/**
* @method HandleDimensionsCommand [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* Called when DIMENSIONS command needs to be parsed from within the
* DISTANCES block. Deals with everything after the token DIMENSIONS
* up to and including the semicolon that terminates the DIMENSIONS
* command.
*/
void DistancesBlock::HandleDimensionsCommand( NexusToken& token )
{
for(;;)
{
token.GetNextToken();
// token should either be ';' or the name of a subcommand
//
if( token.Equals(";") ) {
break;
}
else if( token.Equals("NEWTAXA") ) {
ntax = 0;
newtaxa = 1;
}
else if( token.Equals("NTAX") ) {
if( !newtaxa ) {
errormsg = "Must specify NEWTAXA before NTAX if new taxa are being defined";
throw XNexus( 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 XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
// this should be the number of taxa
token.GetNextToken();
ntax = atoi( token.GetToken().c_str() );
}
else if( token.Equals("NCHAR") ) {
// this should be the equals sign
token.GetNextToken();
if( !token.Equals("=") ) {
errormsg = "Expecting '=' but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
// this should be the number of characters
token.GetNextToken();
nchar = atoi( token.GetToken().c_str() );
}
}
if( ntax == 0 )
ntax = taxa.GetNumTaxonLabels();
}
/**
* @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 HandleMatrixCommand [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* Called when MATRIX command needs to be parsed from within the
* DISTANCES block. Deals with everything after the token MATRIX
* up to and including the semicolon that terminates the MATRIX
* command.
*/
void DistancesBlock::HandleMatrixCommand( NexusToken& token )
{
int i;
if( ntax == 0 )
ntax = taxa.GetNumTaxonLabels();
if( ntax == 0 ) {
errormsg = "MATRIX command cannot be read if NTAX is zero";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
if( triangle == both && !diagonal ) {
errormsg = "Cannot specify NODIAGONAL and TRIANGLE=BOTH at the same time";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
if( newtaxa )
taxa.Reset();
// allocate memory to hold the taxonPos array
//
if( taxonPos != NULL )
delete [] taxonPos;
taxonPos = new int[ntax];
for( i = 0; i < ntax; i++ )
taxonPos[i] = -1;
// allocate memory to hold the matrix
//
if( matrix != NULL )
delete matrix;
matrix = new DistanceDatum*[ntax];
for( i = 0; i < ntax; i++ )
matrix[i] = new DistanceDatum[ntax];
int offset = 0;
int done = 0;
while( !done ) {
done = HandleNextPass( token, offset );
}
// token should be equal to the terminating semicolon
token.GetNextToken();
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate MATRIX command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
/**
* @method HandleTaxset [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* ?
*/
void AssumptionsBlock::HandleTaxset( NexusToken& token )
{
bool asterisked = false;
// Next token should be either an asterisk or the name of a taxset
token.GetNextToken();
if( token.Equals("*") ) {
asterisked = true;
token.GetNextToken();
}
// Token now stored should be the name of a taxset
nxsstring taxset_name = token.GetToken();
// Now grab the equals sign
token.GetNextToken();
if( !token.Equals("=") ) {
errormsg = "Expecting '=' in TAXSET definition but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
IntSet s;
int totalTaxa = taxa.GetNumTaxonLabels();
SetReader( token, totalTaxa, s, *this, SetReader::taxset ).Run();
taxsets[taxset_name] = s;
if( asterisked )
def_taxset = taxset_name;
}
/**
* @method HandleCharset [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* Reads and stores information contained in the command
* CHARSET within an ASSUMPTIONS block.
*/
void AssumptionsBlock::HandleCharset( NexusToken& token )
{
bool asterisked = false;
// Next token should be either an asterisk or the name of a charset
token.GetNextToken();
if( token.Equals("*") ) {
asterisked = true;
token.GetNextToken();
}
// Token now stored should be the name of a charset
nxsstring charset_name = token.GetToken();
// Now grab the equals sign
token.GetNextToken();
if( !token.Equals("=") ) {
errormsg = "Expecting '=' in CHARSET definition but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
assert( charBlockPtr != NULL );
CharactersBlock& charBlock = *charBlockPtr;
IntSet s;
int totalChars = charBlock.GetNCharTotal();
SetReader( token, totalChars, s, charBlock, SetReader::charset ).Run();
charsets[charset_name] = s;
if( asterisked )
def_charset = charset_name;
}
/**
* @method HandleEndblock [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* Called when the END or ENDBLOCK command needs to be parsed
* from within the ASSUMPTIONS block. Basically just checks to make
* sure the next token in the data file is a semicolon.
