Merge pull request #23 from fmichonneau/fix-ncl-cpp20

Author: fmichonneau

src/ncl/nxscharactersblock.h

@@ -23,6 +23,7 @@
 #include <sstream>
 #include <cfloat>
 #include <climits>
+#include <memory>
 
 #include "ncl/nxsdefs.h"
 #include "ncl/nxsdiscretedatum.h"
@@ -480,7 +481,7 @@ class NxsCharactersBlock
 		typedef std::vector<std::string> VecString;
 		typedef std::map<unsigned, std::string> IndexToLabelMap;
 		typedef std::map<std::string, unsigned> LabelToIndexMap;
-		typedef std::pair<NxsDiscreteDatatypeMapper, NxsUnsignedSet> DatatypeMapperAndIndexSet;
+		typedef std::pair<std::shared_ptr<NxsDiscreteDatatypeMapper>, NxsUnsignedSet> DatatypeMapperAndIndexSet;
 		typedef std::vector<DatatypeMapperAndIndexSet> VecDatatypeMapperAndIndexSet;
 
 
@@ -1535,7 +1536,7 @@ inline void NxsCharactersBlock::SetGapSymbol(char g)
 	{
 	gap = g;
 	if (datatypeMapperVec.size() == 1)
-		datatypeMapperVec[0].first.SetGapSymbol(g);
+		 datatypeMapperVec[0].first->SetGapSymbol(g);
 	}
 
 
@@ -1551,7 +1552,7 @@ inline NxsCharactersBlock::DataTypesEnum NxsCharactersBlock::GetDataType() const
 		return datatype;
 	if (datatypeMapperVec.size() > 1)
 		return mixed;
-	return datatypeMapperVec[0].first.GetDatatype();
+	return datatypeMapperVec[0].first->GetDatatype();
 	}
 
 inline NxsCharactersBlock::DataTypesEnum NxsCharactersBlock::GetOriginalDataType() const
@@ -1937,12 +1938,12 @@ inline const NxsCharactersBlock::ContinuousCharRow & NxsCharactersBlock::GetCont
 inline NxsDiscreteDatatypeMapper * NxsCharactersBlock::GetMutableDatatypeMapperForChar(unsigned int charIndex)
 	{
 	if (datatypeMapperVec.size() == 1)
-		return &(datatypeMapperVec[0].first);
+		return datatypeMapperVec[0].first.get();
 	for (VecDatatypeMapperAndIndexSet::iterator dmvIt = datatypeMapperVec.begin(); dmvIt != datatypeMapperVec.end(); ++dmvIt)
 		{
 		const NxsUnsignedSet & currCS = dmvIt->second;
 		if (currCS.count(charIndex) > 0)
-			return &(dmvIt->first);
+			return dmvIt->first.get();
 		}
 	return NULL;
 	}
@@ -1951,7 +1952,7 @@ inline std::vector<const NxsDiscreteDatatypeMapper *> NxsCharactersBlock::GetAll
 	{
 	std::vector<const NxsDiscreteDatatypeMapper *> v;
 	for (VecDatatypeMapperAndIndexSet::const_iterator dmvIt = datatypeMapperVec.begin(); dmvIt != datatypeMapperVec.end(); ++dmvIt)
-		v.push_back(&(dmvIt->first));
+		v.push_back(dmvIt->first.get());
 	return v;
 	}
 

src/nxscharactersblock.cpp

@@ -1542,8 +1542,8 @@ void NxsCharactersBlock::CreateDatatypeMapperObjects(const NxsPartition & dtPart
 		mixedTypeMapping.clear();
 		if (datatype != mixed)
 			{
-			NxsDiscreteDatatypeMapper d(datatype, symbols, missing, gap, matchchar, respectingCase, userEquates);
-			datatype = d.GetDatatype();
+            auto d = std::make_shared<NxsDiscreteDatatypeMapper>(datatype, symbols, missing, gap, matchchar, respectingCase, userEquates);
+            datatype = d->GetDatatype();
 			DatatypeMapperAndIndexSet das(d, NxsUnsignedSet());
 			datatypeMapperVec.clear();
 			datatypeMapperVec.push_back(das);
@@ -1560,7 +1560,7 @@ void NxsCharactersBlock::CreateDatatypeMapperObjects(const NxsPartition & dtPart
 				std::string mt;
 				if (*cIt == standard)
 					mt.assign("0123456789"); /*mrbayes is the only program to support MIXED and it uses a default (not extendable) symbols list of 0123456789 rather than 01*/
-				NxsDiscreteDatatypeMapper d(*cIt, mt, missing, gap, matchchar, respectingCase, userEquates);
+				auto d = std::make_shared<NxsDiscreteDatatypeMapper>(*cIt, mt, missing, gap, matchchar, respectingCase, userEquates);
 				const NxsUnsignedSet & indexSet = pIt->second;
 				DatatypeMapperAndIndexSet das(d, pIt->second);
 				NxsUnsignedSet & mappedInds =  mixedTypeMapping[*cIt];
@@ -1669,27 +1669,27 @@ bool NxsCharactersBlock::AugmentedSymbolsToMixed()
 
