Changes in src/molecule.hpp [8ab0407:24a5e0]

File:

• src/molecule.hpp (modified) (8 diffs)

src/molecule.hpp

@@ -27 +27 @@
 #include <vector>
 
+#include <string>
+
+#include "defs.hpp"
 #include "graph.hpp"
 #include "stackclass.hpp"
 #include "tesselation.hpp"
+#include "Patterns/Observer.hpp"
+#include "Patterns/Cacheable.hpp"
 
 /****************************************** forward declarations *****************************/
@@ -80 +85 @@
  * Class incorporates number of types
  */
-class molecule : public PointCloud {
+class molecule : public PointCloud , public Observable {
+  friend molecule *NewMolecule();
+  friend void DeleteMolecule(molecule *);
   public:
     double cell_size[6];//!< cell size
@@ -99 +106 @@
     bool ActiveFlag;    //!< in a MoleculeListClass used to discern active from inactive molecules
     Vector Center;      //!< Center of molecule in a global box
+    int IndexNr;        //!< index of molecule in a MoleculeListClass
     char name[MAXSTRINGSIZE];         //!< arbitrary name
-    int IndexNr;        //!< index of molecule in a MoleculeListClass
-
-  molecule(const periodentafel * const teil);
-  virtual ~molecule();
+
+  private:
+    Cacheable<string> formula;
+    moleculeId_t id;
+  protected:
+    molecule(const periodentafel * const teil);
+    virtual ~molecule();
+
+
+public:
+  //getter and setter
+  const std::string getName();
+  moleculeId_t getId();
+  void setId(moleculeId_t);
+  void setName(const std::string);
+  const std::string getFormula();
+  std::string calcFormula();
+
 
   // re-definition of virtual functions from PointCloud
@@ -269 +291 @@
   int FragmentMolecule(int Order, config *configuration);
   bool CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
-  bool StoreBondsToFile(char *path, char *filename);
-  bool StoreAdjacencyToFile(char *path, char *filename);
+  bool StoreBondsToFile(char *path);
+  bool StoreAdjacencyToFile(char *path);
   bool CheckAdjacencyFileAgainstMolecule(char *path, atom **ListOfAtoms);
   bool ParseOrderAtSiteFromFile(char *path);
@@ -299 +321 @@
   bool OutputTemperatureFromTrajectories(ofstream * const output, int startstep, int endstep);
 
+  // Manipulation routines
+  void flipActiveFlag();
+
   private:
   int last_atom;      //!< number given to last atom
@@ -304 +329 @@
 };
 
+molecule *NewMolecule();
+void DeleteMolecule(molecule* mol);
+
 #include "molecule_template.hpp"
 
 /** A list of \a molecule classes.
  */
-class MoleculeListClass {
+class MoleculeListClass : public Observable {
   public:
     MoleculeList ListOfMolecules; //!< List of the contained molecules
     int MaxIndex;
 
-  MoleculeListClass();
+  MoleculeListClass(World *world);
   ~MoleculeListClass();
 
@@ -322 +350 @@
   bool OutputConfigForListOfFragments(config *configuration, int *SortIndex);
   int NumberOfActiveMolecules();
-  void Enumerate(ofstream *out);
+  void Enumerate(ostream *out);
   void Output(ofstream *out);
   void DissectMoleculeIntoConnectedSubgraphs(const periodentafel * const periode, config * const configuration);
   int CountAllAtoms() const;
+
+  // Methods moved here from the menus
+  // TODO: more refactoring needed on these methods
+  void flipChosen();
+  void createNewMolecule(periodentafel *periode);
+  void loadFromXYZ(periodentafel *periode);
+  void setMoleculeFilename();
+  void parseXYZIntoMolecule();
+  void eraseMolecule();
+
 
   // merging of molecules
@@ -336 +374 @@
 
   private:
+  World *world; //!< The world this List belongs to. Needed to avoid deadlocks in the destructor
 };