MultiFormatReader * instantiateReader() {
MultiFormatReader * nexusReader = new MultiFormatReader(-1, NxsReader::WARNINGS_TO_STDERR);
if (gQuietMode) {
nexusReader->SetWarningOutputLevel(NxsReader::SKIPPING_CONTENT_WARNING);
}
if (gStrictLevel != 2) {
nexusReader->SetWarningToErrorThreshold((int)NxsReader::FATAL_WARNING + 1 - (int) gStrictLevel);
}
NxsCharactersBlock * charsB = nexusReader->GetCharactersBlockTemplate();
NxsDataBlock * dataB = nexusReader->GetDataBlockTemplate();
charsB->SetAllowAugmentingOfSequenceSymbols(true);
dataB->SetAllowAugmentingOfSequenceSymbols(true);
NxsTreesBlock * treesB = nexusReader->GetTreesBlockTemplate();
assert(treesB);
if (gStrictLevel < 2) {
treesB->SetAllowImplicitNames(true);
}
treesB->setValidateInternalNodeLabels(gValidateInternals);
treesB->setAllowNumericInterpretationOfTaxLabels(true);
if (gStrictLevel < 2) {
NxsStoreTokensBlockReader *storerB = nexusReader->GetUnknownBlockTemplate();
assert(storerB);
storerB->SetTolerateEOFInBlock(true);
}
nexusReader->conversionOutputRecord.addNumbersToDisambiguateNames = true;
return nexusReader;
}
////////////////////////////////////////////////////////////////////////////////
// Creates a NxsReader, and tries to read the file `filename`. If the
// read succeeds, then processContent will be called.
////////////////////////////////////////////////////////////////////////////////
void processFilepath(
const char * filename, // name of the file to be read
ostream *out, // output stream to use (NULL for no output). Not that cerr is used to report errors.
MultiFormatReader::DataFormatType fmt) // enum indicating the file format to expect.
{
assert(filename);
try
{
MultiFormatReader nexusReader(-1, NxsReader::WARNINGS_TO_STDERR);
if (gStrictLevel != 2)
nexusReader.SetWarningToErrorThreshold((int)NxsReader::FATAL_WARNING + 1 - (int) gStrictLevel);
NxsCharactersBlock * charsB = nexusReader.GetCharactersBlockTemplate();
NxsDataBlock * dataB = nexusReader.GetDataBlockTemplate();
charsB->SetAllowAugmentingOfSequenceSymbols(true);
dataB->SetAllowAugmentingOfSequenceSymbols(true);
if (gInterleaveLen > 0)
{
assert(charsB);
charsB->SetWriteInterleaveLen(gInterleaveLen);
dataB->SetWriteInterleaveLen(gInterleaveLen);
}
NxsTreesBlock * treesB = nexusReader.GetTreesBlockTemplate();
assert(treesB);
if (gStrictLevel < 2)
treesB->SetAllowImplicitNames(true);
if (!gTreesToSplitsB)
gTreesToSplitsB = new TreesToSplits();
treesB->setValidationCallbacks(newTreeHook, gTreesToSplitsB);
if (gStrictLevel < 2)
{
NxsStoreTokensBlockReader *storerB = nexusReader.GetUnknownBlockTemplate();
assert(storerB);
storerB->SetTolerateEOFInBlock(true);
}
cerr << "Executing" <<endl;
try {
nexusReader.ReadFilepath(filename, fmt);
processContent(nexusReader, out);
}
catch(...)
