Working on reaction module and RM_interface.

Changed most declarations to protected: from private:

git-svn-id: svn://136.177.114.72/svn_GW/phreeqcpp/branches/ErrorHandling@5688 1feff8c3-07ed-0310-ac33-dd36852eb9cd

Exchange.h

@@ -41,7 +41,7 @@ public:
 	void mpi_pack(std::vector < int >&ints, std::vector < double >&doubles);
 	void mpi_unpack(int *ints, int *ii, double *doubles, int *dd);
 #endif
-private:
+protected:
 	void add(const cxxExchange & addee, double extensive);
 	// not written
 	void dump_xml(std::ostream & os, unsigned int indent = 0) const;

GasPhase.h

@@ -51,7 +51,7 @@ class cxxGasPhase:public cxxNumKeyword
 	double Get_volume(void) const {return volume;};
 	cxxNameDouble & Get_totals(void) {return totals;};
 
-private:
+protected:
 	void add(const cxxGasPhase & addee, double extensive);
 
 protected:
@@ -61,9 +61,6 @@ protected:
 	double volume;
 	cxxNameDouble totals;
 
-public:
-	//static std::map<int, cxxGasPhase>& map;
-
 };
 
 #endif // !defined(GASPHASE_H_INCLUDED)

ISolutionComp.h

@@ -123,7 +123,7 @@ class cxxISolutionComp: public PHRQ_base
 		return ::strcmp(this->description.c_str(), conc.description.c_str()) < 0;
 	}
 
-  private:
+  protected:
 	  std::string description;
 	  double moles;
 	  double input_conc;

NumKeyword.h

@@ -65,7 +65,7 @@ class cxxNumKeyword: public PHRQ_base
 	int n_user_end;
 	std::string description;
 
-  private:
+  protected:
 	void read_number_description(std::istream & is);
 };
 #endif // !defined(NUMKEYWORD_H_INCLUDED)

PHRQ_base.h

@@ -35,7 +35,7 @@ public:
 		return this->base_error_count;
 	}
 	// data
-private:
+protected:
 	PHRQ_io * io;
 	int base_error_count;
 };

PHRQ_io.h

@@ -143,7 +143,7 @@ typedef enum
 		return this->dump_file_on;
 	}
 	// data
-private:
+protected:
 	FILE *input_file;
 	FILE *database_file;
 	FILE *output_file;	/* OUTPUT_MESSAGE */

PPassemblage.h

@@ -44,7 +44,7 @@ class cxxPPassemblage:public cxxNumKeyword
 
 	void totalize(PHREEQC_PTR_ARG);
 
-private:
+protected:
 	void add(const cxxPPassemblage & addee, double extensive);
 	// not written
 	void dump_xml(std::ostream & os, unsigned int indent = 0) const;

Parser.h

@@ -287,7 +287,7 @@ class CParser: public PHRQ_base
   protected:
 	LINE_TYPE get_logical_line();
 
-  private:
+  protected:
 	std::istream & m_input_stream;
 	std::ostream & m_output_stream;
 	std::ostream & m_error_stream;

