From 1ce466df532a17330e456e71a7256932653f41dd Mon Sep 17 00:00:00 2001
From: Tim Melentyev <tim.melentyev@gmail.com>
Date: Sun, 16 Aug 2020 16:39:10 +0200
Subject: [PATCH 1/2] Make food and waste particles easier to see for people
 with colorblindness

---
 virus/Particle.pde |  306 +++++-----
 virus/virus.pde    | 1422 ++++++++++++++++++++++----------------------
 2 files changed, 866 insertions(+), 862 deletions(-)

diff --git a/virus/Particle.pde b/virus/Particle.pde
index c775594..f1a5a11 100644
--- a/virus/Particle.pde
+++ b/virus/Particle.pde
@@ -1,151 +1,155 @@
-class Particle{
-  double[] coor;
-  double[] velo;
-  int type;
-  double laserX = 0;
-  double laserY = 0;
-  int laserT = -9999;
-  int birthFrame;
-  double AGE_GROW_SPEED = 0.08;
-  Genome UGO_genome;
-  
-  public Particle(double[] tcoor, int ttype, int b){
-    coor = tcoor;
-    velo = getRandomVelo();
-    type = ttype;
-    UGO_genome = null;
-    birthFrame = b;
-  }
-  public Particle(double[] tcoor, int ttype, String genomeString, int b){
-    coor = tcoor;
-    double dx = tcoor[2]-tcoor[0];
-    double dy = tcoor[3]-tcoor[1];
-    double dist = Math.sqrt(dx*dx+dy*dy);
-    double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
-    velo = new double[]{dx/dist*sp,dy/dist*sp};
-    type = ttype;
-    UGO_genome = new Genome(genomeString,true);
-    birthFrame = b;
-  }
-  public double[] copyCoor(){
-    double[] result = new double[2];
-    for(int dim = 0; dim < 2; dim++){
-      result[dim] = coor[dim];
-    }
-    return result;
-  }
-  public void moveDim(int d){
-    float visc = (getCellTypeAt(coor,true) == 0) ? 1 : 0.5;
-    double[] future = copyCoor();
-    future[d] = coor[d]+velo[d]*visc*PLAY_SPEED;
-    if(cellTransfer(coor, future)){
-      int currentType = getCellTypeAt(coor,true);
-      int futureType = getCellTypeAt(future,true);
-      if(type == 2 && currentType == 0 && futureType == 2 &&
-      UGO_genome.codons.size()+getCellAt(future,true).genome.codons.size() <= MAX_CODON_COUNT){ // there are few enough codons that we can fit in the new material!
-        injectGeneticMaterial(future);  // UGO is going to inject material into a cell!
-      }else if(futureType == 1 ||
-      (type >= 1 && (currentType != 0 || futureType != 0))){ // bounce
-        Cell b_cell = getCellAt(future,true);
-        if(b_cell.type >= 2){
-          b_cell.hurtWall(1);
-        }
-        if(velo[d] >= 0){
-          velo[d] = -Math.abs(velo[d]);
-          future[d] = Math.ceil(coor[d])-EPS;
-        }else{
-          velo[d] = Math.abs(velo[d]);
-          future[d] = Math.floor(coor[d])+EPS;
-        }
-        Cell t_cell = getCellAt(coor,true);
-        if(t_cell.type >= 2){
-          t_cell.hurtWall(1);
-        }
-      }else{
-        while(future[d] >= WORLD_SIZE){
-          future[d] -= WORLD_SIZE;
-        }
-        while(future[d] < 0){
-          future[d] += WORLD_SIZE;
-        }
-        hurtWalls(coor, future);
-      }
-    }
-    coor = future;
-  }
-  public void injectGeneticMaterial(double[] futureCoor){
-    Cell c = getCellAt(futureCoor,true);
-    int injectionLocation = c.genome.rotateOn;
-    ArrayList<Codon> toInject = UGO_genome.codons;
-    int INJECT_SIZE = UGO_genome.codons.size();
-    
-    for(int i = 0; i < toInject.size(); i++){
-      int[] info = toInject.get(i).codonInfo;
-      c.genome.codons.add(injectionLocation+i,new Codon(info,1.0));
-    }
-    if(c.genome.performerOn >= c.genome.rotateOn){
-      c.genome.performerOn += INJECT_SIZE;
-    }
-    c.genome.rotateOn += INJECT_SIZE;
-    c.tamper();
-    removeParticle();
-    Particle newWaste = new Particle(coor,1,-99999);
-    newWaste.addToCellList();
-    particles.get(1).add(newWaste);
-  }
-  public void hurtWalls(double[] coor, double[] future){
-    Cell p_cell = getCellAt(coor,true);
-    if(p_cell.type >= 2){
-      p_cell.hurtWall(1);
-    }
-    p_cell.removeParticleFromCell(this);
-    Cell n_cell = getCellAt(future,true);
-    if(n_cell.type >= 2){
-      n_cell.hurtWall(1);
-    }
-    n_cell.addParticleToCell(this);
-  }
-  public void iterate(){
-    for(int dim = 0; dim < 2; dim++){
-      moveDim(dim);
-    }
-  }
-  public void drawParticle(double x, double y, double s){
-    pushMatrix();
-    translate((float)x,(float)y);
-    
-    double ageScale = Math.min(1.0,(frameCount-birthFrame)*AGE_GROW_SPEED);
-    scale((float)(s/BIG_FACTOR*ageScale));
-    noStroke();
-    if(type == 0){
-      fill(255,0,0);
-    }else if(type == 1){
-      fill(WASTE_COLOR);
-    }else if(type == 2){
-      fill(0);
-    }
-    ellipseMode(CENTER);
-    ellipse(0,0,0.1*BIG_FACTOR,0.1*BIG_FACTOR);
-    if(UGO_genome != null){
-      UGO_genome.drawCodons();
-    }
-    popMatrix();
-  }
-
-  public void removeParticle(){
-    particles.get(type).remove(this);
-    getCellAt(coor,true).particlesInCell.get(type).remove(this);
-  }
-  public void addToCellList(){
-    Cell cellIn = getCellAt(coor,true);
-    cellIn.addParticleToCell(this);
-  }
-  public void loopCoor(int d){
-    while(coor[d] >= WORLD_SIZE){
-      coor[d] -= WORLD_SIZE;
-    }
-    while(coor[d] < 0){
-      coor[d] += WORLD_SIZE;
-    }
-  }
-}
+class Particle{
+  double[] coor;
+  double[] velo;
+  int type;
+  double laserX = 0;
+  double laserY = 0;
+  int laserT = -9999;
+  int birthFrame;
+  double AGE_GROW_SPEED = 0.08;
+  int outlineThickness = 2;
+  Genome UGO_genome;
+  
+  public Particle(double[] tcoor, int ttype, int b){
+    coor = tcoor;
+    velo = getRandomVelo();
+    type = ttype;
+    UGO_genome = null;
+    birthFrame = b;
+  }
+  public Particle(double[] tcoor, int ttype, String genomeString, int b){
+    coor = tcoor;
+    double dx = tcoor[2]-tcoor[0];
+    double dy = tcoor[3]-tcoor[1];
+    double dist = Math.sqrt(dx*dx+dy*dy);
+    double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
+    velo = new double[]{dx/dist*sp,dy/dist*sp};
+    type = ttype;
+    UGO_genome = new Genome(genomeString,true);
+    birthFrame = b;
+  }
+  public double[] copyCoor(){
+    double[] result = new double[2];
+    for(int dim = 0; dim < 2; dim++){
+      result[dim] = coor[dim];
+    }
+    return result;
+  }
+  public void moveDim(int d){
+    float visc = (getCellTypeAt(coor,true) == 0) ? 1 : 0.5;
+    double[] future = copyCoor();
+    future[d] = coor[d]+velo[d]*visc*PLAY_SPEED;
+    if(cellTransfer(coor, future)){
+      int currentType = getCellTypeAt(coor,true);
+      int futureType = getCellTypeAt(future,true);
+      if(type == 2 && currentType == 0 && futureType == 2 &&
+      UGO_genome.codons.size()+getCellAt(future,true).genome.codons.size() <= MAX_CODON_COUNT){ // there are few enough codons that we can fit in the new material!
+        injectGeneticMaterial(future);  // UGO is going to inject material into a cell!
+      }else if(futureType == 1 ||
+      (type >= 1 && (currentType != 0 || futureType != 0))){ // bounce
+        Cell b_cell = getCellAt(future,true);
+        if(b_cell.type >= 2){
+          b_cell.hurtWall(1);
+        }
+        if(velo[d] >= 0){
+          velo[d] = -Math.abs(velo[d]);
+          future[d] = Math.ceil(coor[d])-EPS;
+        }else{
+          velo[d] = Math.abs(velo[d]);
+          future[d] = Math.floor(coor[d])+EPS;
+        }
+        Cell t_cell = getCellAt(coor,true);
+        if(t_cell.type >= 2){
+          t_cell.hurtWall(1);
+        }
+      }else{
+        while(future[d] >= WORLD_SIZE){
+          future[d] -= WORLD_SIZE;
+        }
+        while(future[d] < 0){
+          future[d] += WORLD_SIZE;
+        }
+        hurtWalls(coor, future);
+      }
+    }
+    coor = future;
+  }
+  public void injectGeneticMaterial(double[] futureCoor){
+    Cell c = getCellAt(futureCoor,true);
+    int injectionLocation = c.genome.rotateOn;
+    ArrayList<Codon> toInject = UGO_genome.codons;
+    int INJECT_SIZE = UGO_genome.codons.size();
+    
+    for(int i = 0; i < toInject.size(); i++){
+      int[] info = toInject.get(i).codonInfo;
+      c.genome.codons.add(injectionLocation+i,new Codon(info,1.0));
+    }
+    if(c.genome.performerOn >= c.genome.rotateOn){
+      c.genome.performerOn += INJECT_SIZE;
+    }
+    c.genome.rotateOn += INJECT_SIZE;
+    c.tamper();
+    removeParticle();
+    Particle newWaste = new Particle(coor,1,-99999);
+    newWaste.addToCellList();
+    particles.get(1).add(newWaste);
+  }
+  public void hurtWalls(double[] coor, double[] future){
+    Cell p_cell = getCellAt(coor,true);
+    if(p_cell.type >= 2){
+      p_cell.hurtWall(1);
+    }
+    p_cell.removeParticleFromCell(this);
+    Cell n_cell = getCellAt(future,true);
+    if(n_cell.type >= 2){
+      n_cell.hurtWall(1);
+    }
+    n_cell.addParticleToCell(this);
+  }
+  public void iterate(){
+    for(int dim = 0; dim < 2; dim++){
+      moveDim(dim);
+    }
+  }
+  public void drawParticle(double x, double y, double s){
+    pushMatrix();
+    translate((float)x,(float)y);
+    
+    double ageScale = Math.min(1.0,(frameCount-birthFrame)*AGE_GROW_SPEED);
+    scale((float)(s/BIG_FACTOR*ageScale));
+    noStroke();
+    strokeWeight(outlineThickness);
+    if(type == 0){
+      fill(255,0,0);
+      stroke(0, 0, 0);
+    }else if(type == 1){
+      fill(WASTE_COLOR);
+      stroke(0, 0, 0);
+    }else if(type == 2){
+      fill(0);
+    }
+    ellipseMode(CENTER);
+    ellipse(0,0,0.1*BIG_FACTOR,0.1*BIG_FACTOR);
+    if(UGO_genome != null){
+      UGO_genome.drawCodons();
+    }
+    popMatrix();
+  }
+
+  public void removeParticle(){
+    particles.get(type).remove(this);
+    getCellAt(coor,true).particlesInCell.get(type).remove(this);
+  }
+  public void addToCellList(){
+    Cell cellIn = getCellAt(coor,true);
+    cellIn.addParticleToCell(this);
+  }
+  public void loopCoor(int d){
+    while(coor[d] >= WORLD_SIZE){
+      coor[d] -= WORLD_SIZE;
+    }
+    while(coor[d] < 0){
+      coor[d] += WORLD_SIZE;
+    }
+  }
+}
diff --git a/virus/virus.pde b/virus/virus.pde
index 76e67da..5890da6 100644
--- a/virus/virus.pde
+++ b/virus/virus.pde
@@ -1,711 +1,711 @@
-int WORLD_SIZE = 12;
-int W_W = 1728;
-int W_H = 972;
-Cell[][] cells = new Cell[WORLD_SIZE][WORLD_SIZE];
-ArrayList<ArrayList<Particle>> particles = new ArrayList<ArrayList<Particle>>(0);
-int foodLimit = 180;
-float BIG_FACTOR = 100;
-float PLAY_SPEED = 0.6;
-double GENE_TICK_TIME = 40.0;
-double margin = 4;
-int START_LIVING_COUNT = 0;
-int[] cellCounts = {0,0,0};
-
-double REMOVE_WASTE_SPEED_MULTI = 0.001;
-double removeWasteTimer = 1.0;
-
-double GENE_TICK_ENERGY = 0.014;
-double WALL_DAMAGE = 0.01;
-double CODON_DEGRADE_SPEED = 0.008;
-double EPS = 0.00000001;
-
-String starterGenome = "46-11-22-33-11-22-33-45-44-57__-67__";
-boolean canDrag = false;
-double clickWorldX = -1;
-double clickWorldY = -1;
-boolean DQclick = false;
-int[] codonToEdit = {-1,-1,0,0};
-double[] genomeListDims = {70,430,360,450};
-double[] editListDims = {550,430,180,450};
-double[] arrowToDraw = null;
-Cell selectedCell = null;
-Cell UGOcell;
-int lastEditTimeStamp = 0;
-color handColor = color(0,128,0);
-color TELOMERE_COLOR = color(0,0,0);
-color WASTE_COLOR = color(100,65,0);
-int MAX_CODON_COUNT = 20; // If a cell were to have more codons in its DNA than this number if it were to absorb a cirus particle, it won't absorb it.
