/**
* @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 BullShell::ParseCodLikeStartValCommand(CodLikeStartOpts &opts, NexusToken& token) const
{
opts.aaFreqs.clear();
DblVector blankRow(21, 1.0/20.0);
blankRow[20] = 0.0; //zero out the freq of the stop codon.
opts.genetic_code = GenCode(MITO);
token.GetNextToken();
opts.gtrParams.assign(N_MUT_PARAMS, .25);
while (token.GetToken()!=";") {
if (token.Abbreviation("CURREntbranchlengths") || token.Abbreviation("CURRBranchlengths")) {
token.GetNextToken();
opts.currbrlen = true;
if (token.Equals("=")) {
token.GetNextToken();
if (token.Abbreviation("No"))
opts.currbrlen = false;
else if (!token.Abbreviation("Yes"))
throw XBull("Expecting YES or NO after CurrentBranchLengths = option to CodLikeStartVal command");
token.GetNextToken();
}
}
else if (token.Abbreviation("GEneticCode")) {
SkipEqualsIfNext(token);
if (token.Abbreviation("Mitochondrial"))
opts.genetic_code = GenCode(MITO);
else if (token.Abbreviation("Nuclear"))
opts.genetic_code = GenCode(NUCLEAR);
else
throw XBull("Expecting either Mito or Nuclear code");
}
else if (token.Abbreviation("BASEfreq")) {
SkipEqualsIfNext(token);
if (!token.Equals("("))
throw XBull("Expecting ( after basefreq option to CodLikeStartVal command");
for (unsigned i = 0; i < 3; i++) {
token.GetNextToken();
opts.gtrParams[i] = atof(token.GetToken().c_str());
if (opts.gtrParams[i] <= 0.0)
throw XBull("basefreqs must be > 0.0 CodLikeStartVal command");
}
if (opts.gtrParams[1] + opts.gtrParams[2] + opts.gtrParams[0] >= 1.0)
throw XBull("Sum of A, C, and G must be <1.0 CodLikeStartVal command");
token.GetNextToken();
if (!token.Equals(")"))
throw XBull("Expecting ) after basefreq option to CodLikeStartVal command");
}
else if (token.Abbreviation("RMATrix")) {
SkipEqualsIfNext(token);
if (!token.Equals("("))
throw XBull("Expecting ( after rmatrix option to CodLikeStartVal command");
for (int i = 0; i < 6; i++) {
token.GetNextToken();
opts.gtrParams[3 + i] = atof(token.GetToken().c_str());
if (opts.gtrParams[3 + i] <= 0.0)
throw XBull("rmatrix must be >0.0 CodLikeStartVal command");
}
token.GetNextToken();
if (!token.Equals(")"))
throw XBull("Expecting ) after rmatrix option to CodLikeStartVal command");
}
# ifdef ALLOWMULTIHITS
else if (token.Abbreviation("DOublehit")) { //not a great name, but allows multiplier abbreviation to work
SkipEqualsIfNext(token);
opts.gtrParams[MULTI_HIT_PARAM_INDEX] = atof(token.GetToken().c_str());
if (opts.gtrParams[MULTI_HIT_PARAM_INDEX] < 0.0)
throw XBull("DOublehit (MultipleHitProb) must be >= 0.0 CodLikeStartVal command");
}
# endif
else if (token.Abbreviation("AAFreq")) {
SkipEqualsIfNext(token);
if (!token.Equals("("))
throw XBull("Expecting ( after aafreq option to CodLikeStartVal command");
token.GetNextToken();
long tmp;
if (!NxsString::to_long(token.GetTokenAsCStr(), &tmp))
throw XBull("Expecting number of codons after aafreq=( option to CodLikeStartVal command");
if (tmp < 1)
throw XBull("number of codons must be >0 in CodLikeStartVal command");
unsigned naa = (unsigned) tmp;
opts.aaFreqs.assign(naa, blankRow);
for (unsigned ii = 0; ii < naa; ii++) {
token.GetNextToken();
if (!token.Equals("("))
throw XBull("Expecting ( for next site in aafreq option to CodLikeStartVal command", token);
DblVector & row = opts.aaFreqs[ii];
for (int j=0; j < 20; j++) {
token.SetLabileFlagBit(NxsToken::hyphenNotPunctuation);
token.GetNextToken();
row[j] = atof(token.GetToken().c_str());
if (row[j]<0.0)
throw XBull("each amino acid freq must be >0.0 CodLikeStartVal command", token);
}
token.GetNextToken();
if (!token.Equals(")"))
throw XBull("Expecting ) for next site in aafreq option to CodLikeStartVal command", token);
}
token.GetNextToken();
if (!token.Equals(")"))
throw XBull("Expecting ) after aafreq option to CodLikeStartVal command");
}
else if (token.Abbreviation("MUlt")) {
SkipEqualsIfNext(token);
if (!token.Equals("("))
throw XBull("Expecting ( after mult option to CodLikeStartVal command");
if (opts.aaFreqs.size() < 1)
throw XBull("number of codons must be specified (in the AAFreq subcommand) before the mult option is used in CodLikeStartVal command");
opts.multipliers.assign(opts.aaFreqs.size(), 1.0);
for (unsigned ii = 0; ii < opts.aaFreqs.size(); ii++) {
token.GetNextToken();
opts.multipliers[ii] = atof(token.GetToken().c_str());
if (opts.multipliers[ii] < 0.0)
throw XBull("multiplier must be > 0.0 CodLikeStartVal command");
}
token.GetNextToken();
if (!token.Equals(")"))
throw XBull("Expecting ) after mult option to CodLikeStartVal command");
}
else if (token.Abbreviation("TReescale")) {
SkipEqualsIfNext(token);
opts.treeScale = atof(token.GetToken().c_str());
if (opts.treeScale < 0.0)
throw XBull("The Tree scaling must be >0.0 CodLikeStartVal command");
}
token.GetNextToken();
}
}
/**
* @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;
}