Phreeqc.h

@@ -944,20 +944,20 @@ public:
 	struct element *element_store(const char *element);
 	int elt_list_combine(void);
 	CLASS_STATIC int elt_list_compare(const void *ptr1, const void *ptr2);
-private:
+protected:
 struct elt_list *elt_list_dup(struct elt_list *elt_list_ptr_old);
 int elt_list_print(struct elt_list *elt_list_ptr);
 struct elt_list *elt_list_save(void);
 public:
 	struct exchange *exchange_alloc(void);
 	struct exchange *exchange_bsearch(int k, int *n);
-private:
+protected:
 int exchange_comp_compare(const void *ptr1, const void *ptr2);
 void exchange_comp_init(struct exch_comp *exch_comp_ptr);
 public:
 	int exchange_copy(struct exchange *exchange_old_ptr,
 		struct exchange *exchange_new_ptr, int n_user_new);
-private:
+protected:
 CLASS_STATIC int exchange_compare(const void *ptr1, const void *ptr2);
 int exchange_copy_to_last(int n, int n_user);
 int exchange_delete(int n_user_old);
@@ -966,7 +966,7 @@ int exchange_init(struct exchange *exchange_ptr, int n_user, int n_user_end,
 				  const char *description);
 public:
 	int exchange_free(struct exchange *exchange_ptr);
-private:
+protected:
 int exchange_ptr_to_user(struct exchange *exchange_old_ptr, int n_user_new);
 struct exchange *exchange_replicate(struct exchange *exchange_old_ptr,
 									int n_user_new);
@@ -976,12 +976,12 @@ CLASS_STATIC int gas_comp_compare(const void *ptr1, const void *ptr2);
 public:
 	struct gas_phase *gas_phase_alloc(void);
 	struct gas_phase *gas_phase_bsearch(int k, int *n);
-private:
+protected:
 CLASS_STATIC int gas_phase_compare(const void *ptr1, const void *ptr2);
 public:
 int gas_phase_copy(struct gas_phase *gas_phase_old_ptr,
 				   struct gas_phase *gas_phase_new_ptr, int n_user_new);
-private:
+protected:
 int gas_phase_copy_to_last(int n, int n_user);
 int gas_phase_delete(int n_user_old);
 int gas_phase_duplicate(int n_user_old, int n_user_new);
@@ -1012,7 +1012,7 @@ int irrev_sort(void);
 public:
 	struct kinetics *kinetics_alloc(void);
 	struct kinetics *kinetics_bsearch(int k, int *n);
-private:
+protected:
 int kinetics_delete(int n_user_old);
 int kinetics_comp_duplicate(struct kinetics_comp *kinetics_comp_new_ptr,
 							struct kinetics_comp *kinetics_comp_old_ptr);
@@ -1020,14 +1020,14 @@ CLASS_STATIC int kinetics_compare(const void *ptr1, const void *ptr2);
 public:
 int kinetics_copy(struct kinetics *kinetics_old_ptr,
 				  struct kinetics *kinetics_new_ptr, int n_user_new);
-private:				 
+protected:				 
 int kinetics_copy_to_last(int n, int n_user);
 int kinetics_duplicate(int n_user_old, int n_user_new);
 int kinetics_init(struct kinetics *kinetics_ptr, int n_user, int n_user_end,
 				  char *description);
 public:
 int kinetics_free(struct kinetics *kinetics_ptr);
-private:
+protected:
 int kinetics_ptr_to_user(struct kinetics *kinetics_ptr_old, int n_user_new);
 struct kinetics *kinetics_replicate(struct kinetics *kinetics_old_ptr,
 									int n_user_new);
@@ -1044,7 +1044,6 @@ public:
 struct master *master_bsearch(const char *ptr);
 struct master *master_bsearch_primary(char *ptr);
 struct master *master_bsearch_secondary(char *ptr);
-//private:
 struct master *master_search(char *ptr, int *n);
 struct mix *mix_bsearch(int k, int *n);
 int mix_copy(struct mix *mix_old_ptr,
@@ -1058,30 +1057,30 @@ struct pe_data *pe_data_alloc(void);
 public:
 	struct pe_data *pe_data_dup(struct pe_data *pe_ptr_old);
 	struct pe_data *pe_data_free(struct pe_data *pe_data_ptr);
-private:
+protected:
 int pe_data_store(struct pe_data **pe, const char *token);
 public:
 struct phase *phase_bsearch(const char *ptr, int *j, int print);
-private:
+protected:
 CLASS_STATIC int phase_compare(const void *ptr1, const void *ptr2);
 int phase_delete(int i);
 struct phase *phase_store(char *name);
 public:
 struct pp_assemblage *pp_assemblage_alloc(void);
 struct pp_assemblage *pp_assemblage_bsearch(int k, int *n);
-private:
+protected:
 CLASS_STATIC int pp_assemblage_compare(const void *ptr1, const void *ptr2);
 public:
 int pp_assemblage_copy(struct pp_assemblage *pp_assemblage_old_ptr,
 					   struct pp_assemblage *pp_assemblage_new_ptr,
 					   int n_user_new);
-private:
+protected:
 int pp_assemblage_copy_to_last(int n, int n_user);
 int pp_assemblage_delete(int n_user_old);
 int pp_assemblage_duplicate(int n_user_old, int n_user_new);
 public:
 int pp_assemblage_free(struct pp_assemblage *pp_assemblage_ptr);
-private:
+protected:
 int pp_assemblage_init(struct pp_assemblage *pp_assemblage_ptr, int n_user,
 					   int n_user_end, char *description);