-
-double SPEED_LOW = 0.01;
-double SPEED_HIGH = 0.02;
-double MIN_ARROW_LENGTH_TO_PRODUCE = 0.4;
-
-double ZOOM_THRESHOLD = 0;//80;
-PFont font;
-void setup(){
-  font = loadFont("Jygquip1-96.vlw");
-  for(int j = 0; j < 3; j++){
-    ArrayList<Particle> newList = new ArrayList<Particle>(0);
-    particles.add(newList);
-  }
-  for(int y = 0; y < WORLD_SIZE; y++){
-    for(int x = 0; x < WORLD_SIZE; x++){
-      int t = getTypeFromXY(x,y);
-      cells[y][x] = new Cell(x,y,t,0,1,starterGenome);
-      if(t == 2){
-        START_LIVING_COUNT++;
-        cellCounts[0]++;
-      }
-    }
-  }
-  size(1728,972);
-  noSmooth();
-  UGOcell = new Cell(-1,-1,2,0,1,"00-00-00-00-00");
-}
-int getTypeFromXY(int preX, int preY){
-  int[] weirdo = {0,1,1,2};
-  int x = (preX/4)*3;
-  x += weirdo[preX%4];
-  int y = (preY/4)*3;
-  y += weirdo[preY%4];
-  int result = 0;
-  for(int i = 1; i < WORLD_SIZE; i *= 3){
-    if((x/i)%3 == 1 && (y/i)%3 == 1){
-      result = 1;
-      int xPart = x%i;
-      int yPart = y%i;
-      boolean left = (xPart == 0);
-      boolean right = (xPart == i-1);
-      boolean top = (yPart == 0);
-      boolean bottom = (yPart == i-1);
-      if(left || right || top || bottom){
-        result = 2;
-      }
-    }
-  }
-  return result;
-}
-
-boolean wasMouseDown = false;
-double camX = 0;
-double camY = 0;
-double MIN_CAM_S = ((float)W_H)/WORLD_SIZE;
-double camS = MIN_CAM_S;
-void draw(){
-  doParticleCountControl();
-  iterate();
-  detectMouse();
-  drawBackground();
-  drawCells();
-  drawParticles();
-  drawExtras();
-  drawUI();
-}
-void drawExtras(){
-  if(arrowToDraw != null){
-    if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
-      stroke(0);
-    }else{
-      stroke(0,0,0,80);
-    }
-    drawArrow(arrowToDraw[0],arrowToDraw[1],arrowToDraw[2],arrowToDraw[3]);
-  }
-}
-void doParticleCountControl(){
-  ArrayList<Particle> foods = particles.get(0);
-  while(foods.size() < foodLimit){
-    int choiceX = -1;
-    int choiceY = -1;
-    while(choiceX == -1 || cells[choiceY][choiceX].type >= 1){
-      choiceX = (int)random(0,WORLD_SIZE);
-      choiceY = (int)random(0,WORLD_SIZE);
-    }
-    double extraX = random(0.3,0.7);
-    double extraY = random(0.3,0.7);
-    double x = choiceX+extraX;
-    double y = choiceY+extraY;
-    double[] coor = {x,y};
-    Particle newFood = new Particle(coor,0,frameCount);
-    foods.add(newFood);
-    newFood.addToCellList();
-  }
-  
-  ArrayList<Particle> wastes = particles.get(1);
-  if(wastes.size() > foodLimit){
-    removeWasteTimer -= (wastes.size()-foodLimit)*REMOVE_WASTE_SPEED_MULTI;
-    if(removeWasteTimer < 0){
-      int choiceIndex = -1;
-      int iter = 0;
-      while(iter < 50 && (choiceIndex == -1 || getCellAt(wastes.get(choiceIndex).coor,true).type == 2)){
-        choiceIndex = (int)(Math.random()*wastes.size());
-      } // If possible, choose a particle that is NOT in a cell at the moment.
-      wastes.get(choiceIndex).removeParticle();
-      removeWasteTimer++;
-    }
-  }
-}
-double[] getRandomVelo(){
-  double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
-  double ang = random(0,2*PI);
-  double vx = sp*Math.cos(ang);
-  double vy = sp*Math.sin(ang);
-  double[] result = {vx, vy};
-  return result;
-}
-void iterate(){
-  for(int z = 0; z < 3; z++){
-    ArrayList<Particle> sparticles = particles.get(z);
-    for(int i = 0; i < sparticles.size(); i++){
-      Particle p = sparticles.get(i);
-      p.iterate();
-    }
-  }
-  for(int y = 0; y < WORLD_SIZE; y++){
-    for(int x = 0; x < WORLD_SIZE; x++){
-      cells[y][x].iterate();
-    }
-  }
-}
-void drawParticles(){
-  for(int z = 0; z < 3; z++){
-    ArrayList<Particle> sparticles = particles.get(z);
-    for(int i = 0; i < sparticles.size(); i++){
-      Particle p = sparticles.get(i);
-      p.drawParticle(trueXtoAppX(p.coor[0]),trueYtoAppY(p.coor[1]),trueStoAppS(1));
-    }
-  }
-}
-void checkGLclick(){
-  double gx = genomeListDims[0];
-  double gy = genomeListDims[1];
-  double gw = genomeListDims[2];
-  double gh = genomeListDims[3];
-  double rMouseX = ((mouseX-W_H)-gx)/gw;
-  double rMouseY = (mouseY-gy)/gh;
-  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0){
-    if(rMouseY < 1){
-      codonToEdit[0] = (int)(rMouseX*2);
-      codonToEdit[1] = (int)(rMouseY*selectedCell.genome.codons.size());
-    }else if(selectedCell == UGOcell){
-      if(rMouseX < 0.5){
-        String genomeString = UGOcell.genome.getGenomeStringShortened();
-        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
-      }else{
-        String genomeString = UGOcell.genome.getGenomeStringLengthened();
-        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
-      }
-    }
-  }
-}
-void checkETclick(){
-  double ex = editListDims[0];
-  double ey = editListDims[1];
-  double ew = editListDims[2];
-  double eh = editListDims[3];
-  double rMouseX = ((mouseX-W_H)-ex)/ew;
-  double rMouseY = (mouseY-ey)/eh;
-  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0 && rMouseY < 1){
-    int optionCount = CodonInfo.getOptionSize(codonToEdit[0]);
-    int choice = (int)(rMouseY*optionCount);
-    if(codonToEdit[0] == 1 && choice >= optionCount-2){
-      int diff = 1;
-      if(rMouseX < 0.5){
-        diff = -1;
-      }
-      if(choice == optionCount-2){
-        codonToEdit[2] = loopCodonInfo(codonToEdit[2]+diff);
-      }else{
-        codonToEdit[3] = loopCodonInfo(codonToEdit[3]+diff);
-      }
-    }else{
-      Codon thisCodon = selectedCell.genome.codons.get(codonToEdit[1]);
-      if(codonToEdit[0] == 1 && choice == 7){
-        if(thisCodon.codonInfo[1] != 7 ||
-        thisCodon.codonInfo[2] != codonToEdit[2] || thisCodon.codonInfo[3] != codonToEdit[3]){
-          thisCodon.setInfo(1,choice);
-          thisCodon.setInfo(2,codonToEdit[2]);
-          thisCodon.setInfo(3,codonToEdit[3]);
-          if(selectedCell != UGOcell){
-            lastEditTimeStamp = frameCount;
-            selectedCell.tamper();
-          }
-        }
-      }else{
-        if(thisCodon.codonInfo[codonToEdit[0]] != choice){
-          thisCodon.setInfo(codonToEdit[0],choice);
-          if(selectedCell != UGOcell){
-            lastEditTimeStamp = frameCount;
-            selectedCell.tamper();
-          }
-        }
-      }
-    }
-  }else{
-    codonToEdit[0] = codonToEdit[1] = -1;
-  }
-}
-int loopCodonInfo(int val){
-  while(val < -30){
-    val += 61;
-  }
-  while(val > 30){
-    val -= 61;
-  }
-  return val;
-}
-int codonCharToVal(char c){
-  int val = (int)(c) - (int)('A');
-  return val-30;
-}
-String codonValToChar(int i){
-  int val = (i+30) + (int)('A');
-  return (char)val+"";
-}
-void detectMouse(){
-  if (mousePressed){
-    arrowToDraw = null;
-    if(!wasMouseDown) {
-      if(mouseX < W_H){
-        codonToEdit[0] = codonToEdit[1] = -1;
-        clickWorldX = appXtoTrueX(mouseX);
-        clickWorldY = appYtoTrueY(mouseY);
-        canDrag = true;
-      }else{
-        if(selectedCell != null){
-          if(codonToEdit[0] >= 0){
-            checkETclick();
-          }
-          checkGLclick();
-        }
-        if(selectedCell == UGOcell){
-          if((mouseX >= W_H+530 && codonToEdit[0] == -1) || mouseY < 160){
-            selectedCell = null;
-          }
-        }else if(mouseX > W_W-160 && mouseY < 160){
-          selectedCell = UGOcell;
-        }
-        canDrag = false;
-      }
-      DQclick = false;
-    }else if(canDrag){
-      double newCX = appXtoTrueX(mouseX);
-      double newCY = appYtoTrueY(mouseY);
-      if(newCX != clickWorldX || newCY != clickWorldY){
-        DQclick = true;
-      }
-      if(selectedCell == UGOcell){
-        stroke(0,0,0);
-        arrowToDraw = new double[]{clickWorldX,clickWorldY,newCX,newCY};
-      }else{
-        camX -= (newCX-clickWorldX);
-        camY -= (newCY-clickWorldY);
-      }
-    }
-  }
-  if(!mousePressed){
-    if(wasMouseDown){
-      if(selectedCell == UGOcell && arrowToDraw != null){
-        if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
-          produceUGO(arrowToDraw);
-        }
-      }
-      if(!DQclick && canDrag){
-        double[] mCoor = {clickWorldX,clickWorldY};
-        Cell clickedCell = getCellAt(mCoor,false);
-        if(selectedCell != UGOcell){
-          selectedCell = null;
-        }
-        if(clickedCell != null && clickedCell.type == 2){
-          selectedCell = clickedCell;
-        }
-      }
-    }
-    clickWorldX = -1;
-    clickWorldY = -1;
-    arrowToDraw = null;
-  }
-  wasMouseDown = mousePressed;
-}
-void mouseWheel(MouseEvent event) {
-  double ZOOM_F = 1.05;
-  double thisZoomF = 1;
-  float e = event.getCount();
-  if(e == 1){
-    thisZoomF = 1/ZOOM_F;
-  }else{
-    thisZoomF = ZOOM_F;
-  }
-  double worldX = mouseX/camS+camX;
-  double worldY = mouseY/camS+camY;
-  camX = (camX-worldX)/thisZoomF+worldX;
-  camY = (camY-worldY)/thisZoomF+worldY;
-  camS *= thisZoomF;
-}
-double euclidLength(double[] coor){
-  return Math.sqrt(Math.pow(coor[0]-coor[2],2)+Math.pow(coor[1]-coor[3],2));
-}
-void produceUGO(double[] coor){
-  if(getCellAt(coor,false) != null && getCellAt(coor,false).type == 0){
-    String genomeString = UGOcell.genome.getGenomeString();
-    Particle newUGO = new Particle(coor,2,genomeString,frameCount);
-    particles.get(2).add(newUGO);
-    newUGO.addToCellList();
-    lastEditTimeStamp = frameCount;
-  }
-}
-void drawBackground(){
-  background(255);
-}
-void drawArrow(double dx1, double dx2, double dy1, double dy2){
-  float x1 = (float)trueXtoAppX(dx1);
-  float y1 = (float)trueYtoAppY(dx2);
-  float x2 = (float)trueXtoAppX(dy1);
-  float y2 = (float)trueYtoAppY(dy2);
-  strokeWeight((float)(0.03*camS));
-  line(x1,y1,x2,y2);
-  float angle = atan2(y2-y1,x2-x1);
-  float head_size = (float)(0.2*camS);
-  float x3 = x2+head_size*cos(angle+PI*0.8);
-  float y3 = y2+head_size*sin(angle+PI*0.8);
-  line(x2,y2,x3,y3);
-  float x4 = x2+head_size*cos(angle-PI*0.8);
-  float y4 = y2+head_size*sin(angle-PI*0.8);
-  line(x2,y2,x4,y4);
-}
-String framesToTime(double f){
-  double ticks = f/GENE_TICK_TIME;
-  String timeStr = nf((float)ticks,0,1);
-  if(ticks >= 1000){
-    timeStr = (int)(Math.round(ticks))+"";
-  }
-  return timeStr+"t since";
-}
-String count(int count, String s){
-  if(count == 1){
-    return count+" "+s;
-  }else{
-    return count+" "+s+"s";
-  }
-}
-void drawUI(){
-  pushMatrix();
-  translate(W_H,0);
-  fill(0);
-  noStroke();
-  rect(0,0,W_W-W_H,W_H);
-  fill(255);
-  textFont(font,48);
-  textAlign(LEFT);
-  text(framesToTime(frameCount)+" start",25,60);
-  text(framesToTime(frameCount-lastEditTimeStamp)+" edit",25,108);
-  textFont(font,36);
-  text("Healthy: "+cellCounts[0]+" / "+START_LIVING_COUNT,360,50);
-  text("Tampered: "+cellCounts[1]+" / "+START_LIVING_COUNT,360,90);
-  text("Dead: "+cellCounts[2]+" / "+START_LIVING_COUNT,360,130);
-  if(selectedCell != null){
-    drawCellStats();
-  }
-  popMatrix();
-  drawUGObutton((selectedCell != UGOcell));
-}
-void drawUGObutton(boolean drawUGO){
-  fill(80);
-  noStroke();
-  rect(W_W-130,10,120,140);
-  fill(255);
-  textAlign(CENTER);
-  if(drawUGO){
-    textFont(font,48);
-    text("MAKE",W_W-70,70);
-    text("UGO",W_W-70,120);
-  }else{
-    textFont(font,36);
-    text("CANCEL",W_W-70,95);
-  }
-}
-void drawCellStats(){
-  boolean isUGO = (selectedCell.x == -1);
-  fill(80);
-  noStroke();
-  rect(10,160,530,W_H-170);
-  if(!isUGO){
-    rect(540,160,200,270);
-  }
-  fill(255);
-  textFont(font,96);
-  textAlign(LEFT);
-  text(selectedCell.getCellName(),25,255);
-  if(!isUGO){
-    textFont(font,32);
-    text("Inside this cell,",555,200);
-    text("there are:",555,232);
-    text(count(selectedCell.getParticleCount(-1),"particle"),555,296);