 	/* copy the incoming matrix and mapper */
 	VecDatatypeMapperAndIndexSet mdm = datatypeMapperVec;
-	const NxsDiscreteDatatypeMapper & oldMapper = mdm[0].first;
+	const NxsDiscreteDatatypeMapper & oldMapper = *mdm[0].first;
 	if (oldMapper.GetUserDefinedEquatesBeforeConversion())
 		return false; /* dealing with equates correctly is not implemented below, so we'll bale out */
 
 	/* add the new mappers */
 	std::map<char, NxsString> noEquates;
 	datatypeMapperVec.clear();
-	NxsDiscreteDatatypeMapper o(odt, origSymb, missing, gap, matchchar, respectingCase, noEquates);
+	auto o = std::make_shared<NxsDiscreteDatatypeMapper>(odt, origSymb, missing, gap, matchchar, respectingCase, noEquates);
 	datatypeMapperVec.push_back(DatatypeMapperAndIndexSet(o, origTypeChars));
-	NxsDiscreteDatatypeMapper s(NxsCharactersBlock::standard, augmentSymbols, missing, gap, matchchar, respectingCase, noEquates);
+	auto s = std::make_shared<NxsDiscreteDatatypeMapper>(NxsCharactersBlock::standard, augmentSymbols, missing, gap, matchchar, respectingCase, noEquates);
 	datatypeMapperVec.push_back(DatatypeMapperAndIndexSet(s, stdTypeChars));
 
 
-	NxsDiscreteDatatypeMapper & newOrigTMapper = datatypeMapperVec[0].first;
-	NxsDiscreteDatatypeMapper & newStdTMapper = datatypeMapperVec[1].first;
+    NxsDiscreteDatatypeMapper & newOrigTMapper = *datatypeMapperVec[0].first;
+    NxsDiscreteDatatypeMapper & newStdTMapper = *datatypeMapperVec[1].first;
 
 	/* now we recode discrete matrix with new state codes */
 	const NxsDiscreteStateCell nOrigStates = (NxsDiscreteStateCell) origSymb.size();
 	std::map<NxsDiscreteStateCell, NxsDiscreteStateCell> oldToNewStateCode;
 	NxsDiscreteStateMatrix::iterator rowIt = discreteMatrix.begin();
-	for (unsigned colIndex = 0; rowIt != discreteMatrix.end(); ++colIndex, ++rowIt)
+	for (; rowIt != discreteMatrix.end(); ++rowIt)
 		{
 		NxsDiscreteStateRow & row = *rowIt;
 		unsigned column = 0;
@@ -2298,7 +2298,7 @@ void NxsCharactersBlock::HandleFormat(
 		if (*b)
 			{
 			DatatypeMapperAndIndexSet &mapper = datatypeMapperVec.at(mapInd);
-			mapper.first.SetWasRestrictionDataype(true);
+			mapper.first->SetWasRestrictionDataype(true);
 			}
 		}
 	}
@@ -3352,7 +3352,6 @@ NxsDiscreteStateCell NxsCharactersBlock::HandleTokenState(
 	*/
 	NxsStringVector::const_iterator ci_begin	= bagIter->second.begin();
 	NxsStringVector::const_iterator ci_end		= bagIter->second.end();
-	NxsStringVector::const_iterator cit;
 	NxsDiscreteStateCell k = 0;
 	for (; ci_begin != ci_end; ++ci_begin, ++k)
 		{
@@ -4943,7 +4942,7 @@ void NxsCharactersBlock::WriteFormatCommand(std::ostream &out) const
 				first = false;
 			else
 				out << ", ";
-			out << GetNameOfDatatype(mIt->first.GetDatatype()) << ':';
+			out << GetNameOfDatatype(mIt->first->GetDatatype()) << ':';
 			NxsSetReader::WriteSetAsNexusValue(mIt->second, out);
 			}
 		out << ')';