Commit b8089f17 authored by Vedran Miletić's avatar Vedran Miletić

Remove using std:: (containers)

parent 69fd7265
......@@ -80,7 +80,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtCell> RbtCellPtr; // Smart pointer
typedef vector<RbtCellPtr> RbtCellList; // Vector of smart pointers
typedef std::vector<RbtCellPtr> RbtCellList; // Vector of smart pointers
typedef RbtCellList::iterator RbtCellListIter;
typedef RbtCellList::const_iterator RbtCellListConstIter;
......
......@@ -53,7 +53,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtCommand> RbtCommandPtr; // Smart pointer
typedef vector<RbtCommandPtr> RbtCommandList; // Vector of smart pointers
typedef std::vector<RbtCommandPtr> RbtCommandList; // Vector of smart pointers
typedef RbtCommandList::iterator RbtCommandListIter;
typedef RbtCommandList::const_iterator RbtCommandListConstIter;
class AddCommand : public RbtCommand {
......
......@@ -46,7 +46,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtGPFFCHK1> RbtGPFFCHK1Ptr; // Smart pointer
typedef vector<RbtGPFFCHK1Ptr> RbtGPFFCHK1List; // Vector of smart pointers
typedef std::vector<RbtGPFFCHK1Ptr> RbtGPFFCHK1List; // Vector of smart pointers
typedef RbtGPFFCHK1List::iterator RbtGPFFCHK1ListIter;
typedef RbtGPFFCHK1List::const_iterator RbtGPFFCHK1ListConstIter;
#endif //_RbtGPFFCHK1
......@@ -39,7 +39,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtGPFFCrossDock> RbtGPFFCrossDockPtr; // Smart pointer
typedef vector<RbtGPFFCrossDockPtr>
typedef std::vector<RbtGPFFCrossDockPtr>
RbtGPFFCrossDockList; // Vector of smart pointers
typedef RbtGPFFCrossDockList::iterator RbtGPFFCrossDockListIter;
typedef RbtGPFFCrossDockList::const_iterator RbtGPFFCrossDockListConstIter;
......
......@@ -35,7 +35,7 @@ public:
// Useful typedefs
typedef SmartPtr<RbtGPFFGold> RbtGPFFGoldPtr; // Smart pointer
typedef vector<RbtGPFFGoldPtr> RbtGPFFGoldList; // Vector of smart pointers
typedef std::vector<RbtGPFFGoldPtr> RbtGPFFGoldList; // Vector of smart pointers
typedef RbtGPFFGoldList::iterator RbtGPFFGoldListIter;
typedef RbtGPFFGoldList::const_iterator RbtGPFFGoldListConstIter;
#endif //_RbtGPFFGold
......@@ -47,7 +47,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtGPFFHSP90> RbtGPFFHSP90Ptr; // Smart pointer
typedef vector<RbtGPFFHSP90Ptr> RbtGPFFHSP90List; // Vector of smart pointers
typedef std::vector<RbtGPFFHSP90Ptr> RbtGPFFHSP90List; // Vector of smart pointers
typedef RbtGPFFHSP90List::iterator RbtGPFFHSP90ListIter;
typedef RbtGPFFHSP90List::const_iterator RbtGPFFHSP90ListConstIter;
#endif //_RbtGPFFHSP90
......@@ -46,7 +46,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtGPFFSpike> RbtGPFFSpikePtr; // Smart pointer
typedef vector<RbtGPFFSpikePtr> RbtGPFFSpikeList; // Vector of smart pointers
typedef std::vector<RbtGPFFSpikePtr> RbtGPFFSpikeList; // Vector of smart pointers
typedef RbtGPFFSpikeList::iterator RbtGPFFSpikeListIter;
typedef RbtGPFFSpikeList::const_iterator RbtGPFFSpikeListConstIter;
#endif //_RbtGPFFSpike
......@@ -58,7 +58,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtGPFitnessFunction> RbtGPFitnessFunctionPtr; // Smart pointer
typedef vector<RbtGPFitnessFunctionPtr>
typedef std::vector<RbtGPFitnessFunctionPtr>
RbtGPFitnessFunctionList; // Vector of smart pointers
typedef RbtGPFitnessFunctionList::iterator RbtGPFitnessFunctionListIter;
typedef RbtGPFitnessFunctionList::const_iterator
......
