void BlockParams::Read(NxsToken &token)
{
DemandEndSemicolon(token, "PARAMS");
nat idCtr = 0;
auto catsFound = std::unordered_set<Category>{};
while(true)
{
token.GetNextToken();
NxsBlock::NxsCommandResult res = HandleBasicBlockCommands(token);
if (res == NxsBlock::NxsCommandResult(STOP_PARSING_BLOCK))
return;
if (res != NxsBlock::NxsCommandResult(HANDLED_COMMAND))
{
auto str = token.GetToken(false);
auto cat = CategoryFuns::getCategoryFromLinkLabel(str);
parseScheme(token, cat, idCtr);
if(catsFound.find(cat) != catsFound.end())
{
cerr << "parsing error: found a linking scheme for category " << CategoryFuns::getShortName(cat) << " twice. Aborting." ;
exitFunction(-1, true);
}
if( cat == Category::TOPOLOGY)
{
cerr << "not implemented";
assert(0);
}
}
}
}
/*----------------------------------------------------------------------------------------------------------------------
| 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;
unsigned nominal_ntax = 0;
isEmpty = false;
isUserSupplied = true;
DemandEndSemicolon(token, "BEGIN TAXA");
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());
}
DemandEquals(token, "after NTAX");
nominal_ntax = DemandPositiveInt(token, "NTAX");
DemandEndSemicolon(token, "DIMENSIONS");
} // 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; i < nominal_ntax; i++)
{
token.GetNextToken();
//@pol should check to make sure this is not punctuation
AddTaxonLabel(token.GetToken());
}
DemandEndSemicolon(token, "TAXLABELS");
} // if (token.Equals("TAXLABELS"))
else if (token.Equals("END") || token.Equals("ENDBLOCK"))
{
DemandEndSemicolon(token, "ENDBLOCK");
break;
} // if (token.Equals("END") || token.Equals("ENDBLOCK"))
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());
}
} // token not END, ENDBLOCK, TAXLABELS, or DIMENSIONS
} // GetNextToken loop
}
