Added photosynthesis, a chloroplast organelle, and environmental CO2 …

…emitters.

Notes:
- Chloroplast organelle is placed in editor with hotkey [P]
- Water and sun are everywhere, so photosynthesis only requires CO2
- New OrganelleFactory streamlines microbe creation and modification
- definitions are now on the git repo

.gitignore

@@ -1,3 +1,16 @@
+# Asset directory
+assets/*
+# We want certain xmls though
+!assets/definitions/
+!assets/definitions/*.xml
+# maybe add these in later
+#!assets/gui/layouts/*.layout
+
+# Website directory
+
+website/*
+index.html
+
 # Standard stuff
 Thumbs.db
 *.obj
@@ -72,5 +85,5 @@ nbproject/
 # Vim swap files
 *.swp
 
-# Asset directory
-assets/*
+# Temporary/backup files
+*~

assets/definitions/compounds.xml

@@ -0,0 +1,47 @@
+<?xml version="1.0" ?>
+<Compounds>
+    <Compound name="atp" weight="1">
+        <Display text="ATP">
+            <Model file="atp.mesh" size="0.1" />
+        </Display>
+	</Compound>
+    <Compound name="oxygen" weight="1">
+        <Display text="Oxygen" >
+            <Model file="molecule.mesh" size="0.3" />
+        </Display>
+	</Compound>
+    <Compound name="reproductase" weight="1">
+        <Display text="Reproductase" >
+            <Model file="hex.mesh" size="0.3" />
+        </Display>
+	</Compound>
+    <Compound name="aminoacids" weight="1">
+        <Display text="Amino Acids">
+            <Model file="hex.mesh" size="0.3" />
+        </Display>
+	</Compound>
+    <Compound name="ammonia" weight="1">
+        <Display text="Ammonia" >
+            <Model file="hex.mesh" size="0.3" />
+        </Display>
+	</Compound>
+    <Compound name="glucose" weight="1">
+        <Display text="Glucose" >
+            <Model file="glucose.mesh" size="0.3" />
+        </Display>
+	</Compound>
+    <Compound name="co2" weight="1">
+        <Display text="CO2" >
+            <Model file="co2.mesh" size="0.16" />
+        </Display>
+	</Compound>
+
+    <AgentCompounds>
+        <Agent name="oxytoxy" weight="1">
+            <Display text="OxyToxy NT" >
+                <Model file="oxytoxy.mesh" size="0.3" />
+            </Display>
+            <Effect function="oxytoxyEffect" />
+        </Agent>
+    </AgentCompounds>
+</Compounds>

assets/definitions/processes.xml

@@ -0,0 +1,52 @@
+<?xml version="1.0" ?>
+<Processes>
+	<Process name="Respiration" speedFactor="0.5" energyCost="0">
+        <Inputs>
+            <Input compound="glucose" amount="1"/>
+            <Input compound="oxygen" amount="6"/>
+        </Inputs>
+        <Outputs>
+            <Output compound="co2" amount="6"/>
+            <Output compound="atp" amount="36"/>
+        </Outputs>
+	</Process>
+    <Process name="ReproductaseSynthesis" speedFactor="2.2" energyCost="30">
+        <Inputs>
+            <Input compound="aminoacids" amount="6"/>
+            <Input compound="glucose" amount="6"/>
+            <Input compound="oxygen" amount="6"/>
+            <Input compound="atp" amount="6"/>
+        </Inputs>
+        <Outputs>
+            <Output compound="reproductase" amount="1"/>
+        </Outputs>
+	</Process>
+    <Process name="AminoAcidSynthesis" speedFactor="3.5" energyCost="0">
+        <Inputs>
+            <Input compound="glucose" amount="1"/>
+            <Input compound="ammonia" amount="1"/>
+        </Inputs>
+        <Outputs>
+            <Output compound="co2" amount="1"/>
+            <Output compound="atp" amount="2"/>
+            <Output compound="aminoacids" amount="1"/>
+        </Outputs>
+	</Process>
+    <Process name="OxyToxySynthesis" speedFactor="0.1" energyCost="1">
+        <Inputs>
+            <Input compound="oxygen" amount="3"/>
+        </Inputs>
+        <Outputs>
+            <Output compound="oxytoxy" amount="1"/>
+        </Outputs>
+	</Process>
+    <Process name="Photosynthesis" speedFactor="0.2" energyCost="0">
+	    <Inputs>
+            <Input compound="co2" amount="6"/>
+        </Inputs>
+        <Outputs>
+            <Output compound="glucose" amount="1"/>
+            <Output compound="oxygen" amount="6"/>
+        </Outputs>
+    </Process>
+</Processes>

scripts/microbe_editor/microbe_editor.lua

@@ -18,6 +18,7 @@ function MicrobeEditor:__init(hudSystem)
     self.placementFunctions = {["nucleus"] = MicrobeEditor.createNewMicrobe,
                                ["flagelium"] = MicrobeEditor.addMovementOrganelle,
                                ["mitochondria"] = MicrobeEditor.addProcessOrganelle,
+                               ["chloroplast"] = MicrobeEditor.addProcessOrganelle,
                                ["toxin"] = MicrobeEditor.addAgentVacuole,
 