......@@ -68,7 +68,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtGPGenome> RbtGPGenomePtr; // Smart pointer
typedef vector<RbtGPGenomePtr> RbtGPGenomeList; // Vector of smart pointers
typedef std::vector<RbtGPGenomePtr> RbtGPGenomeList; // Vector of smart pointers
typedef RbtGPGenomeList::iterator RbtGPGenomeListIter;
typedef RbtGPGenomeList::const_iterator RbtGPGenomeListConstIter;
......
......@@ -81,7 +81,7 @@ private:
RbtReturnTypeArray ittrain, sfttrain;
};
typedef SmartPtr<RbtGPPopulation> RbtGPPopulationPtr;
typedef vector<RbtGPPopulationPtr> RbtGPPopulationList;
typedef std::vector<RbtGPPopulationPtr> RbtGPPopulationList;
typedef RbtGPPopulationList::iterator RbtGPPopulationListIter;
// Compare class to compare different populations. Use to find the
......
......@@ -21,8 +21,8 @@
// operator[] and size() defined on it
typedef float RbtReturnType;
typedef SmartPtr<RbtReturnType> RbtReturnTypePtr; // Smart pointer
typedef vector<RbtReturnTypePtr> RbtReturnTypeList; // Vector of smart pointers
typedef vector<RbtReturnTypeList> RbtReturnTypeArray; // Vector of smart
typedef std::vector<RbtReturnTypePtr> RbtReturnTypeList; // Vector of smart pointers
typedef std::vector<RbtReturnTypeList> RbtReturnTypeArray; // Vector of smart
// pointers
typedef RbtReturnTypeList::iterator RbtReturnTypeListIter;
typedef RbtReturnTypeList::const_iterator RbtReturnTypeListConstIter;
......
......@@ -82,7 +82,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtAnnotation> RbtAnnotationPtr; // Smart pointer
typedef vector<RbtAnnotationPtr> RbtAnnotationList; // Vector of smart pointers
typedef std::vector<RbtAnnotationPtr> RbtAnnotationList; // Vector of smart pointers
typedef RbtAnnotationList::iterator RbtAnnotationListIter;
typedef RbtAnnotationList::const_iterator RbtAnnotationListConstIter;
......
......@@ -36,7 +36,7 @@ public:
// Map of bonds the atom is bonded to
// Key is regular RbtBond*, value is RbtBool
// RbtBool is true if this atom is atom1 in the bond, false if atom2
typedef map<RbtBond *, bool, Rbt::RbtBondPCmp_BondId> RbtBondMap;
typedef std::map<RbtBond *, bool, Rbt::RbtBondPCmp_BondId> RbtBondMap;
typedef RbtBondMap::iterator RbtBondMapIter;
typedef RbtBondMap::const_iterator RbtBondMapConstIter;
......@@ -261,7 +261,7 @@ public:
///////////////////////////////////////////////
// DM 11 Jan 1999 - give atoms the ability to save their current coords
// and revert to the saved coords. Useful for Monte Carlo simulations.
// DM 08 Feb 1999 - all saved coords are now saved in a map<RbtUInt,RbtCoord>
// DM 08 Feb 1999 - all saved coords are now saved in a std::map<RbtUInt,RbtCoord>
// map key=0 is reserved for the default SaveCoords and RevertCoords
void SaveCoords(unsigned int coordNum = 0);
void RevertCoords(unsigned int coordNum = 0);
......@@ -336,30 +336,30 @@ private:
double m_dReweight; // XB reweighting factor
RbtUIntCoordMap m_savedCoords; // DM 08 Feb 1999 - now store all saved coords
// in a map<RbtUInt,RbtCoord>
// in a std::map<RbtUInt,RbtCoord>
};
// Useful typedefs
typedef SmartPtr<RbtAtom> RbtAtomPtr; // Smart pointer
typedef vector<RbtAtomPtr> RbtAtomList; // Vector of smart pointers
typedef std::vector<RbtAtomPtr> RbtAtomList; // Vector of smart pointers
typedef RbtAtomList::iterator RbtAtomListIter;
typedef RbtAtomList::const_iterator RbtAtomListConstIter;
typedef vector<RbtAtom *> RbtAtomRList; // Vector of regular pointers
typedef std::vector<RbtAtom *> RbtAtomRList; // Vector of regular pointers
typedef RbtAtomRList::iterator RbtAtomRListIter;
