsString stateAsNexus = token.GetToken();
	const NxsDiscreteStateCell stateCode = mapper.EncodeNexusStateString(stateAsNexus, token, taxNum, charNum, NULL, nameStr);
	if (charNum < row.size())
		row[charNum] = stateCode;
	else
		{
		while (charNum < row.size())
			row.push_back(NXS_INVALID_STATE_CODE);
		row.push_back(stateCode);
		}
	return true;
	}

void NxsTaxaAssociationBlock::Read(
    NxsToken &token) /* the token used to read from `in' */
{
    isEmpty = false;

    DemandEndSemicolon(token, "BEGIN TAXAASSOCIATION");

    for (;; )
    {
        token.GetNextToken();
        NxsBlock::NxsCommandResult res = HandleBasicBlockCommands(token);
        if (res == NxsBlock::NxsCommandResult(STOP_PARSING_BLOCK))
        {
            return;
        }
        if (res != NxsBlock::NxsCommandResult(HANDLED_COMMAND))
        {
            if (token.Equals("TAXA"))
            {
                HandleTaxaCommand(token);
            }
            else if (token.Equals("ASSOCIATES"))
            {
                HandleAssociatesCommand(token);
            }
            else
            {
                SkipCommand(token);
            }
        }
    }
}

/*----------------------------------------------------------------------------------------------------------------------
|	Called when the HELP command needs to be parsed from within the GarliReader block.
*/
void GarliReader::HandleHelp(
  NxsToken &token)	/* the token used to read from `in' */
	{
	// Retrieve all tokens for this command, stopping only in the event
	// of a semicolon or an unrecognized keyword
	//
	for (;;)
		{
		token.GetNextToken();

		if (token.Equals(";"))
			{
			break;
			}
		else
			{
			errormsg = "Unexpected keyword (";
			errormsg += token.GetToken();
			errormsg += ") encountered reading HELP command";
			throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
			}
		}

	message = "\nExamples of use of available commands:";
	message += "\n  help                     -> shows this message";
	message += "\n  log file=mylog.txt start -> opens log file named mylog.txt";
	message += "\n  log stop                 -> closes current log file";
	message += "\n  exe mydata.nex           -> executes nexus file mydata.nex";
	message += "\n  show                     -> reports on blocks currently stored";
	message += "\n  quit                     -> terminates application";
	message += "\n";
	PrintMessage();
	}

/*----------------------------------------------------------------------------------------------------------------------
|	Stores the next token as the this->blockid field.
*/
void NxsBlock::HandleBlockIDCommand(NxsToken & token)
	{
	token.GetNextToken();
	if (token.Equals(";"))
		GenerateUnexpectedTokenNxsException(token, "an id for the block");
	blockIDString = token.GetToken();
	DemandEndSemicolon(token, "BLOCKID");
	}

/*----------------------------------------------------------------------------------------------------------------------
	Called whenever a file name needs to be read from either the command line or a file. Expects next token to be "="
	followed by the token representing the file name. Call this function after, say, the keyword "file" has been read
	in the following LOG command:
>
	log file=doofus.txt start replace;
>
	Note that this function will read only the "=doofus.txt " leaving "start replace;" in the stream for reading at
	a later time.
*/
NxsString BASICCMDLINE::GetFileName(
  NxsToken & token)	/* is the token used to read from `in' */
	{
	// Eat the equals sign
	token.GetNextToken();

	if (!token.Equals("="))
		{
		errormsg = "Expecting an equals sign, but found ";
		errormsg += token.GetToken();
		errormsg += " instead";
		throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
		}

	// Now get the filename itself
	token.GetNextToken();

	return token.GetToken();
	}

void NxsTaxaAssociationBlock::HandleTaxaCommand(
    NxsToken &token)
{
    if (!this->nexusReader)
    {
        NxsNCLAPIException("No NxsReader when reading TaxaAssociation block.");
    }

    token.GetNextToken();
    this->firstTaxaBlock = this->ProcessTaxaBlockName(token.GetTokenReference(), token);
    token.GetNextToken();
    if (!token.Equals(","))
    {
        errormsg << "Expecting comma in the TAXA command, found \"" << token.GetTokenReference() << "\".";
        throw NxsException(errormsg, token);
    }
    token.GetNextToken();
    this->secondTaxaBlock = this->ProcessTaxaBlockName(token.GetTokenReference(), token);
    NxsToken::DemandEndSemicolon(token, this->errormsg, "TAXA");
}

bool NxsReader::ReadUntilEndblock(NxsToken &token, const std::string & )
	{
	for (;;)
		{
		token.GetNextToken();
		if (token.Equals("END") || token.Equals("ENDBLOCK")) 
			{
			token.GetNextToken();
			if (!token.Equals(";")) 
				{
				std::string errormsg = "Expecting ';' after END or ENDBLOCK command, but found ";
				errormsg += token.GetToken();
				errormsg += " instead";
				NexusError(NxsString(errormsg.c_str()), token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
				return false;
				}
			return true;
			}
		}
	}