*/
void AssumptionsBlock::HandleEndblock( NexusToken& token )
{
// get the semicolon following END or ENDBLOCK token
//
token.GetNextToken();
if( !token.Equals(";") ) {
errormsg = "Expecting ';' to terminate the END or ENDBLOCK command, but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
/**
* @method HandleTaxlabelsCommand [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* Called when TAXLABELS command needs to be parsed from within the
* DISTANCES block. Deals with everything after the token TAXLABELS
* up to and including the semicolon that terminates the TAXLABELS
* command.
*/
void DistancesBlock::HandleTaxlabelsCommand( NexusToken& token )
{
if( !newtaxa ) {
errormsg = "NEWTAXA must have been specified in DIMENSIONS command to use the TAXLABELS command in a ";
errormsg += id;
errormsg += " block";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
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();
taxa.AddTaxonLabel( 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() );
}
// OPEN ISSUE: Some may object to setting newtaxa to 0 here, because then the
// fact that new taxa were specified in this DISTANCES block rather than in
// a preceding TAXA block is lost. This will only be important if we wish to
// recreate the original data file, which I don't anticipate anyone doing with
// this code (too difficult to remember all comments, the order of blocks in
// the file, etc.)
newtaxa = 0;
}
/**
* @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();
}
void MyCharactersBlock::HandleMatrix (NexusToken& token)
{
int i, j;
if (ntax == 0)
{
errormsg = "Must precede ";
errormsg += id;
errormsg += " block with a TAXA block or specify NEWTAXA and NTAX in the DIMENSIONS command";
throw XNexus (errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn());
}
if (ntaxTotal == 0)
ntaxTotal = taxa.GetNumTaxonLabels();
// We use >= rather than just > below because someone might have
// ELIMINATEd all characters, and we should allow that (even though it
// is absurd)
assert (nchar >= 0);
if (matrix != NULL)
delete matrix;
mContData.clear();
if (GetDataType() != continuous)
{
matrix = new DiscreteMatrix (ntax, nchar);
}
// Allocate memory for (and initialize) the arrays activeTaxon and
// activeChar.
// All characters and all taxa are initially active.
activeTaxon = new bool[ntax];
for (i = 0; i < ntax; i++)
activeTaxon[i] = true;
activeChar = new bool[nchar];
for (j = 0; j < nchar; j++)
activeChar[j] = true;
// The value of ncharTotal is normally identical to the value of nchar
// specified in the CHARACTERS block DIMENSIONS command. If an
// ELIMINATE command is processed, however, nchar < ncharTotal. Note
// that the ELIMINATE command will have already been read by now, and
// the ELIMINATEd character numbers will be stored in the IntSet
// eliminated.
//
// Note that if an ELIMINATE command has been read, charPos will have
// already been created; thus, we only need to allocate and initialize
// charPos if user did not specify an ELIMINATE command
if (charPos == NULL)
BuildCharPosArray();
// The value of ntaxTotal equals the number of taxa specified in the
// TAXA block, whereas ntax equals the number of taxa specified in
// the DIMENSIONS command of the CHARACTERS block. These two numbers
// will be identical unless some taxa were left out of the MATRIX
// command of the CHARACTERS block, in which case ntax < ntaxTotal.
if (taxonPos != NULL)
delete [] taxonPos;
taxonPos = new int[ntaxTotal];
for (i = 0; i < ntaxTotal; i++)
taxonPos[i] = -1;
if (GetDataType() == continuous)
handleContMatrix (token);
else if (transposing)
HandleTransposedMatrix (token);
else
HandleStdMatrix (token);
// If we've gotten this far, presumably it is safe to
// tell the ASSUMPTIONS block that were ready to take on
// the responsibility of being the current character-containing
// block (to be consulted if characters are excluded or included
// or if taxa are deleted or restored)
assumptionsBlock.SetCallback(this);
// this should be the terminating semicolon at the end of the matrix command
if (GetDataType() != continuous)
token.GetNextToken();
if (!token.Equals(";")) {
errormsg = "Expecting ';' at the end of the MATRIX command; found ";
errormsg += token.GetToken();
errormsg += " instead";
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 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() );
}
}
}
}
/**
* @method HandleNextPass [int:protected]
* @param token [NexusToken&] the token we are using for reading the data file
* @param offset [int&] the offset (see below)
*
* Called from within HandleMatrix, this function is used to deal with interleaved
* matrices. It is called once for each pass through the taxa.
*
* <P>The local variable jmax records the number of columns read in the current
* interleaved page and is used to determine the offset used for j in subsequent
* pages.