typedef RbtAtomRList::const_iterator RbtAtomRListConstIter;
typedef vector<RbtAtomList>
typedef std::vector<RbtAtomList>
RbtAtomListList; // A vector of atom vectors (e.g. for storing ring systems)
typedef RbtAtomListList::iterator RbtAtomListListIter;
typedef RbtAtomListList::const_iterator RbtAtomListListConstIter;
typedef vector<RbtAtomRList>
typedef std::vector<RbtAtomRList>
RbtAtomRListList; // A vector of atom vectors (regular pointer version)
typedef RbtAtomRListList::iterator RbtAtomRListListIter;
typedef RbtAtomRListList::const_iterator RbtAtomRListListConstIter;
typedef list<RbtAtomPtr> RbtAtomTrueList; // A real list of smart pointers
typedef std::list<RbtAtomPtr> RbtAtomTrueList; // A real list of smart pointers
typedef RbtAtomTrueList::iterator RbtAtomTrueListIter;
typedef RbtAtomTrueList::const_iterator RbtAtomTrueListConstIter;
......@@ -1111,7 +1111,7 @@ inline RbtAtomList GetPlanarAtomList(const RbtAtomList &atomList) {
// Helper function to return the atom pointer for the "other" atom in the bond
// i.e. return (bondPair.second) ? bondPair.first->GetAtom2Ptr() :
// bondPair.first->GetAtom1Ptr();
RbtAtomPtr GetBondedAtomPtr(pair<RbtBond *, bool> bondBoolPair);
RbtAtomPtr GetBondedAtomPtr(std::pair<RbtBond *, bool> bondBoolPair);
// This pair of functions is a little different to the above
// They convert a RbtBondMap to an RbtAtomList. The BondMap is assumed to
......
......@@ -21,7 +21,7 @@
// useful typedefs
typedef std::string RbtFileRec;
typedef vector<RbtFileRec> RbtFileRecList;
typedef std::vector<RbtFileRec> RbtFileRecList;
typedef RbtFileRecList::iterator RbtFileRecListIter;
// Max line length expected in file
......
......@@ -183,7 +183,7 @@ public:
RbtCoordList GetCoordList(const RbtUIntSet &iXYZSet) const;
// DM 17 May 1999 - returns the set of valid grid points within a sphere of a
// given center and radius DM 17 Jul 2000 - use vector<RbtUInt> and return by
// given center and radius DM 17 Jul 2000 - use std::vector<RbtUInt> and return by
// reference, for performance boost
void GetSphereIndices(const RbtCoord &c, double radius,
RbtUIntList &sIndices) const;
......
......@@ -114,7 +114,7 @@ private:
};
// Useful typedefs
typedef vector<RbtBaseObject *> RbtBaseObjectList; // Vector of smart pointers
typedef std::vector<RbtBaseObject *> RbtBaseObjectList; // Vector of smart pointers
typedef RbtBaseObjectList::iterator RbtBaseObjectListIter;
typedef RbtBaseObjectList::const_iterator RbtBaseObjectListConstIter;
......
......@@ -105,7 +105,7 @@ private:
};
// Useful typedefs
typedef vector<RbtBaseSF *> RbtBaseSFList; // Vector of smart pointers
typedef std::vector<RbtBaseSF *> RbtBaseSFList; // Vector of smart pointers
typedef RbtBaseSFList::iterator RbtBaseSFListIter;
typedef RbtBaseSFList::const_iterator RbtBaseSFListConstIter;
......
......@@ -94,7 +94,7 @@ private:
};
// Useful typedefs
typedef vector<RbtBaseTransform *>
typedef std::vector<RbtBaseTransform *>
RbtBaseTransformList; // Vector of smart pointers
typedef RbtBaseTransformList::iterator RbtBaseTransformListIter;
typedef RbtBaseTransformList::const_iterator RbtBaseTransformListConstIter;
......
......@@ -119,7 +119,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtBond> RbtBondPtr; // Smart pointer
typedef vector<RbtBondPtr> RbtBondList; // Vector of smart pointers
typedef std::vector<RbtBondPtr> RbtBondList; // Vector of smart pointers
typedef RbtBondList::iterator RbtBondListIter;
typedef RbtBondList::const_iterator RbtBondListConstIter;
......