/*!
	This function provides the ability to read everything following the block name (which is read by the NxsReader
	object) to the END or ENDBLOCK statement. Characters are read from the input stream `in'. Overrides the abstract
	virtual function in the base class.
*/
void NxsUnalignedBlock::Read(
  NxsToken & token)	/* is the token used to read from `in' */
	{
	isEmpty = false;
	isUserSupplied = true;

	// This should be the semicolon after the block name
	token.GetNextToken();
	if (!token.Equals(";"))
		{
		errormsg = "Expecting ';' after ";
		errormsg += NCL_BLOCKTYPE_ATTR_NAME;
		errormsg += " block name, but found ";
		errormsg += token.GetToken();
		errormsg += " instead";
		throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
		}
	nTaxWithData = 0;

	for (;;)
		{
		token.GetNextToken();
		NxsBlock::NxsCommandResult res = HandleBasicBlockCommands(token);
		if (res == NxsBlock::NxsCommandResult(STOP_PARSING_BLOCK))
			return;
		if (res != NxsBlock::NxsCommandResult(HANDLED_COMMAND))
			{
			if (token.Equals("DIMENSIONS"))
				HandleDimensions(token);
			else if (token.Equals("FORMAT"))
				HandleFormat(token);
			else if (token.Equals("TAXLABELS"))
				HandleTaxLabels(token);
			else if (token.Equals("MATRIX"))
				HandleMatrix(token);
			else
				SkipCommand(token);
			}
		}	// for (;;)
	}

/*only used it the linkAPI is enabled*/
void NxsTaxaBlockSurrogate::HandleLinkTaxaCommand(NxsToken & token)
	{
	token.GetNextToken();
	const std::map<std::string, std::string> kv = token.ProcessAsSimpleKeyValuePairs("LINK");
	std::map<std::string, std::string>::const_iterator pairIt = kv.begin();
	for (;pairIt != kv.end(); ++pairIt)
		{
		NxsTaxaBlockAPI *entryTaxa = taxa;
		int entryTaxaLinkStatus = taxaLinkStatus;
		NxsString key(pairIt->first.c_str());
		key.ToUpper();
		NxsString value(pairIt->second.c_str());
		if (key == "TAXA")
			{
			if (taxa && !taxa->GetID().EqualsCaseInsensitive(value))
				{
				if (GetTaxaLinkStatus() & NxsBlock::BLOCK_LINK_USED)
					{
					NxsString errormsg = "LINK to a Taxa block must occur before commands that use a taxa block";
					throw NxsException(errormsg, token);
					}
				SetTaxaBlockPtr(NULL, NxsBlock::BLOCK_LINK_UNINITIALIZED);
				}
			if (!taxa)
				{
				if (!nxsReader)
					{
					NxsString errormsg =  "API Error: No nxsReader during parse in NxsTaxaBlockSurrogate::HandleLinkTaxaCommand";
					throw NxsNCLAPIException(errormsg, token);
					}
				NxsTaxaBlockAPI * cb = nxsReader->GetTaxaBlockByTitle(value.c_str(), NULL);
				if (cb == NULL)
					{
					NxsString errormsg = "Unknown TAXA block (";
					errormsg += value;
					errormsg +=") referred to in the LINK command";
					taxa = entryTaxa;
					taxaLinkStatus = entryTaxaLinkStatus;
					throw NxsException(errormsg, token);
					}
				SetTaxaBlockPtr(cb, NxsBlock::BLOCK_LINK_FROM_LINK_CMD);
				}				
			}
		else
			{
			NxsString errormsg = "Skipping unknown LINK subcommand: ";
			errormsg += pairIt->first.c_str();
			nxsReader->NexusWarnToken(errormsg, NxsReader::SKIPPING_CONTENT_WARNING, token);
			errormsg.clear(); //this token pos will be off a bit.
			}
		}
	}

/*!
	Advances the token, and returns the unsigned int that the token represents

 	Sets errormsg and raises a NxsException on failure.
	`contextString` is used in error messages:
		"Expecting ';' to terminate the ${contextString} command"
*/
void NxsToken::DemandEndSemicolon(NxsToken &token, NxsString & errormsg, const char *contextString)
	{
	token.GetNextToken();
	if (!token.Equals(";"))
		{
		errormsg = "Expecting ';' to terminate the ";
		errormsg += contextString;
		errormsg += " command, but found ";
		errormsg += token.GetToken();
		errormsg += " instead";
		throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
		}
	}

/*! Other than the commands handled by NxsBlock::HandleBasicBlockCommands(), this
	function will deal with Dimensions and call NxsTaxaBlock::HandleTaxLabels()
	to parse the TaxLabels commands.