-    text("("+count(selectedCell.getParticleCount(0),"food")+")",555,328);
-    text("("+count(selectedCell.getParticleCount(1),"waste")+")",555,360);
-    text("("+count(selectedCell.getParticleCount(2),"UGO")+")",555,392);
-    drawBar(color(255,255,0),selectedCell.energy,"Energy",290);
-    drawBar(color(210,50,210),selectedCell.wallHealth,"Wall health",360);
-  }
-  drawGenomeAsList(selectedCell.genome,genomeListDims);
-  drawEditTable(editListDims);
-  if(!isUGO){
-    textFont(font,32);
-    textAlign(LEFT);
-    text("Memory: "+getMemory(selectedCell),25,940);
-  }
-}
-String getMemory(Cell c){
-  if(c.memory.length() == 0){
-    return "[NOTHING]";
-  }else{
-    return "\""+c.memory+"\"";
-  }
-}
-void drawGenomeAsList(Genome g, double[] dims){
-  double x = dims[0];
-  double y = dims[1];
-  double w = dims[2];
-  double h = dims[3];
-  int GENOME_LENGTH = g.codons.size();
-  double appCodonHeight = h/GENOME_LENGTH;
-  double appW = w*0.5-margin;
-  textFont(font,30);
-  textAlign(CENTER);
-  pushMatrix();
-  dTranslate(x,y);
-  pushMatrix();
-  dTranslate(0,appCodonHeight*(g.appRO+0.5));
-  if(selectedCell != UGOcell){
-    drawGenomeArrows(w,appCodonHeight);
-  }
-  popMatrix();
-  for(int i = 0; i < GENOME_LENGTH; i++){
-    double appY = appCodonHeight*i;
-    Codon codon = g.codons.get(i);
-    for(int p = 0; p < 2; p++){
-      double extraX = (w*0.5-margin)*p;
-      color fillColor = codon.getColor(p);
-      color textColor = codon.getTextColor(p);
-      fill(0);
-      dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
-      if(codon.hasSubstance()){
-        fill(fillColor);
-        double trueW = appW*codon.codonHealth;
-        double trueX = extraX+margin;
-        if(p == 0){
-          trueX += appW*(1-codon.codonHealth);
-        }
-        dRect(trueX,appY+margin,trueW,appCodonHeight-margin*2);
-      }
-      fill(textColor);
-      dText(codon.getText(p),extraX+w*0.25,appY+appCodonHeight/2+11);
-      
-      if(p == codonToEdit[0] && i == codonToEdit[1]){
-        double highlightFac = 0.5+0.5*sin(frameCount*0.25);
-        fill(255,255,255,(float)(highlightFac*140));
-        dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
-      }
-    }
-  }
-  if(selectedCell == UGOcell){
-    fill(255);
-    textFont(font,60);
-    double avgY = (h+height-y)/2;
-    dText("( - )",w*0.25,avgY+11);
-    dText("( + )",w*0.75-margin,avgY+11);
-  }
-  popMatrix();
-}
-void drawEditTable(double[] dims){
-  double x = dims[0];
-  double y = dims[1];
-  double w = dims[2];
-  double h = dims[3];
-  
-  double appW = w-margin*2;
-  textFont(font,30);
-  textAlign(CENTER);
-  
-  int p = codonToEdit[0];
-  int s = codonToEdit[2];
-  int e = codonToEdit[3];
-  if(p >= 0){
-    pushMatrix();
-    dTranslate(x,y);
-    int choiceCount = CodonInfo.getOptionSize(codonToEdit[0]);
-    double appChoiceHeight = h/choiceCount;
-    for(int i = 0; i < choiceCount; i++){
-      double appY = appChoiceHeight*i;
-      color fillColor = intToColor(CodonInfo.getColor(p,i));
-      color textColor = intToColor(CodonInfo.getTextColor(p,i));
-      fill(fillColor);
-      dRect(margin,appY+margin,appW,appChoiceHeight-margin*2);
-      fill(textColor);
-      dText(CodonInfo.getTextSimple(p, i, s, e),w*0.5,appY+appChoiceHeight/2+11);
-    }
-    popMatrix();
-  }
-}
-color colorInterp(color a, color b, double x){
-  float newR = (float)(red(a)+(red(b)-red(a))*x);
-  float newG = (float)(green(a)+(green(b)-green(a))*x);
-  float newB = (float)(blue(a)+(blue(b)-blue(a))*x);
-  return color(newR, newG, newB);
-}
-void drawGenomeArrows(double dw, double dh){
-  float w = (float)dw;
-  float h = (float)dh;
-  fill(255);
-  beginShape();
-  vertex(-5,0);
-  vertex(-45,-40);
-  vertex(-45,40);
-  endShape(CLOSE);
-  beginShape();
-  vertex(w+5,0);
-  vertex(w+45,-40);
-  vertex(w+45,40);
-  endShape(CLOSE);
-  noStroke();
-  rect(0,-h/2,w,h);
-}
-void dRect(double x, double y, double w, double h){
-  noStroke();
-  rect((float)x, (float)y, (float)w, (float)h);
-}
-void dText(String s, double x, double y){
-  text(s, (float)x, (float)y);
-}
-void dTranslate(double x, double y){
-  translate((float)x, (float)y);
-}
-void daLine(double[] a, double[] b){
-  float x1 = (float)trueXtoAppX(a[0]);
-  float y1 = (float)trueYtoAppY(a[1]);
-  float x2 = (float)trueXtoAppX(b[0]);
-  float y2 = (float)trueYtoAppY(b[1]);
-  strokeWeight((float)(0.03*camS));
-  line(x1,y1,x2,y2);
-}
-void drawBar(color col, double stat, String s, double y){
-  fill(150);
-  rect(25,(float)y,500,60);
-  fill(col);
-  rect(25,(float)y,(float)(stat*500),60);
-  fill(0);
-  textFont(font,48);
-  textAlign(LEFT);
-  text(s+": "+nf((float)(stat*100),0,1)+"%",35,(float)y+47);
-}
-void drawCells(){
-  for(int y = 0; y < WORLD_SIZE; y++){
-    for(int x = 0; x < WORLD_SIZE; x++){
-      cells[y][x].drawCell(trueXtoAppX(x),trueYtoAppY(y),trueStoAppS(1));
-    }
-  }
-}
-double trueXtoAppX(double x){
-  return (x-camX)*camS;
-}
-double trueYtoAppY(double y){
-  return (y-camY)*camS;
-}
-double appXtoTrueX(double x){
-  return x/camS+camX;
-}
-double appYtoTrueY(double y){
-  return y/camS+camY;
-}
-double trueStoAppS(double s){
-  return s*camS;
-}
-int getCellTypeAt(double x, double y, boolean allowLoop){
-  int ix = (int)x;
-  int iy = (int)y;
-  if(allowLoop){
-    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
-    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
-  }else{
-    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
-      return 0;
-    }
-  }
-  return cells[iy][ix].type;
-}
-int getCellTypeAt(double[] coor, boolean allowLoop){
-  return getCellTypeAt(coor[0],coor[1],allowLoop);
-}
-Cell getCellAt(double x, double y, boolean allowLoop){
-  int ix = (int)x;
-  int iy = (int)y;
-  if(allowLoop){
-    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
-    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
-  }else{
-    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
-      return null;
-    }
-  }
-  return cells[iy][ix];
-}
-Cell getCellAt(double[] coor, boolean allowLoop){
-  return getCellAt(coor[0],coor[1],allowLoop);
-}
-boolean cellTransfer(double x1, double y1, double x2, double y2){
-  int ix1 = (int)Math.floor(x1);
-  int iy1 = (int)Math.floor(y1);
-  int ix2 = (int)Math.floor(x2);
-  int iy2 = (int)Math.floor(y2);
-  return (ix1 != ix2 || iy1 != iy2);
-}
-boolean cellTransfer(double[] coor1, double[] coor2){
-  return cellTransfer(coor1[0], coor1[1], coor2[0], coor2[1]);
-}
-double loopIt(double x, double len, boolean evenSplit){
-  if(evenSplit){
-    while(x >= len*0.5){
-      x -= len;
-    }
-    while(x < -len*0.5){
-      x += len;
-    }
-  }else{
-    while(x > len-0.5){
-      x -= len;
-    }
-    while(x < -0.5){
-      x += len;
-    }
-  }
-  return x;
-}
-int loopItInt(int x, int len){
-  return (x+len*10)%len;
-}
-color intToColor(int[] c){
-  return color(c[0],c[1],c[2]);
-}
-color transperize(color col, double trans){
-  float alpha = (float)(trans*255);
-  return color(red(col),green(col),blue(col),alpha);
-}
-String infoToString(int[] info){
-  String result = info[0]+""+info[1];
-  if(info[1] == 7){
-    result += codonValToChar(info[2])+""+codonValToChar(info[3]);
-  }
-  return result;
-}
-int[] stringToInfo(String str){
-  int[] info = new int[4];
-  for(int i = 0; i < 2; i++){
-    info[i] = Integer.parseInt(str.substring(i,i+1));
-  }
-  if(info[1] == 7){
-    for(int i = 2; i < 4; i++){
-      char c = str.charAt(i);
-      info[i] = codonCharToVal(c);
-    }
-  }
-  return info;
-}
\ No newline at end of file
+int WORLD_SIZE = 12;
+int W_W = 1728;
+int W_H = 972;
+Cell[][] cells = new Cell[WORLD_SIZE][WORLD_SIZE];
+ArrayList<ArrayList<Particle>> particles = new ArrayList<ArrayList<Particle>>(0);
+int foodLimit = 180;
+float BIG_FACTOR = 100;
+float PLAY_SPEED = 0.6;
+double GENE_TICK_TIME = 40.0;
+double margin = 4;
+int START_LIVING_COUNT = 0;
+int[] cellCounts = {0,0,0};
+
+double REMOVE_WASTE_SPEED_MULTI = 0.001;
+double removeWasteTimer = 1.0;
+
+double GENE_TICK_ENERGY = 0.014;
+double WALL_DAMAGE = 0.01;
+double CODON_DEGRADE_SPEED = 0.008;
+double EPS = 0.00000001;
+
+String starterGenome = "46-11-22-33-11-22-33-45-44-57__-67__";
+boolean canDrag = false;
+double clickWorldX = -1;
+double clickWorldY = -1;
+boolean DQclick = false;
+int[] codonToEdit = {-1,-1,0,0};
+double[] genomeListDims = {70,430,360,450};
+double[] editListDims = {550,430,180,450};
+double[] arrowToDraw = null;
+Cell selectedCell = null;
+Cell UGOcell;
+int lastEditTimeStamp = 0;
+color handColor = color(0,128,0);
+color TELOMERE_COLOR = color(0,0,0);
+color WASTE_COLOR = color(255,255,255);
+int MAX_CODON_COUNT = 20; // If a cell were to have more codons in its DNA than this number if it were to absorb a cirus particle, it won't absorb it.
+
+double SPEED_LOW = 0.01;
+double SPEED_HIGH = 0.02;
+double MIN_ARROW_LENGTH_TO_PRODUCE = 0.4;
+
+double ZOOM_THRESHOLD = 0;//80;
+PFont font;
+void setup(){
+  font = loadFont("Jygquip1-96.vlw");
+  for(int j = 0; j < 3; j++){
+    ArrayList<Particle> newList = new ArrayList<Particle>(0);
+    particles.add(newList);
+  }
+  for(int y = 0; y < WORLD_SIZE; y++){
+    for(int x = 0; x < WORLD_SIZE; x++){
+      int t = getTypeFromXY(x,y);
+      cells[y][x] = new Cell(x,y,t,0,1,starterGenome);
+      if(t == 2){
+        START_LIVING_COUNT++;
+        cellCounts[0]++;
+      }
+    }
+  }
+  size(1728,972);
+  noSmooth();
+  UGOcell = new Cell(-1,-1,2,0,1,"00-00-00-00-00");
+}
+int getTypeFromXY(int preX, int preY){
+  int[] weirdo = {0,1,1,2};
+  int x = (preX/4)*3;
+  x += weirdo[preX%4];
+  int y = (preY/4)*3;
+  y += weirdo[preY%4];
+  int result = 0;
+  for(int i = 1; i < WORLD_SIZE; i *= 3){
+    if((x/i)%3 == 1 && (y/i)%3 == 1){
+      result = 1;
+      int xPart = x%i;
+      int yPart = y%i;
+      boolean left = (xPart == 0);
+      boolean right = (xPart == i-1);
+      boolean top = (yPart == 0);
+      boolean bottom = (yPart == i-1);
+      if(left || right || top || bottom){
+        result = 2;
+      }
+    }
+  }
+  return result;
+}
+
+boolean wasMouseDown = false;
+double camX = 0;
+double camY = 0;
+double MIN_CAM_S = ((float)W_H)/WORLD_SIZE;
+double camS = MIN_CAM_S;
+void draw(){
+  doParticleCountControl();
+  iterate();
+  detectMouse();
+  drawBackground();
+  drawCells();
+  drawParticles();
+  drawExtras();
+  drawUI();
+}
+void drawExtras(){
+  if(arrowToDraw != null){
+    if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
+      stroke(0);
+    }else{
+      stroke(0,0,0,80);
+    }
+    drawArrow(arrowToDraw[0],arrowToDraw[1],arrowToDraw[2],arrowToDraw[3]);
+  }
+}
+void doParticleCountControl(){
+  ArrayList<Particle> foods = particles.get(0);
+  while(foods.size() < foodLimit){
+    int choiceX = -1;
+    int choiceY = -1;
+    while(choiceX == -1 || cells[choiceY][choiceX].type >= 1){
+      choiceX = (int)random(0,WORLD_SIZE);
+      choiceY = (int)random(0,WORLD_SIZE);
+    }
+    double extraX = random(0.3,0.7);
+    double extraY = random(0.3,0.7);
+    double x = choiceX+extraX;
+    double y = choiceY+extraY;
+    double[] coor = {x,y};
+    Particle newFood = new Particle(coor,0,frameCount);
+    foods.add(newFood);
+    newFood.addToCellList();
+  }
+  
+  ArrayList<Particle> wastes = particles.get(1);
+  if(wastes.size() > foodLimit){
+    removeWasteTimer -= (wastes.size()-foodLimit)*REMOVE_WASTE_SPEED_MULTI;
+    if(removeWasteTimer < 0){
+      int choiceIndex = -1;
+      int iter = 0;
+      while(iter < 50 && (choiceIndex == -1 || getCellAt(wastes.get(choiceIndex).coor,true).type == 2)){
+        choiceIndex = (int)(Math.random()*wastes.size());
+      } // If possible, choose a particle that is NOT in a cell at the moment.
