/*----------------------------------------------------------------------------------------------------------------------
| 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());
}
}
}
}
/*----------------------------------------------------------------------------------------------------------------------
| 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
}
/*----------------------------------------------------------------------------------------------------------------------
| 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 virtual
| function in the base class.
*/
void GarliReader::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.Abbreviation("ENdblock"))
{
HandleEndblock(token);
break;
}
else if (token.Abbreviation("GarliReader"))
{
HandleGarliReader(token);
}
else if (token.Abbreviation("Help"))
{
HandleHelp(token);
}
else if (token.Abbreviation("Log"))
{
HandleLog(token);
}
else if (token.Abbreviation("EXecute"))
{
HandleExecute(token);
}
else if (token.Abbreviation("Show"))
{
HandleShow(token);
}
else if (token.Abbreviation("Quit"))
{
quit_now = true;
message = "\nGarliReader says goodbye\n";
PrintMessage();
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());
}
}
}
}
/*----------------------------------------------------------------------------------------------------------------------
| 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();
if (!token.Equals(";"))
{
errormsg = "Expecting ';' to terminate TAXLABELS command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
}
} // if (token.Equals("TAXLABELS"))
else if (token.Equals("END") || token.Equals("ENDBLOCK"))
{
// Get the semicolon following END
//
token.GetNextToken();
if (!token.Equals(";"))
{
errormsg = "Expecting ';' to terminate the ENDBLOCK command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw NxsException(errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
}
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
}