......@@ -153,7 +153,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtCavity> RbtCavityPtr; // Smart pointer
typedef vector<RbtCavityPtr> RbtCavityList; // Vector of smart pointers
typedef std::vector<RbtCavityPtr> RbtCavityList; // Vector of smart pointers
typedef RbtCavityList::iterator RbtCavityListIter;
typedef RbtCavityList::const_iterator RbtCavityListConstIter;
......
......@@ -57,7 +57,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtCellTokenIter> RbtCellTokenIterPtr; // Smart pointer
typedef vector<RbtCellTokenIterPtr>
typedef std::vector<RbtCellTokenIterPtr>
RbtCellTokenIterList; // Vector of smart pointers
typedef RbtCellTokenIterList::iterator RbtCellTokenIterListIter;
typedef RbtCellTokenIterList::const_iterator RbtCellTokenIterListConstIter;
......
......@@ -19,7 +19,7 @@
#include "RbtConfig.h"
// Added by DM, 8 Dec 1998 for HybridState lookup method
typedef map<std::string, RbtAtom::eHybridState> RbtStringHybridStateMap;
typedef std::map<std::string, RbtAtom::eHybridState> RbtStringHybridStateMap;
typedef RbtStringHybridStateMap::iterator RbtStringHybridStateMapIter;
typedef RbtStringHybridStateMap::const_iterator
RbtStringHybridStateMapConstIter;
......
......@@ -30,7 +30,7 @@ public:
std::string comment;
};
typedef vector<CharmmType> RbtCharmmTypeList;
typedef std::vector<CharmmType> RbtCharmmTypeList;
typedef RbtCharmmTypeList::iterator RbtCharmmTypeListIter;
class RbtCharmmTypesFileSource : public RbtBaseFileSource {
......
......@@ -24,10 +24,10 @@
// GetVector(RbtDoubleList&) returns a flat vector of doubles (for use by
// Simplex) GetVector(RbtXOverList&) returns a vector of RbtXOverElements (for
// use by crossover)
typedef vector<double> RbtXOverElement;
typedef std::vector<double> RbtXOverElement;
typedef RbtXOverElement::iterator RbtXOverElementIter;
typedef RbtXOverElement::const_iterator RbtXOverElementConstIter;
typedef vector<RbtXOverElement> RbtXOverList;
typedef std::vector<RbtXOverElement> RbtXOverList;
typedef RbtXOverList::iterator RbtXOverListIter;
typedef RbtXOverList::const_iterator RbtXOverListConstIter;
......@@ -154,7 +154,7 @@ private:
};
typedef SmartPtr<RbtChromElement> RbtChromElementPtr;
typedef vector<RbtChromElement *>
typedef std::vector<RbtChromElement *>
RbtChromElementList; // Vector of regular pointers
typedef RbtChromElementList::iterator RbtChromElementListIter;
typedef RbtChromElementList::const_iterator RbtChromElementListConstIter;
......
......@@ -96,7 +96,7 @@ private:
// Useful typedefs
// typedef SmartPtr<RbtCommands> RbtCommandsPtr; //Smart pointer
// typedef vector<RbtCommandsPtr> RbtCommandsList;//Vector of smart pointers
// typedef std::vector<RbtCommandsPtr> RbtCommandsList;//Vector of smart pointers
// typedef RbtCommandsList::iterator RbtCommandsListIter;
// typedef RbtCommandsList::const_iterator RbtCommandsListConstIter;
......
......@@ -60,7 +60,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtConstraint> RbtConstraintPtr; // Smart pointer
typedef vector<RbtConstraintPtr> RbtConstraintList; // Vector of smart pointers
typedef std::vector<RbtConstraintPtr> RbtConstraintList; // Vector of smart pointers
typedef RbtConstraintList::iterator RbtConstraintListIter;
typedef RbtConstraintList::const_iterator RbtConstraintListConstIter;
......
