cart_cell comments fixed

Author: salva24

src/cart_cell.h

@@ -30,31 +30,21 @@
 
 namespace bdm {
 
-
-/**
- * @brief Enumeration defining the possible states of a CAR-T cell
- * 
- * This enum class represents the different states that a CAR-T cell can be in
- * during its lifecycle in the simulation.
- */
+/// Enumeration defining the possible states of a CAR-T cell
+/// 
+/// This enum class represents the different states that a CAR-T cell can be in
+/// during its lifecycle in the simulation.
 enum class CartCellState : int {
-  /** @brief Living cell state - the cell is alive and functioning normally */
-  kAlive=0,
-
-  /** @brief Apoptotic phase - the cell is undergoing programmed cell death
-   *  characterized by cell shrinkage and controlled death
-   */
-  kApoptotic=1
+  kAlive=0,///< Living cell state - the cell is alive and functioning normally
+  kApoptotic=1///< Apoptotic phase - the cell is undergoing programmed cell death characterized by cell shrinkage and controlled death
 };
 
-/**
- * @brief CAR-T cell class implementation
- * 
- * This class represents a CAR-T (Chimeric Antigen Receptor T-cell) in the simulation.
- * It inherits from the base Cell class and includes specific behaviors and properties
- * related to CAR-T cell biology, including states, volume dynamics, and interactions
- * with tumor cells.
- */
+/// CAR-T cell class implementation
+/// 
+/// This class represents a CAR-T (Chimeric Antigen Receptor T-cell) in the simulation.
+/// It inherits from the base Cell class and includes specific behaviors and properties
+/// related to CAR-T cell biology, including states, volume dynamics, and interactions
+/// with tumor cells.
 class CartCell : public Cell {
   BDM_AGENT_HEADER(CartCell, Cell, 1);
 
@@ -113,137 +103,121 @@ class CartCell : public Cell {
   /// Returns the diffusion grid for immunostimulatory factors
   DiffusionGrid* GetImmunostimulatoryFactorDiffusionGrid() const { return immunostimulatory_factor_dgrid_; }
 
-  /** @brief Change volume using exponential relaxation equation
-   * 
-   * This method explicitly solves the system of exponential relaxation differential
-   * equations using a discrete update step. It is used to grow or shrink the volume
-   * (and proportions) smoothly toward a desired target volume over time. The relaxation
-   * rate controls the speed of convergence and dt=1 (the time_step).
-   * 
-   * @param relaxation_rate_cytoplasm Relaxation rate for cytoplasm volume changes
-   * @param relaxation_rate_nucleus Relaxation rate for nucleus volume changes
-   * @param relaxation_rate_fluid Relaxation rate for fluid volume changes
-   */
+  /// Change volume using exponential relaxation equation
+  /// 
+  /// This method explicitly solves the system of exponential relaxation differential
+  /// equations using a discrete update step. It is used to grow or shrink the volume
+  /// (and proportions) smoothly toward a desired target volume over time. The relaxation
+  /// rate controls the speed of convergence and dt=1 (the time_step).
+  /// 
+  /// @param relaxation_rate_cytoplasm Relaxation rate for cytoplasm volume changes
+  /// @param relaxation_rate_nucleus Relaxation rate for nucleus volume changes
+  /// @param relaxation_rate_fluid Relaxation rate for fluid volume changes
   void ChangeVolumeExponentialRelaxationEquation(real_t relaxation_rate_cytoplasm, real_t relaxation_rate_nucleus, real_t relaxation_rate_fluid);
 
-  /** @brief Calculate displacement of the cell
-   * 
-   * Computes the displacement of the cell based on interaction forces.
-   * 
-   * @param force Pointer to the interaction force object
-   * @param squared_radius The squared radius of the cell
-   * @param dt The time step for the simulation
-   * @return The calculated displacement vector
-   */
+  /// Calculate displacement of the cell
+  /// 
+  /// Computes the displacement of the cell based on interaction forces.
+  /// 
+  /// @param force Pointer to the interaction force object
+  /// @param squared_radius The squared radius of the cell
+  /// @param dt The time step for the simulation
+  /// @return The calculated displacement vector
   Real3 CalculateDisplacement(const InteractionForce* force,
                               real_t squared_radius, real_t dt) override;
 
-  /** @brief Consume or secrete substances
-   * 
-   * Computes new oxygen or immunostimulatory factor concentration after
-   * consumption or secretion by the cell.
-   * 
-   * @param substance_id The ID of the substance (oxygen or immunostimulatory factor)
-   * @param old_concentration The previous concentration of the substance
-   * @return The new concentration after consumption/secretion
-   */
+  /// Consume or secrete substances
+  /// 
+  /// Computes new oxygen or immunostimulatory factor concentration after
+  /// consumption or secretion by the cell.
+  /// 
+  /// @param substance_id The ID of the substance (oxygen or immunostimulatory factor)
+  /// @param old_concentration The previous concentration of the substance
+  /// @return The new concentration after consumption/secretion
   real_t ConsumeSecreteSubstance(int substance_id, real_t old_concentration);
 