+      wastes.get(choiceIndex).removeParticle();
+      removeWasteTimer++;
+    }
+  }
+}
+double[] getRandomVelo(){
+  double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
+  double ang = random(0,2*PI);
+  double vx = sp*Math.cos(ang);
+  double vy = sp*Math.sin(ang);
+  double[] result = {vx, vy};
+  return result;
+}
+void iterate(){
+  for(int z = 0; z < 3; z++){
+    ArrayList<Particle> sparticles = particles.get(z);
+    for(int i = 0; i < sparticles.size(); i++){
+      Particle p = sparticles.get(i);
+      p.iterate();
+    }
+  }
+  for(int y = 0; y < WORLD_SIZE; y++){
+    for(int x = 0; x < WORLD_SIZE; x++){
+      cells[y][x].iterate();
+    }
+  }
+}
+void drawParticles(){
+  for(int z = 0; z < 3; z++){
+    ArrayList<Particle> sparticles = particles.get(z);
+    for(int i = 0; i < sparticles.size(); i++){
+      Particle p = sparticles.get(i);
+      p.drawParticle(trueXtoAppX(p.coor[0]),trueYtoAppY(p.coor[1]),trueStoAppS(1));
+    }
+  }
+}
+void checkGLclick(){
+  double gx = genomeListDims[0];
+  double gy = genomeListDims[1];
+  double gw = genomeListDims[2];
+  double gh = genomeListDims[3];
+  double rMouseX = ((mouseX-W_H)-gx)/gw;
+  double rMouseY = (mouseY-gy)/gh;
+  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0){
+    if(rMouseY < 1){
+      codonToEdit[0] = (int)(rMouseX*2);
+      codonToEdit[1] = (int)(rMouseY*selectedCell.genome.codons.size());
+    }else if(selectedCell == UGOcell){
+      if(rMouseX < 0.5){
+        String genomeString = UGOcell.genome.getGenomeStringShortened();
+        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
+      }else{
+        String genomeString = UGOcell.genome.getGenomeStringLengthened();
+        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
+      }
+    }
+  }
+}
+void checkETclick(){
+  double ex = editListDims[0];
+  double ey = editListDims[1];
+  double ew = editListDims[2];
+  double eh = editListDims[3];
+  double rMouseX = ((mouseX-W_H)-ex)/ew;
+  double rMouseY = (mouseY-ey)/eh;
+  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0 && rMouseY < 1){
+    int optionCount = CodonInfo.getOptionSize(codonToEdit[0]);
+    int choice = (int)(rMouseY*optionCount);
+    if(codonToEdit[0] == 1 && choice >= optionCount-2){
+      int diff = 1;
+      if(rMouseX < 0.5){
+        diff = -1;
+      }
+      if(choice == optionCount-2){
+        codonToEdit[2] = loopCodonInfo(codonToEdit[2]+diff);
+      }else{
+        codonToEdit[3] = loopCodonInfo(codonToEdit[3]+diff);
+      }
+    }else{
+      Codon thisCodon = selectedCell.genome.codons.get(codonToEdit[1]);
+      if(codonToEdit[0] == 1 && choice == 7){
+        if(thisCodon.codonInfo[1] != 7 ||
+        thisCodon.codonInfo[2] != codonToEdit[2] || thisCodon.codonInfo[3] != codonToEdit[3]){
+          thisCodon.setInfo(1,choice);
+          thisCodon.setInfo(2,codonToEdit[2]);
+          thisCodon.setInfo(3,codonToEdit[3]);
+          if(selectedCell != UGOcell){
+            lastEditTimeStamp = frameCount;
+            selectedCell.tamper();
+          }
+        }
+      }else{
+        if(thisCodon.codonInfo[codonToEdit[0]] != choice){
+          thisCodon.setInfo(codonToEdit[0],choice);
+          if(selectedCell != UGOcell){
+            lastEditTimeStamp = frameCount;
+            selectedCell.tamper();
+          }
+        }
+      }
+    }
+  }else{
+    codonToEdit[0] = codonToEdit[1] = -1;
+  }
+}
+int loopCodonInfo(int val){
+  while(val < -30){
+    val += 61;
+  }
+  while(val > 30){
+    val -= 61;
+  }
+  return val;
+}
+int codonCharToVal(char c){
+  int val = (int)(c) - (int)('A');
+  return val-30;
+}
+String codonValToChar(int i){
+  int val = (i+30) + (int)('A');
+  return (char)val+"";
+}
+void detectMouse(){
+  if (mousePressed){
+    arrowToDraw = null;
+    if(!wasMouseDown) {
+      if(mouseX < W_H){
+        codonToEdit[0] = codonToEdit[1] = -1;
+        clickWorldX = appXtoTrueX(mouseX);
+        clickWorldY = appYtoTrueY(mouseY);
+        canDrag = true;
+      }else{
+        if(selectedCell != null){
+          if(codonToEdit[0] >= 0){
+            checkETclick();
+          }
+          checkGLclick();
+        }
+        if(selectedCell == UGOcell){
+          if((mouseX >= W_H+530 && codonToEdit[0] == -1) || mouseY < 160){
+            selectedCell = null;
+          }
+        }else if(mouseX > W_W-160 && mouseY < 160){
+          selectedCell = UGOcell;
+        }
+        canDrag = false;
+      }
+      DQclick = false;
+    }else if(canDrag){
+      double newCX = appXtoTrueX(mouseX);
+      double newCY = appYtoTrueY(mouseY);
+      if(newCX != clickWorldX || newCY != clickWorldY){
+        DQclick = true;
+      }
+      if(selectedCell == UGOcell){
+        stroke(0,0,0);
+        arrowToDraw = new double[]{clickWorldX,clickWorldY,newCX,newCY};
+      }else{
+        camX -= (newCX-clickWorldX);
+        camY -= (newCY-clickWorldY);
+      }
+    }
+  }
+  if(!mousePressed){
+    if(wasMouseDown){
+      if(selectedCell == UGOcell && arrowToDraw != null){
+        if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
+          produceUGO(arrowToDraw);
+        }
+      }
+      if(!DQclick && canDrag){
+        double[] mCoor = {clickWorldX,clickWorldY};
+        Cell clickedCell = getCellAt(mCoor,false);
+        if(selectedCell != UGOcell){
+          selectedCell = null;
+        }
+        if(clickedCell != null && clickedCell.type == 2){
+          selectedCell = clickedCell;
+        }
+      }
+    }
+    clickWorldX = -1;
+    clickWorldY = -1;
+    arrowToDraw = null;
+  }
+  wasMouseDown = mousePressed;
+}
+void mouseWheel(MouseEvent event) {
+  double ZOOM_F = 1.05;
+  double thisZoomF = 1;
+  float e = event.getCount();
+  if(e == 1){
+    thisZoomF = 1/ZOOM_F;
+  }else{
+    thisZoomF = ZOOM_F;
+  }
+  double worldX = mouseX/camS+camX;
+  double worldY = mouseY/camS+camY;
+  camX = (camX-worldX)/thisZoomF+worldX;
+  camY = (camY-worldY)/thisZoomF+worldY;
+  camS *= thisZoomF;
+}
+double euclidLength(double[] coor){
+  return Math.sqrt(Math.pow(coor[0]-coor[2],2)+Math.pow(coor[1]-coor[3],2));
+}
+void produceUGO(double[] coor){
+  if(getCellAt(coor,false) != null && getCellAt(coor,false).type == 0){
+    String genomeString = UGOcell.genome.getGenomeString();
+    Particle newUGO = new Particle(coor,2,genomeString,frameCount);
+    particles.get(2).add(newUGO);
+    newUGO.addToCellList();
+    lastEditTimeStamp = frameCount;
+  }
+}
+void drawBackground(){
+  background(255);
+}
+void drawArrow(double dx1, double dx2, double dy1, double dy2){
+  float x1 = (float)trueXtoAppX(dx1);
+  float y1 = (float)trueYtoAppY(dx2);
+  float x2 = (float)trueXtoAppX(dy1);
+  float y2 = (float)trueYtoAppY(dy2);
+  strokeWeight((float)(0.03*camS));
+  line(x1,y1,x2,y2);
+  float angle = atan2(y2-y1,x2-x1);
+  float head_size = (float)(0.2*camS);
+  float x3 = x2+head_size*cos(angle+PI*0.8);
+  float y3 = y2+head_size*sin(angle+PI*0.8);
+  line(x2,y2,x3,y3);
+  float x4 = x2+head_size*cos(angle-PI*0.8);
+  float y4 = y2+head_size*sin(angle-PI*0.8);
+  line(x2,y2,x4,y4);
+}
+String framesToTime(double f){
+  double ticks = f/GENE_TICK_TIME;
+  String timeStr = nf((float)ticks,0,1);
+  if(ticks >= 1000){
+    timeStr = (int)(Math.round(ticks))+"";
+  }
+  return timeStr+"t since";
+}
+String count(int count, String s){
+  if(count == 1){
+    return count+" "+s;
+  }else{
+    return count+" "+s+"s";
+  }
+}
+void drawUI(){
+  pushMatrix();
+  translate(W_H,0);
+  fill(0);
+  noStroke();
+  rect(0,0,W_W-W_H,W_H);
+  fill(255);
+  textFont(font,48);
+  textAlign(LEFT);
+  text(framesToTime(frameCount)+" start",25,60);
+  text(framesToTime(frameCount-lastEditTimeStamp)+" edit",25,108);
+  textFont(font,36);
+  text("Healthy: "+cellCounts[0]+" / "+START_LIVING_COUNT,360,50);
+  text("Tampered: "+cellCounts[1]+" / "+START_LIVING_COUNT,360,90);
+  text("Dead: "+cellCounts[2]+" / "+START_LIVING_COUNT,360,130);
+  if(selectedCell != null){
+    drawCellStats();
+  }
+  popMatrix();
+  drawUGObutton((selectedCell != UGOcell));
+}
+void drawUGObutton(boolean drawUGO){
+  fill(80);
+  noStroke();
+  rect(W_W-130,10,120,140);
+  fill(255);
+  textAlign(CENTER);
+  if(drawUGO){
+    textFont(font,48);
+    text("MAKE",W_W-70,70);
+    text("UGO",W_W-70,120);
+  }else{
+    textFont(font,36);
+    text("CANCEL",W_W-70,95);
+  }
+}
+void drawCellStats(){
+  boolean isUGO = (selectedCell.x == -1);
+  fill(80);
+  noStroke();
+  rect(10,160,530,W_H-170);
+  if(!isUGO){
+    rect(540,160,200,270);
+  }
+  fill(255);
+  textFont(font,96);
+  textAlign(LEFT);
+  text(selectedCell.getCellName(),25,255);
+  if(!isUGO){
+    textFont(font,32);
+    text("Inside this cell,",555,200);
+    text("there are:",555,232);
+    text(count(selectedCell.getParticleCount(-1),"particle"),555,296);
+    text("("+count(selectedCell.getParticleCount(0),"food")+")",555,328);
+    text("("+count(selectedCell.getParticleCount(1),"waste")+")",555,360);
+    text("("+count(selectedCell.getParticleCount(2),"UGO")+")",555,392);
+    drawBar(color(255,255,0),selectedCell.energy,"Energy",290);
+    drawBar(color(210,50,210),selectedCell.wallHealth,"Wall health",360);
+  }
+  drawGenomeAsList(selectedCell.genome,genomeListDims);
+  drawEditTable(editListDims);
+  if(!isUGO){
+    textFont(font,32);
+    textAlign(LEFT);
+    text("Memory: "+getMemory(selectedCell),25,940);
+  }
+}
+String getMemory(Cell c){
+  if(c.memory.length() == 0){
+    return "[NOTHING]";
+  }else{
+    return "\""+c.memory+"\"";
+  }
+}
+void drawGenomeAsList(Genome g, double[] dims){
+  double x = dims[0];
+  double y = dims[1];
+  double w = dims[2];
+  double h = dims[3];
+  int GENOME_LENGTH = g.codons.size();
+  double appCodonHeight = h/GENOME_LENGTH;
+  double appW = w*0.5-margin;
+  textFont(font,30);
+  textAlign(CENTER);
+  pushMatrix();
+  dTranslate(x,y);
+  pushMatrix();
+  dTranslate(0,appCodonHeight*(g.appRO+0.5));
+  if(selectedCell != UGOcell){
+    drawGenomeArrows(w,appCodonHeight);
+  }
+  popMatrix();
+  for(int i = 0; i < GENOME_LENGTH; i++){
+    double appY = appCodonHeight*i;
+    Codon codon = g.codons.get(i);
+    for(int p = 0; p < 2; p++){
+      double extraX = (w*0.5-margin)*p;
+      color fillColor = codon.getColor(p);
+      color textColor = codon.getTextColor(p);
+      fill(0);
+      dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
+      if(codon.hasSubstance()){
+        fill(fillColor);
+        double trueW = appW*codon.codonHealth;
+        double trueX = extraX+margin;
+        if(p == 0){
+          trueX += appW*(1-codon.codonHealth);
+        }
+        dRect(trueX,appY+margin,trueW,appCodonHeight-margin*2);
+      }
+      fill(textColor);
+      dText(codon.getText(p),extraX+w*0.25,appY+appCodonHeight/2+11);
+      
+      if(p == codonToEdit[0] && i == codonToEdit[1]){
+        double highlightFac = 0.5+0.5*sin(frameCount*0.25);
+        fill(255,255,255,(float)(highlightFac*140));
+        dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
+      }
+    }
+  }
+  if(selectedCell == UGOcell){
+    fill(255);
+    textFont(font,60);
+    double avgY = (h+height-y)/2;
+    dText("( - )",w*0.25,avgY+11);
+    dText("( + )",w*0.75-margin,avgY+11);
+  }
+  popMatrix();
+}
+void drawEditTable(double[] dims){
+  double x = dims[0];
+  double y = dims[1];
+  double w = dims[2];
+  double h = dims[3];
+  
+  double appW = w-margin*2;
+  textFont(font,30);
+  textAlign(CENTER);
+  
+  int p = codonToEdit[0];
+  int s = codonToEdit[2];
+  int e = codonToEdit[3];
+  if(p >= 0){
+    pushMatrix();