{
nexusReader.DeleteBlocksFromFactories();
throw;
}
nexusReader.DeleteBlocksFromFactories();
}
catch (const NxsException &x)
{
cerr << "Error:\n " << x.msg << endl;
if (x.line >=0)
cerr << "at line " << x.line << ", column (approximately) " << x.col << " (and file position "<< x.pos << ")" << endl;
exit(2);
}
}
MultiFormatReader * instantiateReader() {
MultiFormatReader * nexusReader = new MultiFormatReader(-1, NxsReader::WARNINGS_TO_STDERR);
if (gQuietMode)
nexusReader->SetWarningOutputLevel(NxsReader::SKIPPING_CONTENT_WARNING);
if (gStrictLevel != 2)
nexusReader->SetWarningToErrorThreshold((int)NxsReader::FATAL_WARNING + 1 - (int) gStrictLevel);
if (gUnderscoresToSpaces)
nexusReader->SetCoerceUnderscoresToSpaces(true);
NxsCharactersBlock * charsB = nexusReader->GetCharactersBlockTemplate();
NxsDataBlock * dataB = nexusReader->GetDataBlockTemplate();
charsB->SetAllowAugmentingOfSequenceSymbols(true);
dataB->SetAllowAugmentingOfSequenceSymbols(true);
if (gInterleaveLen > 0) {
assert(charsB);
charsB->SetWriteInterleaveLen(gInterleaveLen);
dataB->SetWriteInterleaveLen(gInterleaveLen);
}
NxsTreesBlock * treesB = nexusReader->GetTreesBlockTemplate();
assert(treesB);
if (gStrictLevel < 2)
treesB->SetAllowImplicitNames(true);
treesB->SetWriteFromNodeEdgeDataStructure(gTreesViaInMemoryStruct);
treesB->setValidateInternalNodeLabels(gValidateInternals);
if (gAltNexus)
treesB->setWriteTranslateTable(false);
if (gStrictLevel < 2) {
NxsStoreTokensBlockReader *storerB = nexusReader->GetUnknownBlockTemplate();
assert(storerB);
storerB->SetTolerateEOFInBlock(true);
}
nexusReader->conversionOutputRecord.addNumbersToDisambiguateNames = true;
if (gSuppressingNameTranslationFile)
nexusReader->conversionOutputRecord.writeNameTranslationFile = false;
return nexusReader;
}
extern "C" SEXP GetNCL(SEXP params, SEXP paramsVecR) {
Rcpp::List list(params);
Rcpp::LogicalVector paramsVec(paramsVecR);
bool charall = paramsVec[0];
bool polyconvert = paramsVec[1];
bool levelsUnif = paramsVec[2];
bool returnTrees = paramsVec[3];
bool returnData = paramsVec[4];
int nCharToReturn = 0;
std::vector<std::string> dataTypes; //vector of datatypes for each character block
std::vector<int> nbCharacters; //number of characters for each character block
std::vector<std::string> dataChr; //characters
std::vector<std::string> charLabels; //labels for the characters
std::vector<std::string> stateLabels; //labels for the states
std::vector<int> nbStates; //number of states for each character (for Standard datatype)
std::vector<std::string> trees; //vector of Newick strings holding the names
std::vector<std::string> treeNames; //vector of tree names
std::vector<std::string> taxaNames; //vector of taxa names
std::vector<bool> test(3);
test[0] = charall;
test[1] = polyconvert;
test[2] = levelsUnif;
# if defined(FILENAME_AS_NEXUS)
std::string filename = "'" + list["fileName"] + "'";
# else
std::string filename = list["fileName"];
# endif
MultiFormatReader nexusReader(-1, NxsReader::WARNINGS_TO_STDERR);
/* make NCL less strict */
NxsTreesBlock * treesB = nexusReader.GetTreesBlockTemplate();
treesB->SetAllowImplicitNames(true);
nexusReader.cullIdenticalTaxaBlocks(true);
/* End of making NCL less strict */
nexusReader.ReadFilepath(const_cast < char* > (filename.c_str()), MultiFormatReader::NEXUS_FORMAT);
const unsigned nTaxaBlocks = nexusReader.GetNumTaxaBlocks();
