/**
* @method HandleLog [void:protected]
* @param token [NexusToken&] the token used to read from in
* @throws XBull
*
* Called when the LOG command needs to be parsed
* from within the BullShell block.
*/
void BullShell::HandleLog( NexusToken& token )
{
bool starting = false;
bool stopping = false;
bool appending = false;
bool replacing = false;
std::string logfname;
errormsg.clear();
// Retrieve all tokens for this command, stopping only in the event
// of a semicolon or an unrecognized keyword
//
for (token.GetNextToken(); !token.Equals(";"); token.GetNextToken()) {
if ( token.Abbreviation("STOp") )
stopping = true;
else if ( token.Abbreviation("STArt") )
starting = true;
else if ( token.Abbreviation("Replace") )
replacing = true;
else if ( token.Abbreviation("Append") )
appending = true;
else if ( token.Abbreviation("File") ) {
DemandEquals(token, "after file subcommand of Log command");
token.GetNextToken();
logfname = token.GetTokenReference();
}
else {
errormsg << "Unexpected keyword (" << token.GetToken() << ") encountered reading LOG command";
throw XBull( errormsg, token);
}
}
// Check for incompatible combinations of keywords
if ( stopping && ( starting || appending || replacing || !logfname.empty() ) ) {
errormsg = "Cannot specify STOP with any of the following START, APPEND, REPLACE, FILE";
throw XBull( errormsg, token);
}
if ( appending && replacing ) {
errormsg = "Cannot specify APPEND and REPLACE at the same time";
throw XBull( errormsg, token);
}
if ( stopping ) {
ioObject.stopLogging();
kernel.logEachStep=false;
return;
}
if (logfname.empty() ) {
errormsg << "Must provide a file name when opening a log file\ne.g., log file=doofus.txt start replace;";
throw XBull(errormsg, token);
}
if (!appending && !replacing && FileExists(logfname.c_str())) {
errormsg << "File " << logfname << " exists.\n APPEND or REPLACE must be specified in the LOG command.";
throw XBull( errormsg, token);
}
ioObject.startLogging(logfname, appending);
}
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;
}
GetTreesOpts BullShell::ParseGetTrees(NexusToken& token ) const {
errormsg.clear();
if (kernel.getNumTaxa() == 0) {
errormsg="You can't get trees without an active set of taxa";
throw XBull( errormsg, token);
}
GetTreesOpts gto;
bool readingMostRecent = false;
gto.fromTree = -1;
gto.toTree = -1;
gto.mode = 7;
std::string filePref;
token.GetNextToken();
while (token.GetToken()!=";") {
if (token.Abbreviation("STOREBrlens")) {
token.GetNextToken();
gto.storeBrLensFromFile=true;
if (token.GetToken() == "=") {
token.GetNextToken();
if (token.Abbreviation("No"))
gto.storeBrLensFromFile=false;
else if (!token.Abbreviation("Yes")) {
errormsg="Expecting YES or NO after CurrentBranchLengths = option to LSCORE command";
throw XBull(errormsg, token);
}
}
}
else if (token.Abbreviation("FRom")) {
DemandEquals(token, "after From subcommand of GetTrees command");
gto.fromTree = DemandPositiveInt(token, "after From subcommand of GetTrees command");
if (gto.fromTree < 0) {
errormsg="Expecting positive integer after FROM option of GETTREES";
throw XBull(errormsg, token);
}
}
else if (token.Abbreviation("To")) {
DemandEquals(token, "after To subcommand of GetTrees command");
gto.toTree = DemandPositiveInt(token, "after To subcommand of GetTrees command");
if (gto.toTree < 0) {
errormsg="Expecting positive integer after TO option of GETTREES";
throw XBull(errormsg, token);
}
}
else if (token.Abbreviation("REplace"))
gto.mode=3;
else if (token.Abbreviation("Mode")) {
DemandEquals(token, "after Mode subcommand of GetTrees command");
gto.mode = DemandPositiveInt(token, "after Mode subcommand of GetTrees command");
if (gto.mode!=3 && gto.mode!=7) {
errormsg="Right now bull only get trees with mode 3 or mode 7";
throw XBull(errormsg, token);
}
}
else if (token.Abbreviation("FIle")) {
DemandEquals(token, "after File subcommand of GetTrees command");
token.GetNextToken();
gto.filename = token.GetTokenReference();
}
else if (token.Abbreviation("PREfix")) {
token.GetNextToken();
if (token.GetToken() == "=")
token.GetNextToken();
filePref = token.GetToken();
}
else if (token.Abbreviation("MOStrecent"))
readingMostRecent=true;
else {
errormsg = "Unrecognized subcommand (";
errormsg << token.GetTokenReference() << ") in GetTrees command.";
throw XBull(errormsg, token);
}
token.GetNextToken();
}
if (readingMostRecent) {
int highNum = GetHighestFileNum(filePref);
if (highNum < 0) {
errormsg << "Couldn't open file " << filePref << "0";
throw XBull(errormsg, token);
}
gto.filename = filePref;
gto.filename += highNum;
}
if (gto.fromTree > -1 && gto.toTree > gto.fromTree) {
errormsg << "The FromTree setting (" << gto.fromTree << ") cannot be less than the ToTree setting (" << gto.toTree << ")";
throw XBull(errormsg, token);
}
gto.fromTree = (gto.fromTree < 1 ? -1 : gto.fromTree - 1);
gto.toTree = (gto.toTree < 1 ? -1 : gto.toTree - 1);
return gto;
}