*/
int DistancesBlock::HandleNextPass( NexusToken& token, int& offset )
{
int i, j, k, jmax = 0, done = 0;
int i_first = 0;
if( triangle == lower )
i_first = offset;
int i_last = ntax;
for( i = i_first; i < i_last; i++ )
{
// Deal with taxon label if provided
//
if( labels && ( !newtaxa || offset>0 ) )
{
do {
token.SetLabileFlagBit( NexusToken::newlineIsToken );
token.GetNextToken();
} while( token.AtEOL() );
try {
k = taxa.FindTaxon( token.GetToken() );
if( taxonPos[i]==-1 )
taxonPos[i] = k;
else if( taxonPos[i] != k ) {
errormsg = "Taxon labeled ";
errormsg += token.GetToken();
errormsg += " is out of order compared to previous interleave pages";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
catch (std::out_of_range) {
errormsg = "Could not find ";
errormsg += token.GetToken();
errormsg += " among taxa previously defined";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
else if( labels && newtaxa ) {
do {
token.SetLabileFlagBit( NexusToken::newlineIsToken );
token.GetNextToken();
} while( token.AtEOL() );
taxa.AddTaxonLabel( token.GetToken() );
taxonPos[i] = i;
}
// Now deal with the row of distance values
//
int true_j = 0;
for( j = 0; j < ntax; j++ )
{
if( i == ntax-1 && j == ntax-1 ) {
done = 1;
}
if( i == ntax-1 && true_j == ntax-1 ) {
done = 1;
break;
}
if( i == ntax-1 && !diagonal && triangle==upper ) {
done = 1;
break;
}
if( !diagonal && triangle==lower && j == ntax-offset-1) {
done = 1;
break;
}
token.SetLabileFlagBit( NexusToken::newlineIsToken );
token.GetNextToken();
if( token.AtEOL() ) {
if( j > jmax ) {
jmax = j;
if( !diagonal && triangle == upper && i >= offset )
jmax++;
if( interleave && triangle == upper )
i_last = jmax + offset;
}
break;
}
true_j = j+offset;
if( triangle==upper && i > offset )
true_j += ( i - offset );
if( !diagonal && triangle==upper && i >= offset )
true_j++;
if( true_j == ntax ) {
errormsg = "Too many distances specified in row just read in";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
std::string t = token.GetToken();
if( token.GetTokenLength() == 1 && t[0] == missing )
SetMissing( i, true_j );
else
SetDistance( i, true_j, atof( t.c_str() ) );
}
}
offset += jmax;
if( done )
return 1;
else
return 0;
}
/**
* @method HandleFormatCommand [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XNexus
*
* Called when FORMAT command needs to be parsed from within the
* DISTANCES block. Deals with everything after the token FORMAT
* up to and including the semicolon that terminates the FORMAT
* command.
*/
void DistancesBlock::HandleFormatCommand( NexusToken& token )
{
for(;;)
{
token.GetNextToken();
// token should either be ';' or the name of a subcommand
//
if( token.Equals(";") ) {
break;
}
else if( token.Equals("TRIANGLE") ) {
// this should be the equals sign
token.GetNextToken();
if( !token.Equals("=") ) {
errormsg = "Expecting '=' but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
// this should be LOWER, UPPER, or BOTH
token.GetNextToken();
if( token.Equals("LOWER") )
triangle = lower;
else if( token.Equals("UPPER") )
triangle = upper;
else if( token.Equals("BOTH") )
triangle = both;
else {
errormsg = "Expecting UPPER, LOWER, or BOTH but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
else if( token.Equals("DIAGONAL") ) {
diagonal = 1;
}
else if( token.Equals("NODIAGONAL") ) {
diagonal = 0;
}
else if( token.Equals("LABELS") ) {
labels = 1;
}
else if( token.Equals("NOLABELS") ) {
labels = 0;
}
else if( token.Equals("INTERLEAVE") ) {
interleave = 1;
}
else if( token.Equals("NOINTERLEAVE") ) {
interleave = 0;
}
else if( token.Equals("MISSING") ) {
// this should be the equals sign
token.GetNextToken();
if( !token.Equals("=") ) {
errormsg = "Expecting '=' but found ";
errormsg += token.GetToken();
errormsg += " instead";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
// this should be the missing data symbol
token.GetNextToken();
if( token.GetTokenLength() != 1 ) {
errormsg = "Missing data symbol specified (";
errormsg += token.GetToken();
errormsg += ") is invalid (must be a single character)";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
missing = token.GetToken()[0];
}
else {
errormsg = "Token specified (";
errormsg += token.GetToken();
errormsg += ") is an invalid subcommand for the FORMAT command";
throw XNexus( errormsg, token.GetFilePosition(), token.GetFileLine(), token.GetFileColumn() );
}
}
}