......@@ -16,19 +16,9 @@
#define _RBTCONTAINERS_H_
#include <vector>
using std::vector;
#include <map>
using std::make_pair;
using std::map;
using std::multimap;
using std::pair;
#include <list>
using std::list;
#include <set>
using std::set;
#include <algorithm>
// DM 9 Dec 1998 - add copy_if template to std namespace (not included in STL)
......@@ -54,27 +44,27 @@ OutputIterator copy_if(InputIterator first, InputIterator last,
// Container Typedefs
// double
typedef vector<double> RbtDoubleList;
typedef std::vector<double> RbtDoubleList;
typedef RbtDoubleList::iterator RbtDoubleListIter;
typedef RbtDoubleList::const_iterator RbtDoubleListConstIter;
// int
typedef vector<int> RbtIntList;
typedef std::vector<int> RbtIntList;
typedef RbtIntList::iterator RbtIntListIter;
typedef RbtIntList::const_iterator RbtIntListConstIter;
// uint
typedef vector<unsigned int> RbtUIntList;
typedef std::vector<unsigned int> RbtUIntList;
typedef RbtUIntList::iterator RbtUIntListIter;
typedef RbtUIntList::const_iterator RbtUIntListConstIter;
// string
typedef vector<std::string> RbtStringList;
typedef std::vector<std::string> RbtStringList;
typedef RbtStringList::iterator RbtStringListIter;
typedef RbtStringList::const_iterator RbtStringListConstIter;
// bool
typedef vector<bool> RbtBoolVec; // vector of bools
typedef std::vector<bool> RbtBoolVec; // vector of bools
typedef RbtBoolVec::iterator RbtBoolVecIter;
typedef RbtBoolVec::const_iterator RbtBoolVecConstIter;
......@@ -83,33 +73,33 @@ typedef RbtBoolVec::const_iterator RbtBoolVecConstIter;
// RbtSegmentMap holds a map of (key=unique segment name, value=number of atoms
// in segment)
typedef std::string RbtSegment;
typedef map<RbtSegment, unsigned int> RbtSegmentMap;
typedef std::map<RbtSegment, unsigned int> RbtSegmentMap;
typedef RbtSegmentMap::iterator RbtSegmentMapIter;
typedef RbtSegmentMap::const_iterator RbtSegmentMapConstIter;
// Map of (key=string, value=integer)
typedef map<std::string, int> RbtStringIntMap;
typedef std::map<std::string, int> RbtStringIntMap;
typedef RbtStringIntMap::iterator RbtStringIntMapIter;
typedef RbtStringIntMap::const_iterator RbtStringIntMapConstIter;
// Map of (key=string, value=double)
typedef map<std::string, double> RbtStringDoubleMap;
typedef std::map<std::string, double> RbtStringDoubleMap;
typedef RbtStringDoubleMap::iterator RbtStringDoubleMapIter;
typedef RbtStringDoubleMap::const_iterator RbtStringDoubleMapConstIter;
// Added by DM, 3 Dec 1998
// Map of (key=string, value=bool)
typedef map<std::string, bool> RbtStringBoolMap;
typedef std::map<std::string, bool> RbtStringBoolMap;
typedef RbtStringBoolMap::iterator RbtStringBoolMapIter;
typedef RbtStringBoolMap::const_iterator RbtStringBoolMapConstIter;
// Map of (key=int, value=string)
typedef map<int, std::string> RbtIntStringMap;
typedef std::map<int, std::string> RbtIntStringMap;
typedef RbtIntStringMap::iterator RbtIntStringMapIter;
typedef RbtIntStringMap::const_iterator RbtIntStringMapConstIter;
// Set of (key=uint)
typedef set<unsigned int> RbtUIntSet;
typedef std::set<unsigned int> RbtUIntSet;
typedef RbtUIntSet::iterator RbtUIntSetIter;
typedef RbtUIntSet::const_iterator RbtUIntSetConstIter;
......
......@@ -24,8 +24,8 @@
#include "RbtVble.h"
#include <fstream>
typedef map<std::string, RbtVblePtr> RbtStringVbleMap; // Map of Vbles
typedef map<int, RbtVblePtr> RbtIntVbleMap; // Map of Vbles
typedef std::map<std::string, RbtVblePtr> RbtStringVbleMap; // Map of Vbles
typedef std::map<int, RbtVblePtr> RbtIntVbleMap; // Map of Vbles
typedef RbtStringVbleMap::iterator RbtStringVbleMapIter;
typedef RbtIntVbleMap::iterator RbtIntVbleMapIter;
......@@ -127,17 +127,17 @@ private:
// Useful typedefs
typedef SmartPtr<RbtCellContext> RbtCellContextPtr; // Smart pointer
typedef vector<RbtCellContextPtr> RbtCellContextList; // Vector of smart
typedef std::vector<RbtCellContextPtr> RbtCellContextList; // Vector of smart
// pointers
typedef RbtCellContextList::iterator RbtCellContextListIter;
typedef RbtCellContextList::const_iterator RbtCellContextListConstIter;
typedef SmartPtr<RbtStringContext> RbtStringContextPtr; // Smart pointer
typedef vector<RbtStringContextPtr>
typedef std::vector<RbtStringContextPtr>
RbtStringContextList; // Vector of smart pointers
typedef RbtStringContextList::iterator RbtStringContextListIter;
typedef RbtStringContextList::const_iterator RbtStringContextListConstIter;
typedef SmartPtr<RbtContext> RbtContextPtr; // Smart pointer
typedef vector<RbtContextPtr> RbtContextList; // Vector of smart pointers
typedef std::vector<RbtContextPtr> RbtContextList; // Vector of smart pointers
typedef RbtContextList::iterator RbtContextListIter;
typedef RbtContextList::const_iterator RbtContextListConstIter;
......
