/**
* @method Read [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* This function provides the ability to read everything following
* the block name (which is read by the Nexus 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 AssumptionsBlock::Read( NexusToken& token )
{
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 XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
for(;;)
{
token.GetNextToken();
if( token.Equals("EXSET") ) {
HandleExset( token );
}
else if( token.Equals("TAXSET") ) {
HandleTaxset( token );
}
else if( token.Equals("CHARSET") ) {
HandleCharset( token );
}
else 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 XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
}
}
/**
* @method Read [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* This function provides the ability to read everything following the block name
* (which is read by the Nexus 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 TaxaBlock::Read( NexusToken& token )
{
isEmpty = false;
token.GetNextToken(); // this should be the semicolon after the block name
if( !token.Equals(";") ) {
errormsg = "Expecting ';' after TAXA block name, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
for(;;)
{
token.GetNextToken();
if( token.Equals("DIMENSIONS") ) {
token.GetNextToken(); // this should be the NTAX keyword
if( !token.Equals("NTAX") ) {
errormsg = "Expecting NTAX keyword, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
token.GetNextToken(); // this should be the equals sign
if( !token.Equals("=") ) {
errormsg = "Expecting '=', but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
token.GetNextToken(); // this should be the number of taxa
ntax = atoi( token.GetToken().c_str() );
if( ntax <= 0 ) {
errormsg = "NTAX should be greater than zero (";
errormsg += token.GetToken();
errormsg += " was specified)";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
token.GetNextToken(); // this should be the terminating semicolon
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate DIMENSIONS command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
else if( token.Equals("TAXLABELS") ) {
if( ntax <= 0 ) {
errormsg = "NTAX must be specified before TAXLABELS command";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
for( int i = 0; i < ntax; i++ ) {
token.GetNextToken();
taxonLabels.push_back( token.GetToken() );
}
token.GetNextToken(); // this should be terminating semicolon
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate TAXLABELS command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
else if( token.Equals("END") ) {
// get the semicolon following END
token.GetNextToken();
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate the END command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
break;
}
else if( token.Equals("ENDBLOCK") ) {
// get the semicolon following ENDBLOCK
token.GetNextToken();
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate the ENDBLOCK command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
break;
}
else {
SkippingCommand( token.GetToken() );
do {
token.GetNextToken();
} while( !token.AtEOF() && !token.Equals(";") );
if( token.AtEOF() ) {
errormsg = "Unexpected end of file encountered";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
}
}
/**
* @method Execute [void:public]
* @param token [NexusToken&] the token object used to grab Nexus tokens
* @param notifyStartStop [bool] if true, ExecuteStarting and ExecuteStopping will be called (true by default)
*
* Reads the Nexus data file from the input stream provided by token. This function
* is responsible for reading through the name of a each block. Once
* it has read a block name, it searches blockList for a block object
* to handle reading the remainder of the block's contents. The block
* object is responsible for reading the end or endblock command as well
* as the trailing semicolon. This function also handles reading
* comments that are outside of blocks, as well as the initial #NEXUS
* keyword. The notifyStartStop argument is provided in case you do not
* wish the ExecuteStart and ExecuteStop functions to be called. These functions
* are primarily used for creating and destroying a dialog box to show progress,
* and nested Execute calls can thus cause problems (e.g., a dialog box is
* destroyed when the inner Execute calls ExecuteStop and the outer Execute
* still expects the dialog box to be available). Specifying notifyStartStop
* false for all the nested Execute calls thus allows the outermost Execute call
* to control creation and destruction of the dialog box.
*/
void Nexus::Execute( NexusToken& token, bool notifyStartStop /* = true */ )
{
char id_str[256];
bool disabledBlock = false;
nxsstring errormsg;
try {
token.GetNextToken();
}
catch( XNexus x ) {
NexusError( token.errormsg, 0, 0, 0 );
return;
}
if( !token.Equals("#NEXUS") ) {
errormsg = "Expecting #NEXUS to be the first token in the file, but found ";
errormsg += token.GetToken();
errormsg += " instead";
NexusError( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
return;
}
if( notifyStartStop )
ExecuteStarting();
for(;;)
{
token.SetLabileFlagBit( NexusToken::saveCommandComments );
token.GetNextToken();
if( token.AtEOF() )
break;
if( token.Equals("BEGIN") )
{
disabledBlock = false;
token.GetNextToken();
NexusBlock* curr;
for( curr = blockList; curr != NULL; curr = curr->next )
{
if( !token.Equals( curr->GetID() ) )
continue;
if( !curr->IsEnabled() ) {
disabledBlock = true;
SkippingDisabledBlock( token.GetToken() );
continue;
}
strcpy( id_str, curr->GetID().c_str() );
EnteringBlock( id_str /*curr->GetID()*/ );
curr->Reset();
try {
curr->Read( token );
}
catch( XNexus x ) {
NexusError( curr->errormsg, x.pos, x.line, x.col );
curr->Reset();
return;
}
ExitingBlock( id_str /*curr->GetID()*/ );
break;
}
if( curr == NULL )
{
token.BlanksToUnderscores();
nxsstring currBlock = token.GetToken();
if( !disabledBlock )
SkippingBlock( currBlock );
for(;;)
{
token.GetNextToken();
if( token.Equals("END") || token.Equals("ENDBLOCK") ) {
token.GetNextToken();
if( !token.Equals(";") ) {
errormsg = "Expecting ';' after END or ENDBLOCK command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
NexusError( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
return;
}
break;
}
if( token.AtEOF() ) {
errormsg = "Encountered end of file before END or ENDBLOCK in block ";
errormsg += currBlock;
NexusError( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
return;
}
}
} // if token not found amongst known block IDs
} // if token equals BEGIN
else if( token.Equals("&SHOWALL") ) {
NexusBlock* curr;
for( curr = blockList; curr != NULL; curr = curr->next )
{
DebugReportBlock(*curr);
}
}
else if( token.Equals("&LEAVE") ) {
break;
}
} // for(;;)
if( notifyStartStop )
ExecuteStopping();
}
/**
* @method Read [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* This function provides the ability to read everything following the block name
* (which is read by the Nexus 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 DistancesBlock::Read( NexusToken& token )
{
isEmpty = false;
token.GetNextToken(); // this should be the semicolon after the block name
if( !token.Equals(";") ) {
errormsg = "Expecting ';' after ";
errormsg += id;
errormsg += " block name, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
for(;;)
{
token.GetNextToken();
if( token.Equals("DIMENSIONS") ) {
HandleDimensionsCommand( token );
}
else if( token.Equals("FORMAT") ) {
HandleFormatCommand( token );
}
else if( token.Equals("TAXLABELS") ) {
HandleTaxlabelsCommand( token );
}
else if( token.Equals("MATRIX") ) {
HandleMatrixCommand( token );
}
else if( token.Equals("END") ) {
// get the semicolon following END
token.GetNextToken();
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate the END command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
break;
}
else if( token.Equals("ENDBLOCK") ) {
// get the semicolon following ENDBLOCK
token.GetNextToken();
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate the ENDBLOCK command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
break;
}
else {
SkippingCommand( token.GetToken() );
do {
token.GetNextToken();
} while( !token.AtEOF() && !token.Equals(";") );
if( token.AtEOF() ) {
errormsg = "Unexpected end of file encountered";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
}
}
