Osmia_Nest Class Reference

The Osmia nest is assumed to be a linear element with egg cells added one by one. More...

#include <Osmia.h>

Inheritance diagram for Osmia_Nest:

Public Member Functions
	Osmia_Nest (int a_x, int a_y, int a_polyref, Osmia_Nest_Manager *a_manager)
virtual	~Osmia_Nest ()
void	SetCellLock (void)
	Set the cell lock. More...
void	ReleaseCellLock (void)
	Release the cell lock. More...
void	AddCocoon (TAnimal *a_cocoon)
	Adds a cocoon to the nest, this is only used to initialise the simulation. More...
void	AddEgg (TAnimal *a_egg)
	Adds an egg to the nest. More...
void	ReplaceNestPointer (TAnimal *a_oldpointer, TAnimal *a_newpointer)
void	RemoveCell (TAnimal *a_oldpointer)
bool	Find (TAnimal *a_osmia)
	Debug function - Is this osmia present? More...
void	KillAllSubsequentCells (TAnimal *a_osmia)
	Removes all Osmia from the nest from a target to the end of the tube. More...
int	GetPolyRef ()
	Get the polyref. More...
int	GetNoNests ()
	For debug - get the number of nests currently for this polygon. More...
int	GetNoCells ()
	Get the number of cells for this nest. More...
bool	ZeroCells ()
	Debug - to check if any nests have zero cells. More...
int	GetAspectDelay ()
bool	GetIsOpen ()
	Tells us whether the nest is finished for additions = false or can be added too = true. More...
void	CloseNest ()
	Signals that the nest is closed. More...
Public Member Functions inherited from TAnimal
	TAnimal (int x, int y, Landscape *L)
	The TAnimal constructor saving the x,y, location and the landscape pointer. More...
	TAnimal (int x, int y)
	The TAnimal constructor saving the x,y used if landscape is already set. More...
void	SetGuardMapIndex (int a_index_x, int a_index_y)
	Set the guard map index, this is used to avoid two animals operating in the same location when using multithread. More...
unsigned	SupplyFarmOwnerRef () const
	Get the current location farm ref if any. More...
AnimalPosition	SupplyPosition () const
	Returns the objects location and habitat type and veg type. More...
APoint	SupplyPoint () const
	Returns the objects location in ALMaSS coordinates. More...
int	SupplyPolygonRef () const
	Returns the polygon reference where the object is located. More...
TTypesOfLandscapeElement	SupplyPolygonType () const
	Returns the polygon type where the object is located. More...
int	Supply_m_Location_x () const
	Returns the ALMaSS x-coordinate. More...
int	Supply_m_Location_y () const
	Returns the ALMaSS y-coordinate. More...
int	SupplyGuardCellX () const
	Returns the x-index to the guard cell. More...
int	SupplyGuardCellY () const
	Returns the y-index to the guard cell. More...
int	SupplyAge () const
	Returns the animals age in days. More...
void	SetAge (int a_age)
	Sets the animals age in days. More...
virtual void	KillThis ()
	Sets all parameters ready for object destruction. More...
virtual void	CopyMyself ()
	Used to copy the object details to another in descendent classes. More...
void	SetX (const int a_x)
	Sets the x-coordinate. More...
void	SetY (const int a_y)
	Sets the y-coordinate. More...
virtual void	ReinitialiseObject (int a_x, int a_y, Landscape *a_l_ptr)
virtual void	ReinitialiseObject (int a_x, int a_y)
	Used to re-use an object - must be implemented in descendent classes. More...
virtual int	WhatState ()
	Returns the objects current state number. More...
virtual void	Dying ()
	A wrapped for KillThis - ideally should not be used. More...
void	CheckManagement ()
	Used to start a check for any management related effects at the objects current location. More...
void	CheckManagementXY (int a_x, int a_y)
	Used to start a check for any management related effects at x,y. More...
virtual bool	OnFarmEvent (FarmToDo)
	Must be reimplemented if used in descendent classes. Sets the action on a management event. More...
Public Member Functions inherited from TALMaSSObject
int	GetCurrentStateNo () const
	Returns the current state number. More...
void	SetCurrentStateNo (int a_num)
	Sets the current state number. More...
bool	GetStepDone () const
	Returns the step done indicator flag. More...
void	SetStepDone (bool a_bool)
	Sets the step done indicator flag. More...
virtual void	BeginStep ()
	BeingStep behaviour - must be implemented in descendent classes. More...
virtual void	Step ()
	Step behaviour - must be implemented in descendent classes. More...
virtual void	EndStep ()
	EndStep behaviour - must be implemented in descendent classes. More...
void	ReinitialiseObjectBase ()
	Used to initialise an object. More...
	TALMaSSObject ()
	The constructor for TALMaSSObject. More...
virtual	~TALMaSSObject ()=default
	The destructor for TALMaSSObject. More...