+    dTranslate(x,y);
+    int choiceCount = CodonInfo.getOptionSize(codonToEdit[0]);
+    double appChoiceHeight = h/choiceCount;
+    for(int i = 0; i < choiceCount; i++){
+      double appY = appChoiceHeight*i;
+      color fillColor = intToColor(CodonInfo.getColor(p,i));
+      color textColor = intToColor(CodonInfo.getTextColor(p,i));
+      fill(fillColor);
+      dRect(margin,appY+margin,appW,appChoiceHeight-margin*2);
+      fill(textColor);
+      dText(CodonInfo.getTextSimple(p, i, s, e),w*0.5,appY+appChoiceHeight/2+11);
+    }
+    popMatrix();
+  }
+}
+color colorInterp(color a, color b, double x){
+  float newR = (float)(red(a)+(red(b)-red(a))*x);
+  float newG = (float)(green(a)+(green(b)-green(a))*x);
+  float newB = (float)(blue(a)+(blue(b)-blue(a))*x);
+  return color(newR, newG, newB);
+}
+void drawGenomeArrows(double dw, double dh){
+  float w = (float)dw;
+  float h = (float)dh;
+  fill(255);
+  beginShape();
+  vertex(-5,0);
+  vertex(-45,-40);
+  vertex(-45,40);
+  endShape(CLOSE);
+  beginShape();
+  vertex(w+5,0);
+  vertex(w+45,-40);
+  vertex(w+45,40);
+  endShape(CLOSE);
+  noStroke();
+  rect(0,-h/2,w,h);
+}
+void dRect(double x, double y, double w, double h){
+  noStroke();
+  rect((float)x, (float)y, (float)w, (float)h);
+}
+void dText(String s, double x, double y){
+  text(s, (float)x, (float)y);
+}
+void dTranslate(double x, double y){
+  translate((float)x, (float)y);
+}
+void daLine(double[] a, double[] b){
+  float x1 = (float)trueXtoAppX(a[0]);
+  float y1 = (float)trueYtoAppY(a[1]);
+  float x2 = (float)trueXtoAppX(b[0]);
+  float y2 = (float)trueYtoAppY(b[1]);
+  strokeWeight((float)(0.03*camS));
+  line(x1,y1,x2,y2);
+}
+void drawBar(color col, double stat, String s, double y){
+  fill(150);
+  rect(25,(float)y,500,60);
+  fill(col);
+  rect(25,(float)y,(float)(stat*500),60);
+  fill(0);
+  textFont(font,48);
+  textAlign(LEFT);
+  text(s+": "+nf((float)(stat*100),0,1)+"%",35,(float)y+47);
+}
+void drawCells(){
+  for(int y = 0; y < WORLD_SIZE; y++){
+    for(int x = 0; x < WORLD_SIZE; x++){
+      cells[y][x].drawCell(trueXtoAppX(x),trueYtoAppY(y),trueStoAppS(1));
+    }
+  }
+}
+double trueXtoAppX(double x){
+  return (x-camX)*camS;
+}
+double trueYtoAppY(double y){
+  return (y-camY)*camS;
+}
+double appXtoTrueX(double x){
+  return x/camS+camX;
+}
+double appYtoTrueY(double y){
+  return y/camS+camY;
+}
+double trueStoAppS(double s){
+  return s*camS;
+}
+int getCellTypeAt(double x, double y, boolean allowLoop){
+  int ix = (int)x;
+  int iy = (int)y;
+  if(allowLoop){
+    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
+    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
+  }else{
+    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
+      return 0;
+    }
+  }
+  return cells[iy][ix].type;
+}
+int getCellTypeAt(double[] coor, boolean allowLoop){
+  return getCellTypeAt(coor[0],coor[1],allowLoop);
+}
+Cell getCellAt(double x, double y, boolean allowLoop){
+  int ix = (int)x;
+  int iy = (int)y;
+  if(allowLoop){
+    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
+    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
+  }else{
+    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
+      return null;
+    }
+  }
+  return cells[iy][ix];
+}
+Cell getCellAt(double[] coor, boolean allowLoop){
+  return getCellAt(coor[0],coor[1],allowLoop);
+}
+boolean cellTransfer(double x1, double y1, double x2, double y2){
+  int ix1 = (int)Math.floor(x1);
+  int iy1 = (int)Math.floor(y1);
+  int ix2 = (int)Math.floor(x2);
+  int iy2 = (int)Math.floor(y2);
+  return (ix1 != ix2 || iy1 != iy2);
+}
+boolean cellTransfer(double[] coor1, double[] coor2){
+  return cellTransfer(coor1[0], coor1[1], coor2[0], coor2[1]);
+}
+double loopIt(double x, double len, boolean evenSplit){
+  if(evenSplit){
+    while(x >= len*0.5){
+      x -= len;
+    }
+    while(x < -len*0.5){
+      x += len;
+    }
+  }else{
+    while(x > len-0.5){
+      x -= len;
+    }
+    while(x < -0.5){
+      x += len;
+    }
+  }
+  return x;
+}
+int loopItInt(int x, int len){
+  return (x+len*10)%len;
+}
+color intToColor(int[] c){
+  return color(c[0],c[1],c[2]);
+}
+color transperize(color col, double trans){
+  float alpha = (float)(trans*255);
+  return color(red(col),green(col),blue(col),alpha);
+}
+String infoToString(int[] info){
+  String result = info[0]+""+info[1];
+  if(info[1] == 7){
+    result += codonValToChar(info[2])+""+codonValToChar(info[3]);
+  }
+  return result;
+}
+int[] stringToInfo(String str){
+  int[] info = new int[4];
+  for(int i = 0; i < 2; i++){
+    info[i] = Integer.parseInt(str.substring(i,i+1));
+  }
+  if(info[1] == 7){
+    for(int i = 2; i < 4; i++){
+      char c = str.charAt(i);
+      info[i] = codonCharToVal(c);
+    }
+  }
+  return info;
+}

From 498cf6370f2c0a83b2d8d454593e497a60305689 Mon Sep 17 00:00:00 2001
From: Tim Melentyev <tim.melentyev@gmail.com>
Date: Mon, 17 Aug 2020 18:43:03 +0200
Subject: [PATCH 2/2] Convert line breaks

---
 virus/Particle.pde |  310 +++++-----
 virus/virus.pde    | 1422 ++++++++++++++++++++++----------------------
 2 files changed, 866 insertions(+), 866 deletions(-)

diff --git a/virus/Particle.pde b/virus/Particle.pde
index f1a5a11..8084f96 100644
--- a/virus/Particle.pde
+++ b/virus/Particle.pde
@@ -1,155 +1,155 @@
-class Particle{
-  double[] coor;
-  double[] velo;
-  int type;
-  double laserX = 0;
-  double laserY = 0;
-  int laserT = -9999;
-  int birthFrame;
-  double AGE_GROW_SPEED = 0.08;
-  int outlineThickness = 2;
-  Genome UGO_genome;
-  
-  public Particle(double[] tcoor, int ttype, int b){
-    coor = tcoor;
-    velo = getRandomVelo();
-    type = ttype;
-    UGO_genome = null;
-    birthFrame = b;
-  }
-  public Particle(double[] tcoor, int ttype, String genomeString, int b){
-    coor = tcoor;
-    double dx = tcoor[2]-tcoor[0];
-    double dy = tcoor[3]-tcoor[1];
-    double dist = Math.sqrt(dx*dx+dy*dy);
-    double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
-    velo = new double[]{dx/dist*sp,dy/dist*sp};
-    type = ttype;
-    UGO_genome = new Genome(genomeString,true);
-    birthFrame = b;
-  }
-  public double[] copyCoor(){
-    double[] result = new double[2];
-    for(int dim = 0; dim < 2; dim++){
-      result[dim] = coor[dim];
-    }
-    return result;
-  }
-  public void moveDim(int d){
-    float visc = (getCellTypeAt(coor,true) == 0) ? 1 : 0.5;
-    double[] future = copyCoor();
-    future[d] = coor[d]+velo[d]*visc*PLAY_SPEED;
-    if(cellTransfer(coor, future)){
-      int currentType = getCellTypeAt(coor,true);
-      int futureType = getCellTypeAt(future,true);
-      if(type == 2 && currentType == 0 && futureType == 2 &&
-      UGO_genome.codons.size()+getCellAt(future,true).genome.codons.size() <= MAX_CODON_COUNT){ // there are few enough codons that we can fit in the new material!
-        injectGeneticMaterial(future);  // UGO is going to inject material into a cell!
-      }else if(futureType == 1 ||
-      (type >= 1 && (currentType != 0 || futureType != 0))){ // bounce
-        Cell b_cell = getCellAt(future,true);
-        if(b_cell.type >= 2){
-          b_cell.hurtWall(1);
-        }
-        if(velo[d] >= 0){
-          velo[d] = -Math.abs(velo[d]);
-          future[d] = Math.ceil(coor[d])-EPS;
-        }else{
-          velo[d] = Math.abs(velo[d]);
-          future[d] = Math.floor(coor[d])+EPS;
-        }
-        Cell t_cell = getCellAt(coor,true);
-        if(t_cell.type >= 2){
-          t_cell.hurtWall(1);
-        }
-      }else{
-        while(future[d] >= WORLD_SIZE){
-          future[d] -= WORLD_SIZE;
-        }
-        while(future[d] < 0){
-          future[d] += WORLD_SIZE;
-        }
-        hurtWalls(coor, future);
-      }
-    }
-    coor = future;
-  }
-  public void injectGeneticMaterial(double[] futureCoor){
-    Cell c = getCellAt(futureCoor,true);
-    int injectionLocation = c.genome.rotateOn;
-    ArrayList<Codon> toInject = UGO_genome.codons;
-    int INJECT_SIZE = UGO_genome.codons.size();
-    
-    for(int i = 0; i < toInject.size(); i++){
-      int[] info = toInject.get(i).codonInfo;
-      c.genome.codons.add(injectionLocation+i,new Codon(info,1.0));
-    }
-    if(c.genome.performerOn >= c.genome.rotateOn){
-      c.genome.performerOn += INJECT_SIZE;
-    }
-    c.genome.rotateOn += INJECT_SIZE;
-    c.tamper();
-    removeParticle();
-    Particle newWaste = new Particle(coor,1,-99999);
-    newWaste.addToCellList();
-    particles.get(1).add(newWaste);
-  }
-  public void hurtWalls(double[] coor, double[] future){
-    Cell p_cell = getCellAt(coor,true);
-    if(p_cell.type >= 2){
-      p_cell.hurtWall(1);
-    }
-    p_cell.removeParticleFromCell(this);
-    Cell n_cell = getCellAt(future,true);
-    if(n_cell.type >= 2){
-      n_cell.hurtWall(1);
-    }
-    n_cell.addParticleToCell(this);
-  }
-  public void iterate(){
-    for(int dim = 0; dim < 2; dim++){
-      moveDim(dim);
-    }
-  }
-  public void drawParticle(double x, double y, double s){
-    pushMatrix();
-    translate((float)x,(float)y);
-    
-    double ageScale = Math.min(1.0,(frameCount-birthFrame)*AGE_GROW_SPEED);
-    scale((float)(s/BIG_FACTOR*ageScale));
-    noStroke();
-    strokeWeight(outlineThickness);
-    if(type == 0){
-      fill(255,0,0);
-      stroke(0, 0, 0);
-    }else if(type == 1){
-      fill(WASTE_COLOR);
-      stroke(0, 0, 0);
-    }else if(type == 2){
-      fill(0);
-    }
-    ellipseMode(CENTER);
-    ellipse(0,0,0.1*BIG_FACTOR,0.1*BIG_FACTOR);
-    if(UGO_genome != null){
-      UGO_genome.drawCodons();
-    }
-    popMatrix();
-  }
-
-  public void removeParticle(){
-    particles.get(type).remove(this);
-    getCellAt(coor,true).particlesInCell.get(type).remove(this);
-  }
-  public void addToCellList(){
-    Cell cellIn = getCellAt(coor,true);
-    cellIn.addParticleToCell(this);
-  }
-  public void loopCoor(int d){
-    while(coor[d] >= WORLD_SIZE){
-      coor[d] -= WORLD_SIZE;
-    }
-    while(coor[d] < 0){
-      coor[d] += WORLD_SIZE;
-    }
-  }
-}
+class Particle{
+  double[] coor;
+  double[] velo;
+  int type;
+  double laserX = 0;
+  double laserY = 0;
+  int laserT = -9999;
+  int birthFrame;
+  double AGE_GROW_SPEED = 0.08;
+  int outlineThickness = 2;
+  Genome UGO_genome;
+  
+  public Particle(double[] tcoor, int ttype, int b){
+    coor = tcoor;
+    velo = getRandomVelo();
+    type = ttype;
+    UGO_genome = null;
+    birthFrame = b;
+  }
+  public Particle(double[] tcoor, int ttype, String genomeString, int b){
+    coor = tcoor;
+    double dx = tcoor[2]-tcoor[0];
+    double dy = tcoor[3]-tcoor[1];
+    double dist = Math.sqrt(dx*dx+dy*dy);
+    double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
+    velo = new double[]{dx/dist*sp,dy/dist*sp};
+    type = ttype;
+    UGO_genome = new Genome(genomeString,true);
+    birthFrame = b;
+  }
+  public double[] copyCoor(){
+    double[] result = new double[2];
+    for(int dim = 0; dim < 2; dim++){
+      result[dim] = coor[dim];
+    }
+    return result;
+  }
+  public void moveDim(int d){
+    float visc = (getCellTypeAt(coor,true) == 0) ? 1 : 0.5;
+    double[] future = copyCoor();
+    future[d] = coor[d]+velo[d]*visc*PLAY_SPEED;
+    if(cellTransfer(coor, future)){
+      int currentType = getCellTypeAt(coor,true);
+      int futureType = getCellTypeAt(future,true);
+      if(type == 2 && currentType == 0 && futureType == 2 &&
+      UGO_genome.codons.size()+getCellAt(future,true).genome.codons.size() <= MAX_CODON_COUNT){ // there are few enough codons that we can fit in the new material!