                                ["vacuole"] = MicrobeEditor.addStorageOrganelle,
@@ -92,10 +93,7 @@ function MicrobeEditor:addStorageOrganelle(organelleType)
    -- self.currentMicrobe = Microbe(Entity("working_microbe", GameState.MICROBE))
     local q, r = self:getMouseHex()
     if self.currentMicrobe:getOrganelleAt(q, r) == nil then
-        local storageOrganelle = StorageOrganelle(100.0)
-        storageOrganelle:addHex(0, 0)
-        storageOrganelle:setColour(ColourValue(0, 1, 0, 1))  
-        self.currentMicrobe:addOrganelle(q, r, storageOrganelle)
+        self.currentMicrobe:addOrganelle(q, r, OrganelleFactory.makeVacuole())
         self.organelleCount = self.organelleCount + 1
     end
 end
@@ -104,35 +102,19 @@ end
 function MicrobeEditor:addMovementOrganelle(organelleType)
     local q, r = self:getMouseHex()
     if self.currentMicrobe:getOrganelleAt(q, r) == nil then
-        -- Calculate the momentum of the movement organelle based on angle towards nucleus
-        local organelleX, organelleY = axialToCartesian(q, r)
-        local nucleusX, nucleusY = axialToCartesian(0, 0)
-        local deltaX = nucleusX - organelleX
-        local deltaY = nucleusY - organelleY
-        local dist = math.sqrt(deltaX^2 + deltaY^2) -- For normalizing vector
-        local momentumX = deltaX / dist * FLAGELIUM_MOMENTUM
-        local momentumY = deltaY / dist * FLAGELIUM_MOMENTUM
-        local movementOrganelle = MovementOrganelle(
-            Vector3(momentumX, momentumY, 0.0),
-            300
-        )
-        movementOrganelle:addHex(0, 0)
-        movementOrganelle:setColour(ColourValue(0.8, 0.3, 0.3, 1))
-        self.currentMicrobe:addOrganelle(q,r, movementOrganelle)
+        self.currentMicrobe:addOrganelle(q,r, OrganelleFactory.makeFlagellum(q,r))
         self.organelleCount = self.organelleCount + 1
     end
 end
 
 function MicrobeEditor:addProcessOrganelle(organelleType)
     local q, r = self:getMouseHex()
     if self.currentMicrobe:getOrganelleAt(q, r) == nil then
-        local processOrganelle = ProcessOrganelle()
-        if organelleType == "mitochondria" then         
-            processOrganelle:addProcess(global_processMap["Respiration"])
-            processOrganelle:addHex(0, 0)
-            processOrganelle:setColour(ColourValue(0.8, 0.4, 0.5, 0))
-
-            self.currentMicrobe:addOrganelle(q,r, processOrganelle)
+
+        if organelleType == "mitochondria" then
+            self.currentMicrobe:addOrganelle(q,r, OrganelleFactory.makeMitochondrion())
+        elseif organelleType == "chloroplast" then
+            self.currentMicrobe:addOrganelle(q,r, OrganelleFactory.makeChloroplast())
         else
             assert(false, "organelleType did not exist")
         end
@@ -144,23 +126,16 @@ function MicrobeEditor:addAgentVacuole(organelleType)
     if organelleType == "toxin" then         
         local q, r = self:getMouseHex()
         if self.currentMicrobe:getOrganelleAt(q, r) == nil then
-            local agentVacuole = AgentVacuole(CompoundRegistry.getCompoundId("oxytoxy"), global_processMap["OxyToxySynthesis"])
-            agentVacuole:addHex(0, 0)
-            agentVacuole:setColour(ColourValue(0, 1, 1, 0))
-            self.currentMicrobe:addOrganelle(q, r, agentVacuole)
+            self.currentMicrobe:addOrganelle(q, r, OrganelleFactory.makeOxytoxyVacuole())
             self.organelleCount = self.organelleCount + 1
         end
     end
     self.organelleCount = self.organelleCount + 1
 end
 
 function MicrobeEditor:addNucleus()
-    local nucleusOrganelle = NucleusOrganelle()
-    nucleusOrganelle:addHex(0, 0)
-    nucleusOrganelle:setColour(ColourValue(0.8, 0.2, 0.8, 1))
+    local nucleusOrganelle = OrganelleFactory.makeNucleus()
     self.currentMicrobe:addOrganelle(0, 0, nucleusOrganelle)
-    nucleusOrganelle:addProcess(global_processMap["ReproductaseSynthesis"])
-    nucleusOrganelle:addProcess(global_processMap["AminoAcidSynthesis"])
 end
 
 function MicrobeEditor:createNewMicrobe()
@@ -175,4 +150,4 @@ function MicrobeEditor:createNewMicrobe()
     self.currentMicrobe.collisionHandler:addCollisionGroup("powerupable")
     self:addNucleus()
 
-end
+end