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();
}
}
SimulateOpts BullShell::ParseSimulateCommand(NexusToken& token ) const {
token.GetNextToken();
int nOutputs = 0;
int nSimChars = 0;
SimulateOpts simOpts;
const unsigned nTrees = kernel.getNumTrees();
for (; token.GetToken() != ";"; token.GetNextToken()) {
if (token.Abbreviation("NReps")) {
DemandEquals(token, "after NReps subcommand of Simulate command");
simOpts.nReps = DemandPositiveInt(token, "after NReps subcommand of Simulate command");
}
if (token.Abbreviation("Seed")) {
DemandEquals(token, "after Seed subcommand of Simulate command");
simOpts.seed = DemandPositiveInt(token, "after Seed subcommand of Simulate command");
}
else if (token.Abbreviation("COLLapsefile")) {
DemandEquals(token, "after CollapseFile subcommand of Simulate command");
token.GetNextToken();
simOpts.collapsedTreeFilename = token.GetTokenReference();
}
else if (token.Abbreviation("NChars")) {
DemandEquals(token, "after NChars subcommand of Simulate command");
simOpts.nSimChars = DemandPositiveInt(token, "after NChars subcommand of Simulate command");
}
else if (token.Abbreviation("Concat")) {
DemandEquals(token, "after Concat subcommand of GetTrees command");
simOpts.concatenations = DemandPositiveInt(token, "after Concat subcommand of GetTrees command");
}
else if (token.Abbreviation("Verbose")) {
simOpts.verbose = true;
}
else if (token.Abbreviation("NOUTput")) {
DemandEquals(token, "after NOutput subcommand of Simulate command");
nOutputs = DemandPositiveInt(token, "after NOutput subcommand of Simulate command");
if (nOutputs < 1) {
errormsg="nOutputs must be > 0";
throw XBull( errormsg, token);
}
}
else if (token.Abbreviation("Paupblockfile")) {
DemandEquals(token, "after Paupblockfile subcommand of Simulate");
token.GetNextToken();
ReadNexusVector(&(simOpts.paupBlockFilename), token);
}
else if (token.Abbreviation("OVERWrite"))
simOpts.overwrite = true;
else if (token.Abbreviation("File")) {
DemandEquals(token, "after File subcommand of Simulate");
token.GetNextToken();
ReadNexusVector(&(simOpts.outputFilenames), token);
}
else if (token.Abbreviation("TAg")) {
DemandEquals(token, "after Tag subcommand of Simulate command");
token.GetNextToken();
simOpts.tagname = token.GetTokenReference();
}
else if (token.Abbreviation("AUTOmatic"))
simOpts.automatic = true;
else if (token.Abbreviation("OUTputtypes")) {
DemandEquals(token, "after OutputTypes subcommand of Simulate");
token.GetNextToken();
EncodingType et;
if (token.Equals("(")) {
token.GetNextToken();
while (!token.Equals(")")) {
et = InterpretOutputType(token);
simOpts.outTypes.push_back(et);
token.GetNextToken();
}
}
else {
et = InterpretOutputType(token);
simOpts.outTypes.push_back(et);
}
}
else {
Tree * temptree;
long tn;
if (NxsString::to_long(token.GetTokenAsCStr(), &tn)) {
if ((unsigned) tn > nTrees || tn < 1) {
errormsg = "Tree ";
errormsg += token.GetToken();
errormsg += " unknown. simulation aborted.";
throw XBull( errormsg, token);
}
temptree = kernel.getTree(tn - 1);
}
else {
try {
temptree = kernel.FindTreeFromName(token.GetToken());
}
catch (NoSuchTree) {
errormsg << "Tree " << token.GetToken() << " unknown.";
throw XBull( errormsg, token);
}
}
simOpts.treeNames.push_back(token.GetToken()); //keeps track of what the user called the tree
simOpts.treeAlias.push_back(temptree);
}
}
if (simOpts.outTypes.size() == 0){
simOpts.outTypes.push_back(EncodingType(DNANoGap));
}
if ((nOutputs > 0) && simOpts.outTypes.size() != (unsigned) nOutputs) {
errormsg = "The number of OutputTypes in a Simulate command must match the number of specified in the NOutput option";
throw XBull( errormsg, token);
}
if (simOpts.automatic) {
if (simOpts.tagname.empty()) {
errormsg = "The Tag option of the Simulate command must be used if the Automatic naming mode is requested.";
throw XBull( errormsg, token);
}
if (!simOpts.outputFilenames.empty()) {
errormsg = "The FILE option of the Simulate command cannot be used if the Automatic naming mode is requested (use the Tag instead of file).";
throw XBull( errormsg, token);
}
simOpts.outputFilenames.clear();
std::vector<EncodingType>::const_iterator ot = simOpts.outTypes.begin();
for (; ot != simOpts.outTypes.end(); ot++) {
string ofname = EncodingTypeToString(*ot);
ofname.append(simOpts.tagname);
simOpts.outputFilenames.push_back(ofname);
}
}
else if (simOpts.outTypes.size() != simOpts.outputFilenames.size()) {
errormsg = "The number of OutputTypes in a Simulate command must match the number of Files specified";
throw XBull( errormsg, token);
}
if ((!simOpts.paupBlockFilename.empty()) && simOpts.paupBlockFilename.size() != simOpts.outTypes.size()) {
errormsg = "The number of PaupBlockFile in a Simulate command must match the number of OutputTypes specified";
throw XBull( errormsg, token);
}
//TEMPORARY lots of the interaction with SSettings assumes that you are using SSRFCodonSubModel
if (!kernel.hasModel()) {
errormsg="You can't simulate a codon model without first declaring the models using codLikeStartVal";
throw XBull( errormsg, token);
}
if ( simOpts.concatenations == 0) {
if (nSimChars == 0) {
errormsg="Either the number of characters or the number of concatenations must be specified";
throw XBull( errormsg, token);
}
const unsigned naa = kernel.getModelConstRef().getNumAASites();
const unsigned ndna = 3*naa;
if (nSimChars % ndna) {
errormsg="The number of characters must be a multiple of the number of amino acids";
throw XBull( errormsg, token);
}
simOpts.concatenations = ndna/nSimChars;
}
return simOpts;
}