-  /** @brief Compute constants for consumption and secretion
-   * 
-   * Updates constants after the cell's change of volume or quantities.
-   * These constants are used in the consumption/secretion differential equations.
-   */
+  /// Compute constants for consumption and secretion
+  /// 
+  /// Updates constants after the cell's change of volume or quantities.
+  /// These constants are used in the consumption/secretion differential equations.
   void ComputeConstantsConsumptionSecretion();
 
-
- /** @name Private Member Variables
-  *  @brief Private attributes of the CAR-T cell
-  *  @{
-  */
  private:
-  /** @brief Current state of the CAR-T cell */
+  /// Current state of the CAR-T cell
   CartCellState state_;
 
-  /** @brief Timer to track time in the current state (in minutes)
-   *  Used for apoptotic state timing
-   */
+  /// Timer to track time in the current state (in minutes)
+  /// Used for apoptotic state timing
   int timer_state_;
 
-  /** @brief Pointer to the oxygen diffusion grid */
+  /// Pointer to the oxygen diffusion grid
   DiffusionGrid* oxygen_dgrid_;
 
-  /** @brief Pointer to the immunostimulatory factor diffusion grid */
+  /// Pointer to the immunostimulatory factor diffusion grid
   DiffusionGrid* immunostimulatory_factor_dgrid_;
 
-  /** @brief Flag indicating if the cell is attached to a tumor cell */
+  /// Flag indicating if the cell is attached to a tumor cell
   bool attached_to_tumor_cell_;
 
-  /** @brief Current time until apoptosis */
+  /// Current time until apoptosis
   real_t current_live_time_;
 
-  /** @brief Fluid fraction of the cell volume */
+  /// Fluid fraction of the cell volume
   real_t fluid_fraction_;
 
-  /** @brief Volume of the nucleus */
+  /// Volume of the nucleus
   real_t nuclear_volume_;
 
-  /** @brief Target cytoplasm solid volume for exponential relaxation
-   *  Used during volume changes following exponential relaxation equation
-   */
+  /// Target cytoplasm solid volume for exponential relaxation
+  /// Used during volume changes following exponential relaxation equation
   real_t target_cytoplasm_solid_;
 
-  /** @brief Target nucleus solid volume for exponential relaxation */
+  /// Target nucleus solid volume for exponential relaxation
   real_t target_nucleus_solid_;
 
-  /** @brief Target fluid fraction for exponential relaxation */
+  /// Target fluid fraction for exponential relaxation
   real_t target_fraction_fluid_;
 
-  /** @brief Target relation between cytoplasm and nucleus volumes */
+  /// Target relation between cytoplasm and nucleus volumes
   real_t target_relation_cytoplasm_nucleus_;
 
-  /** @brief Velocity of the cell in the previous time step */
+  /// Velocity of the cell in the previous time step
   Real3 older_velocity_;
 
-  /** @brief Rate of oxygen consumption by the cell */
+  /// Rate of oxygen consumption by the cell
   real_t oxygen_consumption_rate_;
 
-  /** @brief Rate of immunostimulatory factor secretion by the cell */
+  /// Rate of immunostimulatory factor secretion by the cell
   real_t immunostimulatory_factor_secretion_rate_;
 
-  /** @brief Constant 1 for oxygen consumption/secretion differential equation solution */
+  /// Constant 1 for oxygen consumption/secretion differential equation solution
   real_t constant1_oxygen_;
 
-  /** @brief Constant 2 for oxygen consumption/secretion differential equation solution */
+  /// Constant 2 for oxygen consumption/secretion differential equation solution
   real_t constant2_oxygen_;
 
-  /** @brief Pointer to the attached tumor cell */
+  /// Pointer to the attached tumor cell
   TumorCell* attached_cell_;
 
-  /** @} */ // end of Private Member Variables group
 };
 
-/**
- * @brief Behavior class for controlling CAR-T cell state transitions
- * 
- * This behavior handles the state control logic for CAR-T cells, managing
- * transitions between different cell states such as alive and apoptotic phases.
- * It inherits from the base Behavior class and implements the Run method to
- * execute the state control logic during simulation steps.
- */
+/// Behavior class for controlling CAR-T cell state transitions
+/// 
+/// This behavior handles the state control logic for CAR-T cells, managing
+/// transitions between different cell states such as alive and apoptotic phases.
+/// It inherits from the base Behavior class and implements the Run method to
+/// execute the state control logic during simulation steps.
 struct StateControlCart : public Behavior {
   BDM_BEHAVIOR_HEADER(StateControlCart, Behavior, 1);
 
   StateControlCart() { AlwaysCopyToNew(); }
 
   virtual ~StateControlCart() {}
 
-  /** @brief Execute the state control behavior
-   *  @param agent Pointer to the agent (cell) on which to apply the behavior
-   */
+  /// Execute the state control behavior
   void Run(Agent* agent) override;
 };
 
 }  // namespace bdm
 
-#endif  // CART_CELL_H_
+#endif