......@@ -324,16 +324,16 @@ public:
// treated as -3D vectors from those are treated as 3-D points, use this typedef
typedef RbtCoord RbtVector;
typedef vector<RbtCoord> RbtCoordList; // Vector of coords
typedef std::vector<RbtCoord> RbtCoordList; // Vector of coords
typedef RbtCoordList::iterator RbtCoordListIter;
typedef RbtCoordList::const_iterator RbtCoordListConstIter;
// DM 19/1/99 typedefs for a map of key=RbtInt, value=RbtCoord
// typedef map<RbtString,RbtCoord> RbtStringCoordMap;
// typedef std::map<RbtString,RbtCoord> RbtStringCoordMap;
// typedef RbtStringCoordMap::iterator RbtStringCoordMapIter;
// typedef RbtStringCoordMap::const_iterator RbtStringCoordMapConstIter;
// DM 08 Feb 1999 - Changed from key=string to key=int
typedef map<unsigned int, RbtCoord> RbtUIntCoordMap;
typedef std::map<unsigned int, RbtCoord> RbtUIntCoordMap;
typedef RbtUIntCoordMap::iterator RbtUIntCoordMapIter;
typedef RbtUIntCoordMap::const_iterator RbtUIntCoordMapConstIter;
......
......@@ -68,11 +68,11 @@ private:
RbtAtom *m_pAtom2;
RbtAtom *m_pAtom3;
RbtAtom *m_pAtom4;
vector<prms> m_prms;
std::vector<prms> m_prms;
};
// Useful typedefs
typedef vector<RbtDihedral *> RbtDihedralList; // Vector of smart pointers
typedef std::vector<RbtDihedral *> RbtDihedralList; // Vector of smart pointers
typedef RbtDihedralList::iterator RbtDihedralListIter;
typedef RbtDihedralList::const_iterator RbtDihedralListConstIter;
......
......@@ -55,8 +55,8 @@ public:
/**
* ReadFiles should be re-defined by derived classes to match argument
* Ie ReadFile(vector<string> anStrVect) reads file and stores result in
* anStrVect, or ReadFile(map< ... > aMap) in aMap, etc.
* Ie ReadFile(std::vector<string> anStrVect) reads file and stores result in
* anStrVect, or ReadFile(std::map< ... > aMap) in aMap, etc.
*
*/
// virtual void ReadFiles()=0;
......
......@@ -34,12 +34,12 @@ public:
};
// Map with element data indexed by element name
typedef map<std::string, RbtElementData> RbtStringElementDataMap;
typedef std::map<std::string, RbtElementData> RbtStringElementDataMap;
typedef RbtStringElementDataMap::iterator RbtStringElementDataMapIter;
typedef RbtStringElementDataMap::const_iterator
RbtStringElementDataMapConstIter;
// Map with element data indexed by atomic number
typedef map<int, RbtElementData> RbtIntElementDataMap;
typedef std::map<int, RbtElementData> RbtIntElementDataMap;
typedef RbtIntElementDataMap::iterator RbtIntElementDataMapIter;
typedef RbtIntElementDataMap::const_iterator RbtIntElementDataMapConstIter;
......