Public Attributes
Osmia_Female *	m_owner

Protected Attributes
int	m_x
	x-location More...
int	m_y
	y-location More...
int	m_PolyRef
	polygon reference to where the nest is located More...
std::forward_list< TAnimal * >	m_cells
	list of egg objects More...
omp_nest_lock_t *	m_cell_lock
	The lock to for egg cells operation. More...
bool	m_isOpen
	Signals that the nest is closed or open for adding new cells. More...
int	m_aspectdelay
	Simulates the natural variation assumed per nest location based on aspect, exposure etc.. More...
Protected Attributes inherited from TAnimal
int	m_Location_x
	The objects ALMaSS x coordinate. More...
int	m_Location_y
	The objects ALMaSS y coordinate. More...
int	m_guard_cell_x
	The index x to the guard cell. More...
int	m_guard_cell_y
	The index y to the guard cell. More...
int	m_AgeDays {0}
	To hold the age in days. More...
PesticideToxicity	m_my_pesticide
Protected Attributes inherited from TALMaSSObject
int	m_CurrentStateNo
	The basic state number for all objects - '-1' indicates death. More...
bool	m_StepDone
	Indicates whether the iterative step code is done for this timestep. More...

Static Protected Attributes
static Osmia_Nest_Manager *	m_OurManager = NULL
	A pointer to the one and only nest population manager. More...
Static Protected Attributes inherited from TAnimal
static Landscape *	m_OurLandscape = nullptr
	A pointer to the landscape object shared with all TAnimal objects. More...
static int	m_SimulationWidth = 0
	A static member for the simulation width because it is often used by descendent classes. More...
static int	m_SimulationHeight = 0
	A static member for the simulation height because it is often used by descendent classes. More...
static double	m_TemperatureToday = 0.0
	A holder for the temperature today shared with all TAnimal objects. More...
static int	m_DayInYear = 0
	A holder for the day in year shared with all TAnimal objects. More...

Additional Inherited Members
Static Public Member Functions inherited from TAnimal
static void	SetSimulationWidth (int a_value)
	Sets the simulation width. More...
static void	SetSimulationHeight (int a_value)
	Sets the simulation height. More...
static void	SetDayInYear (int a_value)
	Sets the day in year attribute. More...
static void	SetOurLandscape (Landscape *a_value)
	Sets the landscape pointer. More...
static void	SetTempToday (double a_value)
	Sets the temperature today attribute. More...
Static Public Member Functions inherited from TALMaSSObject
static void	OnArrayBoundsError ()
	Used for debugging only, tests basic object properties. More...
Protected Member Functions inherited from TAnimal
void	CorrectWrapRound ()
	Corrects wrap around co-ordinate problems. More...

Detailed Description

The Osmia nest is assumed to be a linear element with egg cells added one by one.

Constructor & Destructor Documentation

Osmia_Nest()

Osmia_Nest::Osmia_Nest	(	int	a_x,
		int	a_y,
		int	a_polyref,
		Osmia_Nest_Manager *	a_manager
	)

                                                                                     :TAnimal(a_x, a_y)
{
    m_x = a_x;
    m_y = a_y;
    m_PolyRef = a_polyref;
    m_cells.clear(); // Ensures there are no cells occupied before we start
    m_OurManager = a_manager;
    m_isOpen = true;
    m_owner = nullptr;
    m_aspectdelay = g_uni_0to15(g_generator);
    m_cell_lock = new omp_nest_lock_t;
    omp_init_nest_lock(m_cell_lock);
}

References g_generator, g_uni_0to15(), m_aspectdelay, m_cell_lock, m_cells, m_isOpen, m_OurManager, m_owner, m_PolyRef, m_x, and m_y.

~Osmia_Nest()

virtual Osmia_Nest::~Osmia_Nest ( )

inlinevirtual

                         {
        omp_destroy_nest_lock(m_cell_lock);
        delete m_cell_lock;
    }

References m_cell_lock.

