fix in peptidedb

git-svn-id: svn+ssh://gitlab/srv/svn-repos/pdb-redo/trunk@209 a1961a4f-ab94-4bcc-80e8-33b5a54de466

src/PDB2Cif.cpp

@@ -5458,6 +5458,9 @@ int PDBFileParser::PDBChain::AlignResToSeqRes()
 		throw;
 		throw;
 	}
 	}
 
 
+	if (VERBOSE > 1)
+		printAlignment();
+	
 	// assign numbers to the residues that don't have them yet
 	// assign numbers to the residues that don't have them yet
 	stack<int> unnumbered;
 	stack<int> unnumbered;
 	for (x = 0; x < dimX; ++x)
 	for (x = 0; x < dimX; ++x)

src/PeptideDB.cpp

@@ -55,8 +55,9 @@ const map<string,char> kBaseMap{
 
 
 // --------------------------------------------------------------------
 // --------------------------------------------------------------------
 
 
-struct PeptideDBImpl
+class PeptideDBImpl
 {
 {
+  public:
 	PeptideDBImpl(istream& data, PeptideDBImpl* next);
 	PeptideDBImpl(istream& data, PeptideDBImpl* next);
 
 
 	~PeptideDBImpl()
 	~PeptideDBImpl()
@@ -64,11 +65,13 @@ struct PeptideDBImpl
 		delete mNext;
 		delete mNext;
 	}
 	}
 	
 	
-	/*unordered_*/set<string>	mKnownPeptides;
-	set<string>					mKnownBases;
-	cif::File					mFile;
-	cif::Category&				mChemComp;
-	PeptideDBImpl*				mNext;
+	PeptideDBImpl* pop()
+	{
+		auto result = mNext;
+		mNext = nullptr;
+		delete this;
+		return result;
+	}
 
 
 	string nameFor(const string& resName) const
 	string nameFor(const string& resName) const
 	{
 	{
@@ -113,6 +116,25 @@ struct PeptideDBImpl
 		
 		
 		return result;
 		return result;
 	}
 	}
+
+	bool isKnownPeptide(const string& resName)
+	{
+		return mKnownPeptides.count(resName) or
+			(mNext != nullptr and mNext->isKnownPeptide(resName));
+	}
+
+	bool isKnownBase(const string& resName)
+	{
+		return mKnownBases.count(resName) or
+			(mNext != nullptr and mNext->isKnownBase(resName));
+	}
+
+  private:
+	/*unordered_*/set<string>	mKnownPeptides;
+	set<string>					mKnownBases;
+	cif::File					mFile;
+	cif::Category&				mChemComp;
+	PeptideDBImpl*				mNext;
 };
 };
 
 
 PeptideDBImpl::PeptideDBImpl(istream& data, PeptideDBImpl* next)
 PeptideDBImpl::PeptideDBImpl(istream& data, PeptideDBImpl* next)
@@ -252,12 +274,7 @@ void PeptideDB::pushDictionary(boost::filesystem::path dict)
 void PeptideDB::popDictionary()
 void PeptideDB::popDictionary()
 {
 {
 	if (mImpl != nullptr)
 	if (mImpl != nullptr)
-	{
-		auto i = mImpl;
-		mImpl = i->mNext;
-		i->mNext = nullptr;
-		delete i;
-	}
+		mImpl = mImpl->pop();
 }
 }
 
 
 PeptideDB::~PeptideDB()
 PeptideDB::~PeptideDB()
@@ -267,12 +284,12 @@ PeptideDB::~PeptideDB()
 
 
 bool PeptideDB::isKnownPeptide(const string& resName) const
 bool PeptideDB::isKnownPeptide(const string& resName) const
 {
 {
-	return mImpl->mKnownPeptides.count(resName) > 0;
+	return mImpl->isKnownPeptide(resName);
 }
 }
 
 
 bool PeptideDB::isKnownBase(const string& resName) const
 bool PeptideDB::isKnownBase(const string& resName) const
 {
 {
-	return mImpl->mKnownBases.count(resName) > 0;
+	return mImpl->isKnownBase(resName);
 }
 }
 
 
 string PeptideDB::nameForResidue(const string& resName) const
 string PeptideDB::nameForResidue(const string& resName) const