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;
}
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;
}