Member Function Documentation

AddCocoon()

void Osmia_Nest::AddCocoon ( TAnimal *  a_cocoon )

inline

Adds a cocoon to the nest, this is only used to initialise the simulation.

                                       {
        m_cells.push_front(a_cocoon);
    }

References m_cells.

Referenced by Osmia_Population_Manager::CreateObjects().

AddEgg()

void Osmia_Nest::AddEgg ( TAnimal *  a_egg )

inline

Adds an egg to the nest.

{ m_cells.push_front(a_egg); }

References m_cells.

Referenced by Osmia_Population_Manager::CreateObjects().

CloseNest()

void Osmia_Nest::CloseNest ( )

inline

Signals that the nest is closed.

{ m_isOpen = false; }

References m_isOpen.

Referenced by Osmia_Female::st_Dying(), and Osmia_Female::st_ReproductiveBehaviour().

Find()

bool Osmia_Nest::Find ( TAnimal *  a_osmia )

inline

Debug function - Is this osmia present?

    {
        if (std::find(m_cells.begin(), m_cells.end(), a_osmia) != m_cells.end()) return true;
        else {
            return false;
        }
    }

References m_cells.

GetAspectDelay()

int Osmia_Nest::GetAspectDelay ( )

inline

{ return m_aspectdelay; }

References m_aspectdelay.

Referenced by Osmia_InCocoon::st_Develop().

GetIsOpen()

bool Osmia_Nest::GetIsOpen ( )

inline

Tells us whether the nest is finished for additions = false or can be added too = true.

{ return m_isOpen; }

References m_isOpen.

Referenced by Osmia_Egg::st_Develop(), and Osmia_Larva::st_Develop().

GetNoCells()

int Osmia_Nest::GetNoCells ( )

inline

Get the number of cells for this nest.

{ return std::distance(std::begin(m_cells), std::end(m_cells)); };

References m_cells.

Referenced by Osmia_Female::st_Dying(), and Osmia_Female::st_ReproductiveBehaviour().

GetNoNests()

int Osmia_Nest::GetNoNests

(

)

For debug - get the number of nests currently for this polygon.

{
    return m_OurManager->GetNoNests(m_PolyRef);
}

References Osmia_Nest_Manager::GetNoNests(), m_OurManager, and m_PolyRef.

GetPolyRef()

int Osmia_Nest::GetPolyRef ( )

inline

Get the polyref.

{ return m_PolyRef; }

References m_PolyRef.

Referenced by Osmia_Female::st_Dying(), and Osmia_Female::st_ReproductiveBehaviour().

KillAllSubsequentCells()

void Osmia_Nest::KillAllSubsequentCells

(

TAnimal *

a_osmia

)

Removes all Osmia from the nest from a target to the end of the tube.

Searches the nest until if finds a specific Osmia, once found it removes that Osmia and deletes all cells created higher up the tube.

{
    auto prev_point = m_cells.before_begin();
    for (auto it = m_cells.begin(); it!=m_cells.end(); ++it)
    {
        if(*it == a_osmia) 
        {
            m_cells.erase_after(prev_point, m_cells.end());
            if (std::distance(std::begin(m_cells), std::end(m_cells)) < 1)
            {
                // Need to remove the nest from the world
                m_OurManager->ReleaseOsmiaNest(m_PolyRef, this);
            }
            return;
        }
        prev_point=it;
    }
}

References m_cells, m_OurManager, m_PolyRef, and Osmia_Nest_Manager::ReleaseOsmiaNest().

ReleaseCellLock()

void Osmia_Nest::ReleaseCellLock ( void  )

inline

Release the cell lock.

{ omp_unset_nest_lock(m_cell_lock); }

References m_cell_lock.

Referenced by Osmia_Population_Manager::CreateObjects(), RemoveCell(), Osmia_Female::st_Dying(), and Osmia_Female::st_ReproductiveBehaviour().