	All other commands will be skipped
*/
void NxsTaxaBlock::Read(
  NxsToken &token)	/* the token used to read from in */
	{
	Reset();
	isEmpty				= false;
	isUserSupplied		= true;

	DemandEndSemicolon(token, "BEGIN TAXA");

	for (;;)
		{
		token.GetNextToken();
		NxsBlock::NxsCommandResult res = HandleBasicBlockCommands(token);
		if (res == NxsBlock::NxsCommandResult(STOP_PARSING_BLOCK))
			return;
		if (res != NxsBlock::NxsCommandResult(HANDLED_COMMAND))
			{
			if (token.Equals("DIMENSIONS"))
				{
				token.GetNextToken();
				if (!token.Equals("NTAX"))
					{
					errormsg = "Expecting NTAX keyword, but found ";
					errormsg += token.GetToken();
					errormsg += " instead";
					throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
					}
				DemandEquals(token, "after NTAX");
				dimNTax = DemandPositiveInt(token, "NTAX");
				taxLabels.reserve(dimNTax);
				DemandEndSemicolon(token, "DIMENSIONS");
				}	// if (token.Equals("DIMENSIONS"))
			else if (token.Equals("TAXLABELS"))
				HandleTaxLabels(token);
			else
				SkipCommand(token);
			}
		}	// GetNextToken loop
	}

/*!
	Called when DIMENSIONS command needs to be parsed from within the UNALIGNED block. Deals with everything after the
	token DIMENSIONS up to and including the semicolon that terminates the DIMENSIONS command.
*/
void NxsUnalignedBlock::HandleDimensions(
  NxsToken & token)			/* the token used to read from `in' */
	{
	unsigned ntaxRead = 0;
	for (;;)
		{
		token.GetNextToken();
		if (token.Equals("NEWTAXA"))
			newtaxa = true;
		else if (token.Equals("NTAX"))
			{
			DemandEquals(token, "after NTAX in DIMENSIONS command");
			ntaxRead = DemandPositiveInt(token, "NTAX");
			}
		else if (token.Equals(";"))
			break;
		}
	if (newtaxa)
		{
		if (ntaxRead == 0)
			{
			errormsg = "DIMENSIONS command must have an NTAX subcommand when the NEWTAXA option is in effect.";
			throw NxsException(errormsg, token);
			}
		AssureTaxaBlock(createImpliedBlock, token, "Dimensions");
		if (!createImpliedBlock)
			{
			taxa->Reset();
			if (nexusReader)
				nexusReader->RemoveBlockFromUsedBlockList(taxa);
			}
		taxa->SetNtax(ntaxRead);
		nTaxWithData = ntaxRead;
		}
	else
		{
		AssureTaxaBlock(false, token, "Dimensions");
		const unsigned ntaxinblock = taxa->GetNTax();
		if (ntaxinblock == 0)
			{
			errormsg = "A TAXA block must be read before character data, or the DIMENSIONS command must use the NEWTAXA.";
			throw NxsException(errormsg, token);
			}
		if (ntaxinblock < ntaxRead)
			{
			errormsg = "NTAX in UNALIGNED block must be less than or equal to NTAX in TAXA block\nNote: one circumstance that can cause this error is \nforgetting to specify NTAX in DIMENSIONS command when \na TAXA block has not been provided";
			throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
			}
		nTaxWithData = (ntaxRead == 0 ? ntaxinblock : ntaxRead);
		}
	}

/*----------------------------------------------------------------------------------------------------------------------
	Called when the END or ENDBLOCK command needs to be parsed from within the BASICCMDLINE block. Basically just
	checks to make sure the next token in the data file is a semicolon.
*/
void BASICCMDLINE::HandleEndblock(
  NxsToken & token)	/* is the token used to read from `in' */
	{
	// Get the semicolon following END or ENDBLOCK token
	token.GetNextToken();

	if (!token.Equals(";"))
		{
		errormsg = "Expecting ';' to terminate the END or ENDBLOCK command, but found ";
		errormsg += token.GetToken();
		errormsg += " instead";
		throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
		}
	}

/*----------------------------------------------------------------------------------------------------------------------
|	Advances the token, and returns the unsigned int that the token represents
|
| 	Sets errormsg and raises a NxsException on failure.
|	`contextString` is used in error messages:
|		"${contextString} must be a number greater than 0"
*/
unsigned NxsToken::DemandPositiveInt(NxsToken &token, NxsString & errormsg, const char *contextString)
	{
	token.GetNextToken();
	int i = atoi(token.GetToken().c_str());
	if (i <= 0)
		{
		errormsg.assign(contextString);
		errormsg += " must be a number greater than 0. Found";
		errormsg += token.GetToken();
		errormsg += " instead";
		throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
		}
	return (unsigned) i;
	}