......@@ -35,7 +35,7 @@ public:
typedef SmartPtr<RbtFFTPeak> RbtFFTPeakPtr; // Smart pointer
// Multi-map of key=peak height,value=FFTPeakPtr
typedef multimap<double, RbtFFTPeakPtr> RbtFFTPeakMap;
typedef std::multimap<double, RbtFFTPeakPtr> RbtFFTPeakMap;
typedef RbtFFTPeakMap::iterator RbtFFTPeakMapIter;
typedef RbtFFTPeakMap::reverse_iterator RbtFFTPeakMapRIter;
typedef RbtFFTPeakMap::const_iterator RbtFFTPeakMapConstIter;
......
......@@ -64,7 +64,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtFilter> RbtFilterPtr; // Smart pointer
typedef vector<RbtFilterPtr> RbtFilterList;
typedef std::vector<RbtFilterPtr> RbtFilterList;
// Vector of smart pointers
typedef RbtFilterList::iterator RbtFilterListIter;
typedef RbtFilterList::const_iterator RbtFilterListConstIter;
......
......@@ -47,7 +47,7 @@ protected:
// Useful typedefs
typedef SmartPtr<RbtFilterExpression> RbtFilterExpressionPtr; // Smart pointer
typedef vector<RbtFilterExpressionPtr> RbtFilterExpressionList;
typedef std::vector<RbtFilterExpressionPtr> RbtFilterExpressionList;
// Vector of smart pointers
typedef RbtFilterExpressionList::iterator RbtFilterExpressionListIter;
typedef RbtFilterExpressionList::const_iterator
......
......@@ -91,7 +91,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtGenome> RbtGenomePtr; // Smart pointer
typedef vector<RbtGenomePtr> RbtGenomeList; // Vector of smart pointers
typedef std::vector<RbtGenomePtr> RbtGenomeList; // Vector of smart pointers
typedef RbtGenomeList::iterator RbtGenomeListIter;
typedef RbtGenomeList::const_iterator RbtGenomeListConstIter;
......
......@@ -49,7 +49,7 @@ private:
eLP m_LP;
};
typedef vector<RbtInteractionCenter *>
typedef std::vector<RbtInteractionCenter *>
RbtInteractionCenterList; // Vector of regular pointers
typedef RbtInteractionCenterList::iterator RbtInteractionCenterListIter;
typedef RbtInteractionCenterList::const_iterator
......@@ -106,8 +106,8 @@ public:
// pointer list)
// DM 3 Nov 2000 - replace map by vector for faster lookup
// typedef map<RbtUInt,RbtInteractionCenterList> RbtInteractionListMap;
typedef vector<RbtInteractionCenterList> RbtInteractionListMap;
// typedef std::map<RbtUInt,RbtInteractionCenterList> RbtInteractionListMap;
typedef std::vector<RbtInteractionCenterList> RbtInteractionListMap;
typedef RbtInteractionListMap::iterator RbtInteractionListMapIter;
typedef RbtInteractionListMap::const_iterator RbtInteractionListMapConstIter;
......
......@@ -42,7 +42,7 @@
// single point in a multi-dimensional grid
// the coords contains N values where N is the dimension of the grid
class RbtMOEGridPoint {
vector<double> coords;
std::vector<double> coords;
double value;
public:
......@@ -50,13 +50,13 @@ public:
// see also default ctor for the shape and data vector below
RbtMOEGridPoint();
// parametrized ctor when supplying data as a vector + value pair
RbtMOEGridPoint(vector<double>, double);
RbtMOEGridPoint(std::vector<double>, double);
// parametrized ctor getting coord values from RbtCoord (default 3D
// grid for convenience)
RbtMOEGridPoint(RbtCoord &, double);
// data access methods
double GetValue() { return value; }
const vector<double> &GetCoords() { return coords; }
const std::vector<double> &GetCoords() { return coords; }
void SetCoords(double a_val) { coords.push_back(a_val); }
void SetValue(double a_val) { value = a_val; }
};
......@@ -73,9 +73,9 @@ class RbtMOEGridShape {
// of elements than the total number of the
// shape vector
vector<double> origin; // the starting point
vector<double> extents; // the final points
vector<int> i_extents; // extents in integers: number of
std::vector<double> origin; // the starting point
std::vector<double> extents; // the final points
std::vector<int> i_extents; // extents in integers: number of
// points at the edges (ie 20 X 30 X 40 grid)
double step_size; // grid step size
long data_size; // total number of points
......@@ -87,16 +87,16 @@ public:
// parametrized ctor receives grid as the origin vector, the extent
// vector and stepsize
RbtMOEGridShape(vector<double>, vector<double>, double);
RbtMOEGridShape(std::vector<double>, std::vector<double>, double);
const vector<double> &GetOrigin() { return origin; }
const vector<double> &GetExtents() { return extents; }
const vector<int> &GetIExtents() { return i_extents; }
const std::vector<double> &GetOrigin() { return origin; }
const std::vector<double> &GetExtents() { return extents; }
const std::vector<int> &GetIExtents() { return i_extents; }
double GetStepSize() { return step_size; }
long GetDataSize() { return data_size; }
};
typedef vector<RbtMOEGridPoint> RbtMOEGridData;
typedef std::vector<RbtMOEGridPoint> RbtMOEGridData;
// MOE grid data class for IO
//
......@@ -119,7 +119,7 @@ public:
void SetData(RbtMOEGridData &a_data) { myData = a_data; }
void SetOutputFileName(std::string &a_filename) { stream_name = a_filename; }
// methods to calculate grid extents
void CalculateCommonExtents(vector<std::string> strPrmFiles); // for all
void CalculateCommonExtents(std::vector<std::string> strPrmFiles); // for all
void GetDockingSiteExtents(std::string &a_strPrmFile); // for a single
// get methods
RbtCoord GetMinExtents() { return min; }
......
