====== A simple tomato plant model ======
In this tutorial we will create a simple model of architecture and development of a tomato plant.

===== Organs =====

<code java>
module Organ(super.length) extends M(length);
</code> 

<code java>
module Apex extends Organ;
module Internode extends Organ;
module Leaf extends Organ;
module Leaflet extends Organ;
module Flower extends Organ;
</code> 

==== Parameters for organ geometry ====

<code java>
static double PHYLLOTAXIS_ANGLE	= 137.51;
static double LEAF_ANGLE = 60;
static double LEAF_LENGTH = 0.40;
static double PETIOLE_WIDTH = 0.01;
static double INTERNODE_LENGTH = 0.08;
static double INTERNODE_WIDTH = 0.02;

static int NB_VEG_PHYTOMERS = 8;
</code>

==== Specifying organ geometry ====

<code java>
module Apex extends Organ
==>
    Sphere(0.01).(setShader(RED))
;
</code>

<code java>
module Internode extends Organ 
{
    double width;
    	
    {
        length = INTERNODE_LENGTH;
        width = INTERNODE_WIDTH;
    }
}
==>
    Cylinder(length, width/2).(setShader(YELLOW))
;
</code>

<code java>
module Leaf extends Organ 
{
    double width;
    double angle;
    double petioleLength;
    double petioleWidth;
    
    {
        length = LEAF_LENGTH;
        width = 0.5*LEAF_LENGTH;
        angle = LEAF_ANGLE;
        petioleLength = 0.2*LEAF_LENGTH;
        petioleWidth = PETIOLE_WIDTH;	
    }
}
==> 
    RL(angle)
    Cylinder(petioleLength, petioleWidth/2).(setShader(GREEN))
    Parallelogram(length-petioleLength, width)
;
</code>

<code java>
module Truss extends Organ 
==>
    RL(TRUSS_ANGLE) RH(90)
    for (int i:1:NB_FLOWERS) (
        Cylinder(0.02,0.001).(setShader(YELLOW))  
        [ 
            if(i%2==0) (
                RH(90)
            ) else (
                RH(-90)
            )
            RU(60) 
            Cylinder(0.02,0.001).(setShader(BLUE)) 
            Sphere(0.02).(setShader(RED)) 
        ]
        RU(-20)
    )
;

</code>

===== The initial condition =====

<code java>
protected void init()
[
    Axiom ==> Apex;
]
</code>

===== Rewriting rules =====

First, we specify rewriting rules for vegetative development of the primary shoot in tomato.

<code java>
public void run()
[
    a:Apex ==> 
        Internode
        [Leaf]
        RH(PHYLLOTAXIS_ANGLE)
        a
    ;
]
</code>

After a certain number of phytomers (internodes with leaves), specified by a parameter NB_VEG_PHYTOMERS, primary shoot will change into sympodial shoot. For this, a repetitive pattern with 3 leaves and 1 truss with fruits is typical for many (high-wire) tomato cultivars.

<code java>
public void run()
[
    a:Apex, (a[rank] < NB_VEG_PHYTOMERS) ==> 
        Internode
        [Leaf]
        RH(PHYLLOTAXIS_ANGLE)
        a
        {a[rank]++;}
    ;
	
    a:Apex, (a[rank] >= NB_VEG_PHYTOMERS) ==>
        Internode
        if ((a[rank] - NB_VEG_PHYTOMERS) % 4 == 1) (
            [Truss]
        ) else (
            [Leaf]
        )
        RH(PHYLLOTAXIS_ANGLE)
        a
        {a[rank]++;}
    ;
]
</code>

===== Improving leaf structure =====

===== Introducing timing of organ appearance based on thermal time =====