+        injectGeneticMaterial(future);  // UGO is going to inject material into a cell!
+      }else if(futureType == 1 ||
+      (type >= 1 && (currentType != 0 || futureType != 0))){ // bounce
+        Cell b_cell = getCellAt(future,true);
+        if(b_cell.type >= 2){
+          b_cell.hurtWall(1);
+        }
+        if(velo[d] >= 0){
+          velo[d] = -Math.abs(velo[d]);
+          future[d] = Math.ceil(coor[d])-EPS;
+        }else{
+          velo[d] = Math.abs(velo[d]);
+          future[d] = Math.floor(coor[d])+EPS;
+        }
+        Cell t_cell = getCellAt(coor,true);
+        if(t_cell.type >= 2){
+          t_cell.hurtWall(1);
+        }
+      }else{
+        while(future[d] >= WORLD_SIZE){
+          future[d] -= WORLD_SIZE;
+        }
+        while(future[d] < 0){
+          future[d] += WORLD_SIZE;
+        }
+        hurtWalls(coor, future);
+      }
+    }
+    coor = future;
+  }
+  public void injectGeneticMaterial(double[] futureCoor){
+    Cell c = getCellAt(futureCoor,true);
+    int injectionLocation = c.genome.rotateOn;
+    ArrayList<Codon> toInject = UGO_genome.codons;
+    int INJECT_SIZE = UGO_genome.codons.size();
+    
+    for(int i = 0; i < toInject.size(); i++){
+      int[] info = toInject.get(i).codonInfo;
+      c.genome.codons.add(injectionLocation+i,new Codon(info,1.0));
+    }
+    if(c.genome.performerOn >= c.genome.rotateOn){
+      c.genome.performerOn += INJECT_SIZE;
+    }
+    c.genome.rotateOn += INJECT_SIZE;
+    c.tamper();
+    removeParticle();
+    Particle newWaste = new Particle(coor,1,-99999);
+    newWaste.addToCellList();
+    particles.get(1).add(newWaste);
+  }
+  public void hurtWalls(double[] coor, double[] future){
+    Cell p_cell = getCellAt(coor,true);
+    if(p_cell.type >= 2){
+      p_cell.hurtWall(1);
+    }
+    p_cell.removeParticleFromCell(this);
+    Cell n_cell = getCellAt(future,true);
+    if(n_cell.type >= 2){
+      n_cell.hurtWall(1);
+    }
+    n_cell.addParticleToCell(this);
+  }
+  public void iterate(){
+    for(int dim = 0; dim < 2; dim++){
+      moveDim(dim);
+    }
+  }
+  public void drawParticle(double x, double y, double s){
+    pushMatrix();
+    translate((float)x,(float)y);
+    
+    double ageScale = Math.min(1.0,(frameCount-birthFrame)*AGE_GROW_SPEED);
+    scale((float)(s/BIG_FACTOR*ageScale));
+    noStroke();
+    strokeWeight(outlineThickness);
+    if(type == 0){
+      fill(255,0,0);
+      stroke(0, 0, 0);
+    }else if(type == 1){
+      fill(WASTE_COLOR);
+      stroke(0, 0, 0);
+    }else if(type == 2){
+      fill(0);
+    }
+    ellipseMode(CENTER);
+    ellipse(0,0,0.1*BIG_FACTOR,0.1*BIG_FACTOR);
+    if(UGO_genome != null){
+      UGO_genome.drawCodons();
+    }
+    popMatrix();
+  }
+
+  public void removeParticle(){
+    particles.get(type).remove(this);
+    getCellAt(coor,true).particlesInCell.get(type).remove(this);
+  }
+  public void addToCellList(){
+    Cell cellIn = getCellAt(coor,true);
+    cellIn.addParticleToCell(this);
+  }
+  public void loopCoor(int d){
+    while(coor[d] >= WORLD_SIZE){
+      coor[d] -= WORLD_SIZE;
+    }
+    while(coor[d] < 0){
+      coor[d] += WORLD_SIZE;
+    }
+  }
+}
diff --git a/virus/virus.pde b/virus/virus.pde
index 5890da6..3587b5d 100644
--- a/virus/virus.pde
+++ b/virus/virus.pde
@@ -1,711 +1,711 @@
-int WORLD_SIZE = 12;
-int W_W = 1728;
-int W_H = 972;
-Cell[][] cells = new Cell[WORLD_SIZE][WORLD_SIZE];
-ArrayList<ArrayList<Particle>> particles = new ArrayList<ArrayList<Particle>>(0);
-int foodLimit = 180;
-float BIG_FACTOR = 100;
-float PLAY_SPEED = 0.6;
-double GENE_TICK_TIME = 40.0;
-double margin = 4;
-int START_LIVING_COUNT = 0;
-int[] cellCounts = {0,0,0};
-
-double REMOVE_WASTE_SPEED_MULTI = 0.001;
-double removeWasteTimer = 1.0;
-
-double GENE_TICK_ENERGY = 0.014;
-double WALL_DAMAGE = 0.01;
-double CODON_DEGRADE_SPEED = 0.008;
-double EPS = 0.00000001;
-
-String starterGenome = "46-11-22-33-11-22-33-45-44-57__-67__";
-boolean canDrag = false;
-double clickWorldX = -1;
-double clickWorldY = -1;
-boolean DQclick = false;
-int[] codonToEdit = {-1,-1,0,0};
-double[] genomeListDims = {70,430,360,450};
-double[] editListDims = {550,430,180,450};
-double[] arrowToDraw = null;
-Cell selectedCell = null;
-Cell UGOcell;
-int lastEditTimeStamp = 0;
-color handColor = color(0,128,0);
-color TELOMERE_COLOR = color(0,0,0);
-color WASTE_COLOR = color(255,255,255);
-int MAX_CODON_COUNT = 20; // If a cell were to have more codons in its DNA than this number if it were to absorb a cirus particle, it won't absorb it.
-
-double SPEED_LOW = 0.01;
-double SPEED_HIGH = 0.02;
-double MIN_ARROW_LENGTH_TO_PRODUCE = 0.4;
-
-double ZOOM_THRESHOLD = 0;//80;
-PFont font;
-void setup(){
-  font = loadFont("Jygquip1-96.vlw");
-  for(int j = 0; j < 3; j++){
-    ArrayList<Particle> newList = new ArrayList<Particle>(0);
-    particles.add(newList);
-  }
-  for(int y = 0; y < WORLD_SIZE; y++){
-    for(int x = 0; x < WORLD_SIZE; x++){
-      int t = getTypeFromXY(x,y);
-      cells[y][x] = new Cell(x,y,t,0,1,starterGenome);
-      if(t == 2){
-        START_LIVING_COUNT++;
-        cellCounts[0]++;
-      }
-    }
-  }
-  size(1728,972);
-  noSmooth();
-  UGOcell = new Cell(-1,-1,2,0,1,"00-00-00-00-00");
-}
-int getTypeFromXY(int preX, int preY){
-  int[] weirdo = {0,1,1,2};
-  int x = (preX/4)*3;
-  x += weirdo[preX%4];
-  int y = (preY/4)*3;
-  y += weirdo[preY%4];
-  int result = 0;
-  for(int i = 1; i < WORLD_SIZE; i *= 3){
-    if((x/i)%3 == 1 && (y/i)%3 == 1){
-      result = 1;
-      int xPart = x%i;
-      int yPart = y%i;
-      boolean left = (xPart == 0);
-      boolean right = (xPart == i-1);
-      boolean top = (yPart == 0);
-      boolean bottom = (yPart == i-1);
-      if(left || right || top || bottom){
-        result = 2;
-      }
-    }
-  }
-  return result;
-}
-
-boolean wasMouseDown = false;
-double camX = 0;
-double camY = 0;
-double MIN_CAM_S = ((float)W_H)/WORLD_SIZE;
-double camS = MIN_CAM_S;
-void draw(){
-  doParticleCountControl();
-  iterate();
-  detectMouse();
-  drawBackground();
-  drawCells();
-  drawParticles();
-  drawExtras();
-  drawUI();
-}
-void drawExtras(){
-  if(arrowToDraw != null){
-    if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
-      stroke(0);
-    }else{
-      stroke(0,0,0,80);
-    }
-    drawArrow(arrowToDraw[0],arrowToDraw[1],arrowToDraw[2],arrowToDraw[3]);
-  }
-}
-void doParticleCountControl(){
-  ArrayList<Particle> foods = particles.get(0);
-  while(foods.size() < foodLimit){
-    int choiceX = -1;
-    int choiceY = -1;
-    while(choiceX == -1 || cells[choiceY][choiceX].type >= 1){
-      choiceX = (int)random(0,WORLD_SIZE);
-      choiceY = (int)random(0,WORLD_SIZE);
-    }
-    double extraX = random(0.3,0.7);
-    double extraY = random(0.3,0.7);
-    double x = choiceX+extraX;
-    double y = choiceY+extraY;
-    double[] coor = {x,y};
-    Particle newFood = new Particle(coor,0,frameCount);
-    foods.add(newFood);
-    newFood.addToCellList();
-  }
-  
-  ArrayList<Particle> wastes = particles.get(1);
-  if(wastes.size() > foodLimit){
-    removeWasteTimer -= (wastes.size()-foodLimit)*REMOVE_WASTE_SPEED_MULTI;
-    if(removeWasteTimer < 0){
-      int choiceIndex = -1;
-      int iter = 0;
-      while(iter < 50 && (choiceIndex == -1 || getCellAt(wastes.get(choiceIndex).coor,true).type == 2)){
-        choiceIndex = (int)(Math.random()*wastes.size());
-      } // If possible, choose a particle that is NOT in a cell at the moment.