......@@ -38,7 +38,7 @@ private:
// A MOL2SubstructureMap stores MOL2Substructures keyed by SUBSTRUCTURE ID
// (subst_id)
typedef map<int, RbtMOL2Substructure> RbtMOL2SubstructureMap;
typedef std::map<int, RbtMOL2Substructure> RbtMOL2SubstructureMap;
typedef RbtMOL2SubstructureMap::iterator RbtMOL2SubstructureMapIter;
typedef RbtMOL2SubstructureMap::const_iterator RbtMOL2SubstructureMapConstIter;
......@@ -102,7 +102,7 @@ private:
// and to sort atom list into a more sensible order (ordered by substructure
// ID)
RbtMOL2SubstructureMap m_ssInfo;
map<int, RbtAtomList> m_ssAtoms;
std::map<int, RbtAtomList> m_ssAtoms;
RbtElementFileSourcePtr
m_spElementData; // Elemental data source for vdW radii etc
......
......@@ -27,7 +27,7 @@
// Value = logical atom ID as rendered to file
// Logical atom IDs are consecutive for all atoms rendered
// The actual atom ID (RbtAtom::GetAtomId()) is unchanged
typedef map<RbtAtom *, unsigned int, Rbt::RbtAtomPtrCmp_Ptr> RbtAtomIdMap;
typedef std::map<RbtAtom *, unsigned int, Rbt::RbtAtomPtrCmp_Ptr> RbtAtomIdMap;
class RbtMdlFileSink : public RbtBaseMolecularFileSink {
public:
......
......@@ -345,7 +345,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtModel> RbtModelPtr; // Smart pointer
typedef vector<RbtModelPtr> RbtModelList; // Vector of smart pointers
typedef std::vector<RbtModelPtr> RbtModelList; // Vector of smart pointers
typedef RbtModelList::iterator RbtModelListIter;
typedef RbtModelList::const_iterator RbtModelListConstIter;
......
......@@ -82,7 +82,7 @@ private:
m_rotAtoms; // List of atom lists on smallest side of each rotable bond
// DM 25 Apr 2002
// m_flexIntns is a vector of size N(atoms)
// Each element is an RbtAtomList (i.e. vector<RbtAtomPtr>)
// Each element is an RbtAtomList (i.e. std::vector<RbtAtomPtr>)
//
//*** The vector is indexed by AtomId
//*** We assume all atom IDs in the molecule are assigned sequentially from 1
......
......@@ -97,7 +97,7 @@ private:
// Useful typedefs
typedef SmartPtr<RbtNmrRestraintFileSource>
RbtNmrRestraintFileSourcePtr; // Smart pointer
typedef vector<RbtNmrRestraintFileSourcePtr>
typedef std::vector<RbtNmrRestraintFileSourcePtr>
RbtNmrRestraintFileSourceList; // Vector of smart pointers
typedef RbtNmrRestraintFileSourceList::iterator
RbtNmrRestraintFileSourceListIter;
......
......@@ -144,22 +144,22 @@ public:
std::ostream &operator<<(std::ostream &s, const RbtStdRestraintAtoms &std);
// Useful typedefs