RemoveCell()

void Osmia_Nest::RemoveCell

(

TAnimal *

a_oldpointer

)

{
    SetCellLock();
 
    auto prev_point = m_cells.before_begin();
    for (auto it = m_cells.begin(); it!=m_cells.end(); ++it)
    {
        //cout<< a_oldpointer<<' '<<*it<<endl;
        //cout<<std::distance(std::begin(m_cells), std::end(m_cells))<<endl;
        if((*it) == a_oldpointer) 
        {
            m_cells.erase_after(prev_point);
            //cout<<"cell removed "<<endl;
            if (std::distance(std::begin(m_cells), std::end(m_cells)) < 1)
            {
                // Need to remove the nest from the world
                //cout<<"nest needs removed "<<endl;
                //release the lock before we remove the nest
                ReleaseCellLock();
                m_OurManager->ReleaseOsmiaNest(m_PolyRef, this);
            }
            else
            {
                //cout<<"nest not removed "<<endl;
                ReleaseCellLock();
            }
            return;
        }
 
        prev_point=it;
    }
 
    ReleaseCellLock();
}

References m_cells, m_OurManager, m_PolyRef, ReleaseCellLock(), Osmia_Nest_Manager::ReleaseOsmiaNest(), and SetCellLock().

Referenced by Osmia_Base::st_Dying(), and Osmia_InCocoon::st_Emerge().

ReplaceNestPointer()

void Osmia_Nest::ReplaceNestPointer ( TAnimal *  a_oldpointer, TAnimal *  a_newpointer  )

inline

                                                                          {
        std::replace(m_cells.begin(), m_cells.end(), a_oldpointer, a_newpointer); // replaces the old life stage pointer with the new one in-place
    }

References m_cells.

Referenced by Osmia_Population_Manager::CreateObjects().

SetCellLock()

void Osmia_Nest::SetCellLock ( void  )

inline

Set the cell lock.

{ omp_set_nest_lock(m_cell_lock); }

References m_cell_lock.

Referenced by Osmia_Population_Manager::CreateObjects(), RemoveCell(), Osmia_Female::st_Dying(), and Osmia_Female::st_ReproductiveBehaviour().

ZeroCells()

bool Osmia_Nest::ZeroCells ( )

inline

Debug - to check if any nests have zero cells.

                     {
        if (std::distance(std::begin(m_cells), std::end(m_cells)) < 1) return false; else return true;
    }

References m_cells.

Member Data Documentation

m_aspectdelay

int Osmia_Nest::m_aspectdelay

protected

Simulates the natural variation assumed per nest location based on aspect, exposure etc..

Referenced by GetAspectDelay(), and Osmia_Nest().

m_cell_lock

omp_nest_lock_t* Osmia_Nest::m_cell_lock

protected

The lock to for egg cells operation.

Referenced by Osmia_Nest(), ReleaseCellLock(), SetCellLock(), and ~Osmia_Nest().

m_cells

std::forward_list<TAnimal*> Osmia_Nest::m_cells

protected

list of egg objects

Referenced by AddCocoon(), AddEgg(), Find(), GetNoCells(), KillAllSubsequentCells(), Osmia_Nest(), RemoveCell(), ReplaceNestPointer(), and ZeroCells().

m_isOpen

bool Osmia_Nest::m_isOpen

protected

Signals that the nest is closed or open for adding new cells.

Referenced by CloseNest(), GetIsOpen(), and Osmia_Nest().

m_OurManager

Osmia_Nest_Manager * Osmia_Nest::m_OurManager = NULL

staticprotected

A pointer to the one and only nest population manager.

Referenced by GetNoNests(), KillAllSubsequentCells(), Osmia_Nest(), and RemoveCell().

m_owner

Osmia_Female* Osmia_Nest::m_owner

Referenced by Osmia_Female::FindNestLocation(), and Osmia_Nest().

m_PolyRef

int Osmia_Nest::m_PolyRef

protected

polygon reference to where the nest is located

Referenced by GetNoNests(), GetPolyRef(), KillAllSubsequentCells(), Osmia_Nest(), and RemoveCell().

m_x

int Osmia_Nest::m_x

protected

x-location

The Osmia_Nest class contains a list of Osmia_Egg pointers to objects it contains. It is descended from TAnimal which means it has a location and has access to the TALMaSSObject Step code if needed..however, right now this is not implemented in the population manager. All information about the egg state is held by the egg itself e.g. sex, parasitoids, so this is simply a list of eggs in order of them being added to the nest The nest can however supply the number of current eggs it holds

Referenced by Osmia_Nest().

m_y

int Osmia_Nest::m_y

protected

y-location

Referenced by Osmia_Nest().

---

The documentation for this class was generated from the following files:

• /builds/ALMaSS/ALMaSS_MIDox/Osmia/Osmia.h
• /builds/ALMaSS/ALMaSS_MIDox/Osmia/Osmia.cpp
• /builds/ALMaSS/ALMaSS_MIDox/Osmia/Osmia_Population_Manager.cpp