-      wastes.get(choiceIndex).removeParticle();
-      removeWasteTimer++;
-    }
-  }
-}
-double[] getRandomVelo(){
-  double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
-  double ang = random(0,2*PI);
-  double vx = sp*Math.cos(ang);
-  double vy = sp*Math.sin(ang);
-  double[] result = {vx, vy};
-  return result;
-}
-void iterate(){
-  for(int z = 0; z < 3; z++){
-    ArrayList<Particle> sparticles = particles.get(z);
-    for(int i = 0; i < sparticles.size(); i++){
-      Particle p = sparticles.get(i);
-      p.iterate();
-    }
-  }
-  for(int y = 0; y < WORLD_SIZE; y++){
-    for(int x = 0; x < WORLD_SIZE; x++){
-      cells[y][x].iterate();
-    }
-  }
-}
-void drawParticles(){
-  for(int z = 0; z < 3; z++){
-    ArrayList<Particle> sparticles = particles.get(z);
-    for(int i = 0; i < sparticles.size(); i++){
-      Particle p = sparticles.get(i);
-      p.drawParticle(trueXtoAppX(p.coor[0]),trueYtoAppY(p.coor[1]),trueStoAppS(1));
-    }
-  }
-}
-void checkGLclick(){
-  double gx = genomeListDims[0];
-  double gy = genomeListDims[1];
-  double gw = genomeListDims[2];
-  double gh = genomeListDims[3];
-  double rMouseX = ((mouseX-W_H)-gx)/gw;
-  double rMouseY = (mouseY-gy)/gh;
-  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0){
-    if(rMouseY < 1){
-      codonToEdit[0] = (int)(rMouseX*2);
-      codonToEdit[1] = (int)(rMouseY*selectedCell.genome.codons.size());
-    }else if(selectedCell == UGOcell){
-      if(rMouseX < 0.5){
-        String genomeString = UGOcell.genome.getGenomeStringShortened();
-        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
-      }else{
-        String genomeString = UGOcell.genome.getGenomeStringLengthened();
-        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
-      }
-    }
-  }
-}
-void checkETclick(){
-  double ex = editListDims[0];
-  double ey = editListDims[1];
-  double ew = editListDims[2];
-  double eh = editListDims[3];
-  double rMouseX = ((mouseX-W_H)-ex)/ew;
-  double rMouseY = (mouseY-ey)/eh;
-  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0 && rMouseY < 1){
-    int optionCount = CodonInfo.getOptionSize(codonToEdit[0]);
-    int choice = (int)(rMouseY*optionCount);
-    if(codonToEdit[0] == 1 && choice >= optionCount-2){
-      int diff = 1;
-      if(rMouseX < 0.5){
-        diff = -1;
-      }
-      if(choice == optionCount-2){
-        codonToEdit[2] = loopCodonInfo(codonToEdit[2]+diff);
-      }else{
-        codonToEdit[3] = loopCodonInfo(codonToEdit[3]+diff);
-      }
-    }else{
-      Codon thisCodon = selectedCell.genome.codons.get(codonToEdit[1]);
-      if(codonToEdit[0] == 1 && choice == 7){
-        if(thisCodon.codonInfo[1] != 7 ||
-        thisCodon.codonInfo[2] != codonToEdit[2] || thisCodon.codonInfo[3] != codonToEdit[3]){
-          thisCodon.setInfo(1,choice);
-          thisCodon.setInfo(2,codonToEdit[2]);
-          thisCodon.setInfo(3,codonToEdit[3]);
-          if(selectedCell != UGOcell){
-            lastEditTimeStamp = frameCount;
-            selectedCell.tamper();
-          }
-        }
-      }else{
-        if(thisCodon.codonInfo[codonToEdit[0]] != choice){
-          thisCodon.setInfo(codonToEdit[0],choice);
-          if(selectedCell != UGOcell){
-            lastEditTimeStamp = frameCount;
-            selectedCell.tamper();
-          }
-        }
-      }
-    }
-  }else{
-    codonToEdit[0] = codonToEdit[1] = -1;
-  }
-}
-int loopCodonInfo(int val){
-  while(val < -30){
-    val += 61;
-  }
-  while(val > 30){
-    val -= 61;
-  }
-  return val;
-}
-int codonCharToVal(char c){
-  int val = (int)(c) - (int)('A');
-  return val-30;
-}
-String codonValToChar(int i){
-  int val = (i+30) + (int)('A');
-  return (char)val+"";
-}
-void detectMouse(){
-  if (mousePressed){
-    arrowToDraw = null;
-    if(!wasMouseDown) {
-      if(mouseX < W_H){
-        codonToEdit[0] = codonToEdit[1] = -1;
-        clickWorldX = appXtoTrueX(mouseX);
-        clickWorldY = appYtoTrueY(mouseY);
-        canDrag = true;
-      }else{
-        if(selectedCell != null){
-          if(codonToEdit[0] >= 0){
-            checkETclick();
-          }
-          checkGLclick();
-        }
-        if(selectedCell == UGOcell){
-          if((mouseX >= W_H+530 && codonToEdit[0] == -1) || mouseY < 160){
-            selectedCell = null;
-          }
-        }else if(mouseX > W_W-160 && mouseY < 160){
-          selectedCell = UGOcell;
-        }
-        canDrag = false;
-      }
-      DQclick = false;
-    }else if(canDrag){
-      double newCX = appXtoTrueX(mouseX);
-      double newCY = appYtoTrueY(mouseY);
-      if(newCX != clickWorldX || newCY != clickWorldY){
-        DQclick = true;
-      }
-      if(selectedCell == UGOcell){
-        stroke(0,0,0);
-        arrowToDraw = new double[]{clickWorldX,clickWorldY,newCX,newCY};
-      }else{
-        camX -= (newCX-clickWorldX);
-        camY -= (newCY-clickWorldY);
-      }
-    }
-  }
-  if(!mousePressed){
-    if(wasMouseDown){
-      if(selectedCell == UGOcell && arrowToDraw != null){
-        if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
-          produceUGO(arrowToDraw);
-        }
-      }
-      if(!DQclick && canDrag){
-        double[] mCoor = {clickWorldX,clickWorldY};
-        Cell clickedCell = getCellAt(mCoor,false);
-        if(selectedCell != UGOcell){
-          selectedCell = null;
-        }
-        if(clickedCell != null && clickedCell.type == 2){
-          selectedCell = clickedCell;
-        }
-      }
-    }
-    clickWorldX = -1;
-    clickWorldY = -1;
-    arrowToDraw = null;
-  }
-  wasMouseDown = mousePressed;
-}
-void mouseWheel(MouseEvent event) {
-  double ZOOM_F = 1.05;
-  double thisZoomF = 1;
-  float e = event.getCount();
-  if(e == 1){
-    thisZoomF = 1/ZOOM_F;
-  }else{
-    thisZoomF = ZOOM_F;
-  }
-  double worldX = mouseX/camS+camX;
-  double worldY = mouseY/camS+camY;
-  camX = (camX-worldX)/thisZoomF+worldX;
-  camY = (camY-worldY)/thisZoomF+worldY;
-  camS *= thisZoomF;
-}
-double euclidLength(double[] coor){
-  return Math.sqrt(Math.pow(coor[0]-coor[2],2)+Math.pow(coor[1]-coor[3],2));
-}
-void produceUGO(double[] coor){
-  if(getCellAt(coor,false) != null && getCellAt(coor,false).type == 0){
-    String genomeString = UGOcell.genome.getGenomeString();
-    Particle newUGO = new Particle(coor,2,genomeString,frameCount);
-    particles.get(2).add(newUGO);
-    newUGO.addToCellList();
-    lastEditTimeStamp = frameCount;
-  }
-}
-void drawBackground(){
-  background(255);
-}
-void drawArrow(double dx1, double dx2, double dy1, double dy2){
-  float x1 = (float)trueXtoAppX(dx1);
-  float y1 = (float)trueYtoAppY(dx2);
-  float x2 = (float)trueXtoAppX(dy1);
-  float y2 = (float)trueYtoAppY(dy2);
-  strokeWeight((float)(0.03*camS));
-  line(x1,y1,x2,y2);
-  float angle = atan2(y2-y1,x2-x1);
-  float head_size = (float)(0.2*camS);
-  float x3 = x2+head_size*cos(angle+PI*0.8);
-  float y3 = y2+head_size*sin(angle+PI*0.8);
-  line(x2,y2,x3,y3);
-  float x4 = x2+head_size*cos(angle-PI*0.8);
-  float y4 = y2+head_size*sin(angle-PI*0.8);
-  line(x2,y2,x4,y4);
-}
-String framesToTime(double f){
-  double ticks = f/GENE_TICK_TIME;
-  String timeStr = nf((float)ticks,0,1);
-  if(ticks >= 1000){
-    timeStr = (int)(Math.round(ticks))+"";
-  }
-  return timeStr+"t since";
-}
-String count(int count, String s){
-  if(count == 1){
-    return count+" "+s;
-  }else{
-    return count+" "+s+"s";
-  }
-}
-void drawUI(){
-  pushMatrix();
-  translate(W_H,0);
-  fill(0);
-  noStroke();
-  rect(0,0,W_W-W_H,W_H);
-  fill(255);
-  textFont(font,48);
-  textAlign(LEFT);
-  text(framesToTime(frameCount)+" start",25,60);
-  text(framesToTime(frameCount-lastEditTimeStamp)+" edit",25,108);
-  textFont(font,36);
-  text("Healthy: "+cellCounts[0]+" / "+START_LIVING_COUNT,360,50);
-  text("Tampered: "+cellCounts[1]+" / "+START_LIVING_COUNT,360,90);
-  text("Dead: "+cellCounts[2]+" / "+START_LIVING_COUNT,360,130);
-  if(selectedCell != null){
-    drawCellStats();
-  }
-  popMatrix();
-  drawUGObutton((selectedCell != UGOcell));
-}
-void drawUGObutton(boolean drawUGO){
-  fill(80);
-  noStroke();
-  rect(W_W-130,10,120,140);
-  fill(255);
-  textAlign(CENTER);
-  if(drawUGO){
-    textFont(font,48);
-    text("MAKE",W_W-70,70);
-    text("UGO",W_W-70,120);
-  }else{
-    textFont(font,36);
-    text("CANCEL",W_W-70,95);
-  }
-}
-void drawCellStats(){
-  boolean isUGO = (selectedCell.x == -1);
-  fill(80);
-  noStroke();
-  rect(10,160,530,W_H-170);
-  if(!isUGO){
-    rect(540,160,200,270);
-  }
-  fill(255);
-  textFont(font,96);
-  textAlign(LEFT);
-  text(selectedCell.getCellName(),25,255);
-  if(!isUGO){
-    textFont(font,32);
-    text("Inside this cell,",555,200);
-    text("there are:",555,232);
-    text(count(selectedCell.getParticleCount(-1),"particle"),555,296);
-    text("("+count(selectedCell.getParticleCount(0),"food")+")",555,328);
-    text("("+count(selectedCell.getParticleCount(1),"waste")+")",555,360);
-    text("("+count(selectedCell.getParticleCount(2),"UGO")+")",555,392);
-    drawBar(color(255,255,0),selectedCell.energy,"Energy",290);
-    drawBar(color(210,50,210),selectedCell.wallHealth,"Wall health",360);
-  }
-  drawGenomeAsList(selectedCell.genome,genomeListDims);
-  drawEditTable(editListDims);
-  if(!isUGO){
-    textFont(font,32);
-    textAlign(LEFT);
-    text("Memory: "+getMemory(selectedCell),25,940);
-  }
-}
-String getMemory(Cell c){
-  if(c.memory.length() == 0){
-    return "[NOTHING]";
-  }else{
-    return "\""+c.memory+"\"";
-  }
-}
-void drawGenomeAsList(Genome g, double[] dims){
-  double x = dims[0];
-  double y = dims[1];
-  double w = dims[2];
-  double h = dims[3];
-  int GENOME_LENGTH = g.codons.size();
-  double appCodonHeight = h/GENOME_LENGTH;
-  double appW = w*0.5-margin;
-  textFont(font,30);
-  textAlign(CENTER);
-  pushMatrix();
-  dTranslate(x,y);
-  pushMatrix();
-  dTranslate(0,appCodonHeight*(g.appRO+0.5));
-  if(selectedCell != UGOcell){
-    drawGenomeArrows(w,appCodonHeight);
-  }
-  popMatrix();
-  for(int i = 0; i < GENOME_LENGTH; i++){
-    double appY = appCodonHeight*i;
-    Codon codon = g.codons.get(i);
-    for(int p = 0; p < 2; p++){
-      double extraX = (w*0.5-margin)*p;
-      color fillColor = codon.getColor(p);
-      color textColor = codon.getTextColor(p);
-      fill(0);
-      dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
-      if(codon.hasSubstance()){
-        fill(fillColor);
-        double trueW = appW*codon.codonHealth;
-        double trueX = extraX+margin;
-        if(p == 0){
-          trueX += appW*(1-codon.codonHealth);
-        }
-        dRect(trueX,appY+margin,trueW,appCodonHeight-margin*2);
-      }
-      fill(textColor);
-      dText(codon.getText(p),extraX+w*0.25,appY+appCodonHeight/2+11);
-      
-      if(p == codonToEdit[0] && i == codonToEdit[1]){
-        double highlightFac = 0.5+0.5*sin(frameCount*0.25);
-        fill(255,255,255,(float)(highlightFac*140));
-        dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
-      }
-    }
-  }
-  if(selectedCell == UGOcell){
-    fill(255);
-    textFont(font,60);
-    double avgY = (h+height-y)/2;
-    dText("( - )",w*0.25,avgY+11);
-    dText("( + )",w*0.75-margin,avgY+11);
-  }
-  popMatrix();
-}
-void drawEditTable(double[] dims){
-  double x = dims[0];
-  double y = dims[1];
-  double w = dims[2];
-  double h = dims[3];
-  
-  double appW = w-margin*2;
-  textFont(font,30);
-  textAlign(CENTER);
-  
-  int p = codonToEdit[0];
-  int s = codonToEdit[2];
-  int e = codonToEdit[3];
-  if(p >= 0){
-    pushMatrix();
-    dTranslate(x,y);
-    int choiceCount = CodonInfo.getOptionSize(codonToEdit[0]);
-    double appChoiceHeight = h/choiceCount;
-    for(int i = 0; i < choiceCount; i++){
-      double appY = appChoiceHeight*i;
-      color fillColor = intToColor(CodonInfo.getColor(p,i));
-      color textColor = intToColor(CodonInfo.getTextColor(p,i));
-      fill(fillColor);
-      dRect(margin,appY+margin,appW,appChoiceHeight-margin*2);
-      fill(textColor);
-      dText(CodonInfo.getTextSimple(p, i, s, e),w*0.5,appY+appChoiceHeight/2+11);
-    }
-    popMatrix();
-  }
-}
-color colorInterp(color a, color b, double x){
-  float newR = (float)(red(a)+(red(b)-red(a))*x);
-  float newG = (float)(green(a)+(green(b)-green(a))*x);
-  float newB = (float)(blue(a)+(blue(b)-blue(a))*x);
-  return color(newR, newG, newB);
-}
-void drawGenomeArrows(double dw, double dh){
-  float w = (float)dw;
-  float h = (float)dh;
-  fill(255);
-  beginShape();
-  vertex(-5,0);
-  vertex(-45,-40);
-  vertex(-45,40);
-  endShape(CLOSE);
-  beginShape();
-  vertex(w+5,0);
-  vertex(w+45,-40);
-  vertex(w+45,40);
-  endShape(CLOSE);
-  noStroke();
-  rect(0,-h/2,w,h);
-}
-void dRect(double x, double y, double w, double h){
-  noStroke();
-  rect((float)x, (float)y, (float)w, (float)h);
-}
-void dText(String s, double x, double y){
-  text(s, (float)x, (float)y);
-}
-void dTranslate(double x, double y){
-  translate((float)x, (float)y);
-}
-void daLine(double[] a, double[] b){
-  float x1 = (float)trueXtoAppX(a[0]);
-  float y1 = (float)trueYtoAppY(a[1]);
-  float x2 = (float)trueXtoAppX(b[0]);
-  float y2 = (float)trueYtoAppY(b[1]);
-  strokeWeight((float)(0.03*camS));
-  line(x1,y1,x2,y2);
-}
-void drawBar(color col, double stat, String s, double y){
-  fill(150);
-  rect(25,(float)y,500,60);
-  fill(col);
-  rect(25,(float)y,(float)(stat*500),60);
-  fill(0);
-  textFont(font,48);
-  textAlign(LEFT);
-  text(s+": "+nf((float)(stat*100),0,1)+"%",35,(float)y+47);
-}
-void drawCells(){
-  for(int y = 0; y < WORLD_SIZE; y++){
-    for(int x = 0; x < WORLD_SIZE; x++){
-      cells[y][x].drawCell(trueXtoAppX(x),trueYtoAppY(y),trueStoAppS(1));
-    }
-  }
-}
-double trueXtoAppX(double x){
-  return (x-camX)*camS;
-}
-double trueYtoAppY(double y){
-  return (y-camY)*camS;
-}
-double appXtoTrueX(double x){
-  return x/camS+camX;
-}
-double appYtoTrueY(double y){
-  return y/camS+camY;
-}
-double trueStoAppS(double s){
-  return s*camS;
-}
-int getCellTypeAt(double x, double y, boolean allowLoop){
-  int ix = (int)x;
-  int iy = (int)y;
-  if(allowLoop){
-    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
-    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
-  }else{
-    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
-      return 0;
-    }
-  }
-  return cells[iy][ix].type;
-}
-int getCellTypeAt(double[] coor, boolean allowLoop){
-  return getCellTypeAt(coor[0],coor[1],allowLoop);
-}
-Cell getCellAt(double x, double y, boolean allowLoop){
-  int ix = (int)x;
-  int iy = (int)y;
-  if(allowLoop){
-    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
-    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
-  }else{
-    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
-      return null;
-    }
-  }
-  return cells[iy][ix];
-}
-Cell getCellAt(double[] coor, boolean allowLoop){
-  return getCellAt(coor[0],coor[1],allowLoop);
-}
-boolean cellTransfer(double x1, double y1, double x2, double y2){
-  int ix1 = (int)Math.floor(x1);
-  int iy1 = (int)Math.floor(y1);
-  int ix2 = (int)Math.floor(x2);
-  int iy2 = (int)Math.floor(y2);
-  return (ix1 != ix2 || iy1 != iy2);
-}
-boolean cellTransfer(double[] coor1, double[] coor2){
-  return cellTransfer(coor1[0], coor1[1], coor2[0], coor2[1]);
-}
-double loopIt(double x, double len, boolean evenSplit){
-  if(evenSplit){
-    while(x >= len*0.5){
-      x -= len;
-    }
-    while(x < -len*0.5){
-      x += len;
-    }
-  }else{
-    while(x > len-0.5){
-      x -= len;
-    }
-    while(x < -0.5){
-      x += len;
-    }
-  }
-  return x;
-}
-int loopItInt(int x, int len){
-  return (x+len*10)%len;
-}
-color intToColor(int[] c){
-  return color(c[0],c[1],c[2]);
-}
-color transperize(color col, double trans){
-  float alpha = (float)(trans*255);
-  return color(red(col),green(col),blue(col),alpha);
-}
-String infoToString(int[] info){
-  String result = info[0]+""+info[1];
-  if(info[1] == 7){
-    result += codonValToChar(info[2])+""+codonValToChar(info[3]);
-  }
-  return result;
-}
-int[] stringToInfo(String str){
-  int[] info = new int[4];
-  for(int i = 0; i < 2; i++){
-    info[i] = Integer.parseInt(str.substring(i,i+1));
-  }
-  if(info[1] == 7){
-    for(int i = 2; i < 4; i++){
-      char c = str.charAt(i);
-      info[i] = codonCharToVal(c);
-    }
-  }
-  return info;
-}
+int WORLD_SIZE = 12;
+int W_W = 1728;
+int W_H = 972;
+Cell[][] cells = new Cell[WORLD_SIZE][WORLD_SIZE];
+ArrayList<ArrayList<Particle>> particles = new ArrayList<ArrayList<Particle>>(0);
+int foodLimit = 180;
+float BIG_FACTOR = 100;
+float PLAY_SPEED = 0.6;
+double GENE_TICK_TIME = 40.0;
+double margin = 4;
+int START_LIVING_COUNT = 0;
+int[] cellCounts = {0,0,0};
+
+double REMOVE_WASTE_SPEED_MULTI = 0.001;
+double removeWasteTimer = 1.0;
+
+double GENE_TICK_ENERGY = 0.014;
+double WALL_DAMAGE = 0.01;
+double CODON_DEGRADE_SPEED = 0.008;
+double EPS = 0.00000001;
+
+String starterGenome = "46-11-22-33-11-22-33-45-44-57__-67__";
+boolean canDrag = false;
+double clickWorldX = -1;
+double clickWorldY = -1;
+boolean DQclick = false;
+int[] codonToEdit = {-1,-1,0,0};
+double[] genomeListDims = {70,430,360,450};
+double[] editListDims = {550,430,180,450};
+double[] arrowToDraw = null;
+Cell selectedCell = null;
+Cell UGOcell;
+int lastEditTimeStamp = 0;
+color handColor = color(0,128,0);
+color TELOMERE_COLOR = color(0,0,0);
+color WASTE_COLOR = color(255,255,255);
+int MAX_CODON_COUNT = 20; // If a cell were to have more codons in its DNA than this number if it were to absorb a cirus particle, it won't absorb it.