 int pp_assemblage_ptr_to_user(struct pp_assemblage *pp_assemblage_ptr_old,
@@ -1108,19 +1107,19 @@ struct species *s_store(char *name, LDBLE z, int replace_if_found);
 public:
 	struct s_s_assemblage *s_s_assemblage_alloc(void);
 	struct s_s_assemblage *s_s_assemblage_bsearch(int k, int *n);
-private:
+protected:
 CLASS_STATIC int s_s_assemblage_compare(const void *ptr1, const void *ptr2);
 public:
 	int s_s_assemblage_copy(struct s_s_assemblage *s_s_assemblage_old_ptr,
 						struct s_s_assemblage *s_s_assemblage_new_ptr,
 						int n_user_new);
-private:
+protected:
 int s_s_assemblage_copy_to_last(int n, int n_user);
 int s_s_assemblage_duplicate(int n_user_old, int n_user_new);
 int s_s_assemblage_delete(int n_user_old);
 public:
 	int s_s_assemblage_free(struct s_s_assemblage *s_s_assemblage_ptr);
-private:
+protected:
 int s_s_assemblage_init(struct s_s_assemblage *s_s_assemblage_ptr,
 						int n_user, int n_user_end, char *description);
 int s_s_assemblage_ptr_to_user(struct s_s_assemblage *s_s_assemblage_ptr_old,
@@ -1143,7 +1142,7 @@ public:
 	struct solution *solution_bsearch(int k, int *n, int print);
 	struct solution *solution_copy(struct solution *solution_old_ptr,
 							   int n_user_new);
-private:
+protected:
 int solution_copy_to_last(int n, int n_user_new);
 int solution_duplicate(int n_user_old, int n_user_new);
 int solution_delete(int n_user_old);
@@ -1160,7 +1159,7 @@ struct Change_Surf *change_surf_alloc(int count);
 public:
 	struct surface *surface_alloc(void);
 	struct surface *surface_bsearch(int k, int *n);
-private:
+protected:
 struct master *surface_get_psi_master(const char *name, int plane);
 CLASS_STATIC int surface_comp_compare(const void *ptr1, const void *ptr2);
 CLASS_STATIC int surface_charge_compare(const void *ptr1, const void *ptr2);
@@ -1170,7 +1169,7 @@ CLASS_STATIC int surface_compare(const void *ptr1, const void *ptr2);
 public:
 	int surface_copy(struct surface *surface_old_ptr,
 				 struct surface *surface_new_ptr, int n_user_new);
-private:
+protected:
 int surface_copy_to_last(int n, int n_user);
 int surface_delete(int n_user_old);
 int surface_duplicate(int n_user_old, int n_user_new);
@@ -1379,7 +1378,7 @@ int mix_stag(int i, LDBLE stagkin_time, int punch,
 // utilities.c -------------------------------
 public:
 int add_elt_list(struct elt_list *elt_list_ptr, LDBLE coef);
-private:
+protected:
 int backspace_screen(int spaces);
 LDBLE calc_alk(struct reaction *rxn_ptr);
 public:
@@ -1392,7 +1391,7 @@ int dup_print(const char *ptr, int emphasis);
 int equal(LDBLE a, LDBLE b, LDBLE eps);
 public:
 	void *free_check_null(void *ptr);
-private:
+protected:
 void free_hash_strings(HashTable * Table);
 int get_token(char **eqnaddr, char *string, LDBLE * z, int *l);
 int hcreate_multi(unsigned Count, HashTable ** HashTable_ptr);
@@ -1401,12 +1400,12 @@ ENTRY *hsearch_multi(HashTable * Table, ENTRY item, ACTION action);
 int islegit(const char c);
 public:
 void malloc_error(void);
-private:
+protected:
 int parse_couple(char *token);
 int print_centered(const char *string);
 public:
 CLASS_STATIC int replace(const char *str1, const char *str2, char *str);
-private:
+protected:
 void space(void **ptr, int i, int *max, int struct_size);
 void squeeze_white(char *s_l);
 int status(int count, const char *str);
@@ -1417,7 +1416,7 @@ int strcmp_nocase_arg1(const char *str1, const char *str2);
 public:
 	char *string_duplicate(const char *token);
 	char *string_hsave(const char *str);
-private:
+protected:
 char *string_pad(char *str, int i);
 int string_trim(char *str);
 int string_trim_right(char *str);

SSassemblage.h

@@ -49,7 +49,7 @@ public:
 	};
 
 
-private:
+protected:
 	void add(const cxxSSassemblage & addee, double extensive);
 
 protected:

Solution.h

@@ -163,13 +163,12 @@ class cxxSolution:public cxxNumKeyword
 	void mpi_recv(int task_number);
 #endif
 
-  private:
+  protected:
 	void zero();
 	void add(const cxxSolution & addee, double extensive);
 	// not checked
 	void dump_xml(std::ostream & os, unsigned int indent = 0) const;
 
-  protected:
 	double tc;
 	double ph;
 	double pe;

System.h

@@ -76,7 +76,7 @@ public:
 		return this->totals;
 	}
 	
-private:
+protected:
 	cxxSolution * solution;
 	cxxExchange * exchange;
 	cxxPPassemblage * ppassemblage;

cxxKinetics.h

@@ -47,7 +47,7 @@ class cxxKinetics:public cxxNumKeyword
 	void mpi_unpack(int *ints, int *ii, double *doubles, int *dd);
 	void mpi_pack(std::vector < int >&ints, std::vector < double >&doubles);
 #endif
-  private:
+  protected:
 	void add(const cxxKinetics & addee, double extensive);
 
   protected: