C++ NxsToken::SetLabileFlagBit方法代码示例

/*!
	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;
	}

/*! used internally to  do most of the work of Execute() */
void NxsReader::CoreExecutionTasks(
    NxsToken  &token,           /* the token object used to grab NxsReader tokens */
    bool notifyStartStop)       /* if true, ExecuteStarting and ExecuteStopping will be called */
{
    unsigned numSigInts = NxsReader::getNumSignalIntsCaught();
    const bool checkingSignals = NxsReader::getNCLCatchesSignals();

    lastExecuteBlocksInOrder.clear();
    currBlock = NULL;

    NxsString errormsg;
    token.SetEOFAllowed(true);

    try
    {
        token.SetLabileFlagBit(NxsToken::saveCommandComments);
        token.GetNextToken();
    }
    catch (NxsException x)
    {
        NexusError(token.errormsg, 0, 0, 0);
        return;
    }

    if (token.Equals("#NEXUS"))
    {
        token.SetLabileFlagBit(NxsToken::saveCommandComments);
        token.GetNextToken();
    }
    else
    {
        errormsg = "Expecting #NEXUS to be the first token in the file, but found ";
        errormsg += token.GetToken();
        errormsg += " instead";
        /*mth changed this to a warning instead of an error	 because of the large number
            of files that violate this requirement.
         */
        NexusWarn(errormsg,  NxsReader::AMBIGUOUS_CONTENT_WARNING, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
    }

    if (notifyStartStop)
    {
        ExecuteStarting();
    }
    bool keepReading = true;
    for (; keepReading && !token.AtEOF(); )
    {
        if (checkingSignals && NxsReader::getNumSignalIntsCaught() != numSigInts)
        {
            throw NxsSignalCanceledParseException("Reading NEXUS content");
        }
        if (token.Equals("BEGIN"))
        {
            token.SetEOFAllowed(false); /*must exit the block before and EOF*/
            token.GetNextToken();
            token.SetBlockName(token.GetTokenReference().c_str());
            for (currBlock = blockList; currBlock != NULL; currBlock = currBlock->next)
            {
                if (currBlock->CanReadBlockType(token))
                {
                    break;
                }
            }
            NxsString currBlockName = token.GetToken();
            currBlockName.ToUpper();
            NxsBlockFactory * sourceOfBlock = NULL;
            if (currBlock == NULL)
            {
                try
                {
                    currBlock = CreateBlockFromFactories(currBlockName, token, &sourceOfBlock);
                }
                catch (NxsException x)
                {
                    NexusError(x.msg, x.pos, x.line, x.col);
                    token.SetBlockName(0L);
                    token.SetEOFAllowed(true);
                    return;
                }
            }
            if (currBlock == NULL)
            {
                SkippingBlock(currBlockName);
                if (!ReadUntilEndblock(token, currBlockName))
                {
                    token.SetBlockName(0L);
                    token.SetEOFAllowed(true);
                    return;
                }
            }
            else if (currBlock->IsEnabled())
            {
                keepReading = ExecuteBlock(token, currBlockName, currBlock, sourceOfBlock);
            }
            else
            {
                SkippingDisabledBlock(token.GetToken());
                if (sourceOfBlock)
                {
//.........这里部分代码省略.........

//.........这里部分代码省略.........
				errormsg += " was specified)";
				throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
				}

			missing = token.GetToken()[0];

			ignoreCaseAssumed = true;
			standardDataTypeAssumed = true;
			}
		else if (token.Equals("SYMBOLS") || token.Equals("SYMBOL"))
			{
			NxsDiscreteStateCell numDefStates;
			unsigned maxNewStates;
			switch(datatype)
				{
				case NxsCharactersBlock::dna:
				case NxsCharactersBlock::rna:
				case NxsCharactersBlock::nucleotide:
					numDefStates = 4;
					maxNewStates = NCL_MAX_STATES-4;
					break;
				case NxsCharactersBlock::protein:
					numDefStates = 21;
					maxNewStates = NCL_MAX_STATES-21;
					break;
				default:
					numDefStates = 0; // replace symbols list for standard datatype
					symbols[0] = '\0';
					maxNewStates = NCL_MAX_STATES;
				}
			DemandEquals(token, "after keyword SYMBOLS");

			// This should be the symbols list
			token.SetLabileFlagBit(NxsToken::doubleQuotedToken);
			token.GetNextToken();

			token.StripWhitespace();
			unsigned numNewSymbols = token.GetTokenLength();

			if (numNewSymbols > maxNewStates)
				{
				errormsg = "SYMBOLS defines ";
				errormsg += numNewSymbols;
				errormsg += " new states but only ";
				errormsg += maxNewStates;
				errormsg += " new states allowed for this DATATYPE";
				throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
				}

			NxsString to = token.GetToken();
			unsigned tlen = (unsigned)to.size();
			NxsString processedS;
			// Check to make sure user has not used any symbols already in the
			// default symbols list for this data type
			for (unsigned i = 0; i < tlen; i++)
				{
				if (IsInSymbols(to[i]))
					{
					errormsg = "The character ";
					errormsg << to[i] << " defined in SYMBOLS is predefined for this DATATYPE and shoud not occur in a SYMBOLS subcommand of a FORMAT command.";
					if (nexusReader)
						{
						nexusReader->NexusWarnToken(errormsg, NxsReader::SKIPPING_CONTENT_WARNING, token);
						errormsg.clear();
						}
					}

/*----------------------------------------------------------------------------------------------------------------------
|	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 NxsTaxaBlock::Read(
  NxsToken &token)	/* the token used to read from in */
	{
	ntax				= 0;
	int nominal_ntax	= 0;
	isEmpty				= false;
	isUserSupplied		= true;

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

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

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

		if (token.Equals("DIMENSIONS"))
			{
			// This should be the NTAX keyword
			//
			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());
				}

			// This should be the equals sign
			//
			token.GetNextToken(); 

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

			// This should be the number of taxa
			//
			token.GetNextToken();

			nominal_ntax = atoi(token.GetToken().c_str());
			if (nominal_ntax <= 0)
				{
				errormsg = "NTAX should be greater than zero (";
				errormsg += token.GetToken();
				errormsg += " was specified)";
				throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
				}

			// This should be the terminating semicolon
			//
			token.GetNextToken(); 

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

		else if (token.Equals("TAXLABELS")) 
			{
			if (nominal_ntax <= 0) 
				{
				errormsg = "NTAX must be specified before TAXLABELS command";
				throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
				}

			for (unsigned i = 0; (int)i < nominal_ntax; i++)
				{
                token.SetLabileFlagBit(NxsToken::hyphenNotPunctuation + NxsToken::preserveUnderscores);
				token.GetNextToken();
				//@pol should check to make sure this is not punctuation
				AddTaxonLabel(token.GetToken());
				}

			// This should be terminating semicolon
			//
			token.GetNextToken(); 
//.........这里部分代码省略.........