Exemplo n.º 1
0
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");
}
Exemplo n.º 2
0
void NxsBlock::SkipCommand(NxsToken & token)
	{
	if (nexusReader)
		{
		errormsg = "Skipping command: ";
		errormsg << token.GetTokenReference();
		nexusReader->NexusWarnToken(errormsg, NxsReader::SKIPPING_CONTENT_WARNING, token);
		errormsg.clear();
		}
	if (!token.Equals(";"))
		SkippingCommand(token.GetToken());
	if (storeSkippedCommands)
		{
		ProcessedNxsCommand pnc;
		token.ProcessAsCommand(&pnc);
		skippedCommands.push_back(pnc);
		}
	else
		token.ProcessAsCommand(NULL);
	}
Exemplo n.º 3
0
/*! 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)
                {
                    sourceOfBlock->BlockSkipped(currBlock);
                }
                if (!ReadUntilEndblock(token, currBlockName))
                {
                    token.SetBlockName(0L);
                    token.SetEOFAllowed(true);
                    return;
                }
            }
            currBlock = NULL;
            token.SetEOFAllowed(true);
            token.SetBlockName(0L);
        }       // if (token.Equals("BEGIN"))
        else if (token.Equals("&SHOWALL"))
        {
            for (NxsBlock*  showBlock = blockList; showBlock != NULL; showBlock = showBlock->next) {
                DebugReportBlock(*showBlock);
            }
        }
        else if (token.Equals("&LEAVE"))
        {
            break;
        }
        if (keepReading)
        {
            token.SetLabileFlagBit(NxsToken::saveCommandComments);
            token.GetNextToken();
        }
    }
    if (notifyStartStop)
    {
        ExecuteStopping();
    }

    currBlock = NULL;
}
Exemplo n.º 4
0
void NxsTaxaAssociationBlock::HandleAssociatesCommand(
    NxsToken &token)
{
    if (this->firstTaxaBlock == 0L || this->secondTaxaBlock == 0L)
    {
        errormsg << "Expecting TAXA command to precede an ASSOCIATES command.";
        throw NxsException(errormsg, token);
    }
    token.GetNextToken();
    for (;; )
    {
        std::set<unsigned> fSet;
        while (!token.IsPunctuationToken() || !(token.Equals(";") || token.Equals(",") || token.Equals("/")))
        {
            try {
                this->firstTaxaBlock->GetIndicesForLabel(token.GetTokenReference(), &fSet);
            }
            catch(...)
            {
                errormsg << "Unrecognized taxon \"" << token.GetTokenReference() << "\" in ASSOCIATES command";
                throw NxsException(errormsg, token);
            }
            token.GetNextToken();
        }
        if (!token.Equals("/"))
        {
            errormsg << "Expecting / in ASSOCIATES command, found \"" << token.GetTokenReference() << "\"";
            throw NxsException(errormsg, token);
        }

        if (fSet.empty())
        {
            errormsg << "Expecting taxon labels from the first TAXA block before the / in ASSOCIATES command.";
            throw NxsException(errormsg, token);
        }
        token.GetNextToken();

        std::set<unsigned> sSet;

        while (!token.IsPunctuationToken() || !(token.Equals(";") || token.Equals(",") || token.Equals("/")))
        {
            try {
                this->secondTaxaBlock->GetIndicesForLabel(token.GetTokenReference(), &sSet);
            }
            catch(...)
            {
                errormsg << "Unrecognized taxon \"" << token.GetTokenReference() << "\" in ASSOCIATES command";
                throw NxsException(errormsg, token);
            }
            token.GetNextToken();
        }

        if (!(token.Equals(";") || token.Equals(",")))
        {
            errormsg << "Expecting , or ; in ASSOCIATES command, found \"" << token.GetTokenReference() << "\"";
            throw NxsException(errormsg, token);
        }

        if (sSet.empty())
        {
            errormsg << "Expecting taxon labels from the second TAXA block after the / in ASSOCIATES command.";
            throw NxsException(errormsg, token);
        }

        for (std::set<unsigned>::const_iterator fIt = fSet.begin(); fIt != fSet.end(); ++fIt)
        {
            this->AddAssociation(*fIt, sSet);
        }
        if (token.Equals(";"))
        {
            break;
        }
        token.GetNextToken();
    }
}