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;
}