for (unsigned t = 0; t < nTaxaBlocks; ++t) {
/* Get blocks */
const NxsTaxaBlock * taxaBlock = nexusReader.GetTaxaBlock(t);
const unsigned nTreesBlocks = nexusReader.GetNumTreesBlocks(taxaBlock);
const unsigned nCharBlocks = nexusReader.GetNumCharactersBlocks(taxaBlock);
int nTax = taxaBlock->GetNumTaxonLabels();
/* Get taxa names */
for (int j=0; j < nTax; ++j) {
taxaNames.push_back (taxaBlock->GetTaxonLabel(j));
}
/* Get trees */
if (returnTrees) {
if (nTreesBlocks == 0) {
continue;
}
for (unsigned i = 0; i < nTreesBlocks; ++i) {
NxsTreesBlock* treeBlock = nexusReader.GetTreesBlock(taxaBlock, i);
const unsigned nTrees = treeBlock->GetNumTrees();
if (nTrees > 0) {
for (unsigned k = 0; k < nTrees; k++) {
NxsString ts = treeBlock->GetTreeDescription(k);
NxsString trNm = treeBlock->GetTreeName(k);
treeNames.push_back(trNm);
trees.push_back (ts);
}
}
else {
continue;
}
}
}
/* Get data */
if (returnData) {
for (unsigned k = 0; k < nCharBlocks; ++k) {
NxsCharactersBlock * charBlock = nexusReader.GetCharactersBlock(taxaBlock, k);
if (nCharBlocks == 0) {
continue;
}
else {
NxsString dtType = charBlock->GetNameOfDatatype(charBlock->GetDataType());
dataTypes.push_back(dtType);
if (charall) {
nCharToReturn=charBlock->GetNCharTotal();
}
else {
nCharToReturn=charBlock->GetNumIncludedChars();
}
nbCharacters.push_back (nCharToReturn);
for (int eachChar=0; eachChar < nCharToReturn; ++eachChar) { //We only pass the non-eliminated chars
NxsString charLabel=charBlock->GetCharLabel(eachChar);
if (charLabel.length()>1) {
charLabels.push_back (charLabel);
}
else {
charLabels.push_back ("standard_char"); //FIXME: needs to fixed for sequence data
}
NxsString tmpCharString;
if (std::string("Continuous") == dtType) {
tmpCharString = contData(*charBlock, tmpCharString, eachChar, nTax);
nbStates.push_back (0);
}
else {
if (std::string("Standard") == dtType) {
tmpCharString = stdData(*charBlock, tmpCharString, eachChar, nTax,
polyconvert);
unsigned int nCharStates = charBlock->GetNumObsStates(eachChar, false);
nbStates.push_back (nCharStates);
for (unsigned int l=0; l < nCharStates; ++l) {
NxsString label = charBlock->GetStateLabel(eachChar, l);
stateLabels.push_back (label);
}
}
else {
if (std::string("DNA") == dtType) {
for (int taxon=0; taxon < nTax; ++taxon) {
for (int eachChar=0; eachChar < nCharToReturn; ++eachChar) {
unsigned int nCharStates = charBlock->GetNumStates(taxon, eachChar);
if (charBlock->IsGapState(taxon, eachChar)) {
tmpCharString += "-";
}
else {
if (charBlock->IsMissingState(taxon, eachChar)) {
tmpCharString += "?";
}
else {
if (nCharStates == 1) {
tmpCharString += charBlock->GetState(taxon, eachChar, 0);
}
else {
tmpCharString += "?"; //FIXME
}
}
}
}
}
}
else { // other type of data not yet supported
tmpCharString = "";
nbStates.push_back (0);
stateLabels.push_back (std::string(""));
}
}
}
std::string charString = "c(" + tmpCharString + ");";
dataChr.push_back (charString);
}
}
}
}
}
/* Prepare list to return */
Rcpp::List res = Rcpp::List::create(Rcpp::Named("taxaNames") = taxaNames,
Rcpp::Named("treeNames") = treeNames,
Rcpp::Named("trees") = trees,
Rcpp::Named("dataTypes") = dataTypes,
Rcpp::Named("nbCharacters") = nbCharacters,
Rcpp::Named("charLabels") = charLabels,
Rcpp::Named("nbStates") = nbStates,
Rcpp::Named("stateLabels") = stateLabels,
Rcpp::Named("dataChr") = dataChr,
Rcpp::Named("Test") = test);
return res;
}