+
+double SPEED_LOW = 0.01;
+double SPEED_HIGH = 0.02;
+double MIN_ARROW_LENGTH_TO_PRODUCE = 0.4;
+
+double ZOOM_THRESHOLD = 0;//80;
+PFont font;
+void setup(){
+  font = loadFont("Jygquip1-96.vlw");
+  for(int j = 0; j < 3; j++){
+    ArrayList<Particle> newList = new ArrayList<Particle>(0);
+    particles.add(newList);
+  }
+  for(int y = 0; y < WORLD_SIZE; y++){
+    for(int x = 0; x < WORLD_SIZE; x++){
+      int t = getTypeFromXY(x,y);
+      cells[y][x] = new Cell(x,y,t,0,1,starterGenome);
+      if(t == 2){
+        START_LIVING_COUNT++;
+        cellCounts[0]++;
+      }
+    }
+  }
+  size(1728,972);
+  noSmooth();
+  UGOcell = new Cell(-1,-1,2,0,1,"00-00-00-00-00");
+}
+int getTypeFromXY(int preX, int preY){
+  int[] weirdo = {0,1,1,2};
+  int x = (preX/4)*3;
+  x += weirdo[preX%4];
+  int y = (preY/4)*3;
+  y += weirdo[preY%4];
+  int result = 0;
+  for(int i = 1; i < WORLD_SIZE; i *= 3){
+    if((x/i)%3 == 1 && (y/i)%3 == 1){
+      result = 1;
+      int xPart = x%i;
+      int yPart = y%i;
+      boolean left = (xPart == 0);
+      boolean right = (xPart == i-1);
+      boolean top = (yPart == 0);
+      boolean bottom = (yPart == i-1);
+      if(left || right || top || bottom){
+        result = 2;
+      }
+    }
+  }
+  return result;
+}
+
+boolean wasMouseDown = false;
+double camX = 0;
+double camY = 0;
+double MIN_CAM_S = ((float)W_H)/WORLD_SIZE;
+double camS = MIN_CAM_S;
+void draw(){
+  doParticleCountControl();
+  iterate();
+  detectMouse();
+  drawBackground();
+  drawCells();
+  drawParticles();
+  drawExtras();
+  drawUI();
+}
+void drawExtras(){
+  if(arrowToDraw != null){
+    if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
+      stroke(0);
+    }else{
+      stroke(0,0,0,80);
+    }
+    drawArrow(arrowToDraw[0],arrowToDraw[1],arrowToDraw[2],arrowToDraw[3]);
+  }
+}
+void doParticleCountControl(){
+  ArrayList<Particle> foods = particles.get(0);
+  while(foods.size() < foodLimit){
+    int choiceX = -1;
+    int choiceY = -1;
+    while(choiceX == -1 || cells[choiceY][choiceX].type >= 1){
+      choiceX = (int)random(0,WORLD_SIZE);
+      choiceY = (int)random(0,WORLD_SIZE);
+    }
+    double extraX = random(0.3,0.7);
+    double extraY = random(0.3,0.7);
+    double x = choiceX+extraX;
+    double y = choiceY+extraY;
+    double[] coor = {x,y};
+    Particle newFood = new Particle(coor,0,frameCount);
+    foods.add(newFood);
+    newFood.addToCellList();
+  }
+  
+  ArrayList<Particle> wastes = particles.get(1);
+  if(wastes.size() > foodLimit){
+    removeWasteTimer -= (wastes.size()-foodLimit)*REMOVE_WASTE_SPEED_MULTI;
+    if(removeWasteTimer < 0){
+      int choiceIndex = -1;
+      int iter = 0;
+      while(iter < 50 && (choiceIndex == -1 || getCellAt(wastes.get(choiceIndex).coor,true).type == 2)){
+        choiceIndex = (int)(Math.random()*wastes.size());
+      } // If possible, choose a particle that is NOT in a cell at the moment.
+      wastes.get(choiceIndex).removeParticle();
+      removeWasteTimer++;
+    }
+  }
+}
+double[] getRandomVelo(){
+  double sp = Math.random()*(SPEED_HIGH-SPEED_LOW)+SPEED_LOW;
+  double ang = random(0,2*PI);
+  double vx = sp*Math.cos(ang);
+  double vy = sp*Math.sin(ang);
+  double[] result = {vx, vy};
+  return result;
+}
+void iterate(){
+  for(int z = 0; z < 3; z++){
+    ArrayList<Particle> sparticles = particles.get(z);
+    for(int i = 0; i < sparticles.size(); i++){
+      Particle p = sparticles.get(i);
+      p.iterate();
+    }
+  }
+  for(int y = 0; y < WORLD_SIZE; y++){
+    for(int x = 0; x < WORLD_SIZE; x++){
+      cells[y][x].iterate();
+    }
+  }
+}
+void drawParticles(){
+  for(int z = 0; z < 3; z++){
+    ArrayList<Particle> sparticles = particles.get(z);
+    for(int i = 0; i < sparticles.size(); i++){
+      Particle p = sparticles.get(i);
+      p.drawParticle(trueXtoAppX(p.coor[0]),trueYtoAppY(p.coor[1]),trueStoAppS(1));
+    }
+  }
+}
+void checkGLclick(){
+  double gx = genomeListDims[0];
+  double gy = genomeListDims[1];
+  double gw = genomeListDims[2];
+  double gh = genomeListDims[3];
+  double rMouseX = ((mouseX-W_H)-gx)/gw;
+  double rMouseY = (mouseY-gy)/gh;
+  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0){
+    if(rMouseY < 1){
+      codonToEdit[0] = (int)(rMouseX*2);
+      codonToEdit[1] = (int)(rMouseY*selectedCell.genome.codons.size());
+    }else if(selectedCell == UGOcell){
+      if(rMouseX < 0.5){
+        String genomeString = UGOcell.genome.getGenomeStringShortened();
+        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
+      }else{
+        String genomeString = UGOcell.genome.getGenomeStringLengthened();
+        selectedCell = UGOcell = new Cell(-1,-1,2,0,1,genomeString);
+      }
+    }
+  }
+}
+void checkETclick(){
+  double ex = editListDims[0];
+  double ey = editListDims[1];
+  double ew = editListDims[2];
+  double eh = editListDims[3];
+  double rMouseX = ((mouseX-W_H)-ex)/ew;
+  double rMouseY = (mouseY-ey)/eh;
+  if(rMouseX >= 0 && rMouseX < 1 && rMouseY >= 0 && rMouseY < 1){
+    int optionCount = CodonInfo.getOptionSize(codonToEdit[0]);
+    int choice = (int)(rMouseY*optionCount);
+    if(codonToEdit[0] == 1 && choice >= optionCount-2){
+      int diff = 1;
+      if(rMouseX < 0.5){
+        diff = -1;
+      }
+      if(choice == optionCount-2){
+        codonToEdit[2] = loopCodonInfo(codonToEdit[2]+diff);
+      }else{
+        codonToEdit[3] = loopCodonInfo(codonToEdit[3]+diff);
+      }
+    }else{
+      Codon thisCodon = selectedCell.genome.codons.get(codonToEdit[1]);
+      if(codonToEdit[0] == 1 && choice == 7){
+        if(thisCodon.codonInfo[1] != 7 ||
+        thisCodon.codonInfo[2] != codonToEdit[2] || thisCodon.codonInfo[3] != codonToEdit[3]){
+          thisCodon.setInfo(1,choice);
+          thisCodon.setInfo(2,codonToEdit[2]);
+          thisCodon.setInfo(3,codonToEdit[3]);
+          if(selectedCell != UGOcell){
+            lastEditTimeStamp = frameCount;
+            selectedCell.tamper();
+          }
+        }
+      }else{
+        if(thisCodon.codonInfo[codonToEdit[0]] != choice){
+          thisCodon.setInfo(codonToEdit[0],choice);
+          if(selectedCell != UGOcell){
+            lastEditTimeStamp = frameCount;
+            selectedCell.tamper();
+          }
+        }
+      }
+    }
+  }else{
+    codonToEdit[0] = codonToEdit[1] = -1;
+  }
+}
+int loopCodonInfo(int val){
+  while(val < -30){
+    val += 61;
+  }
+  while(val > 30){
+    val -= 61;
+  }
+  return val;
+}
+int codonCharToVal(char c){
+  int val = (int)(c) - (int)('A');
+  return val-30;
+}
+String codonValToChar(int i){
+  int val = (i+30) + (int)('A');
+  return (char)val+"";
+}
+void detectMouse(){
+  if (mousePressed){
+    arrowToDraw = null;
+    if(!wasMouseDown) {
+      if(mouseX < W_H){
+        codonToEdit[0] = codonToEdit[1] = -1;
+        clickWorldX = appXtoTrueX(mouseX);
+        clickWorldY = appYtoTrueY(mouseY);
+        canDrag = true;
+      }else{
+        if(selectedCell != null){
+          if(codonToEdit[0] >= 0){
+            checkETclick();
+          }
+          checkGLclick();
+        }
+        if(selectedCell == UGOcell){
+          if((mouseX >= W_H+530 && codonToEdit[0] == -1) || mouseY < 160){
+            selectedCell = null;
+          }
+        }else if(mouseX > W_W-160 && mouseY < 160){
+          selectedCell = UGOcell;
+        }
+        canDrag = false;
+      }
+      DQclick = false;
+    }else if(canDrag){
+      double newCX = appXtoTrueX(mouseX);
+      double newCY = appYtoTrueY(mouseY);
+      if(newCX != clickWorldX || newCY != clickWorldY){
+        DQclick = true;
+      }
+      if(selectedCell == UGOcell){
+        stroke(0,0,0);
+        arrowToDraw = new double[]{clickWorldX,clickWorldY,newCX,newCY};
+      }else{
+        camX -= (newCX-clickWorldX);
+        camY -= (newCY-clickWorldY);
+      }
+    }
+  }
+  if(!mousePressed){
+    if(wasMouseDown){
+      if(selectedCell == UGOcell && arrowToDraw != null){
+        if(euclidLength(arrowToDraw) > MIN_ARROW_LENGTH_TO_PRODUCE){
+          produceUGO(arrowToDraw);
+        }
+      }
+      if(!DQclick && canDrag){
+        double[] mCoor = {clickWorldX,clickWorldY};
+        Cell clickedCell = getCellAt(mCoor,false);
+        if(selectedCell != UGOcell){
+          selectedCell = null;
+        }
+        if(clickedCell != null && clickedCell.type == 2){
+          selectedCell = clickedCell;
+        }
+      }
+    }
+    clickWorldX = -1;
+    clickWorldY = -1;
+    arrowToDraw = null;
+  }
+  wasMouseDown = mousePressed;
+}
+void mouseWheel(MouseEvent event) {
+  double ZOOM_F = 1.05;
+  double thisZoomF = 1;
+  float e = event.getCount();
+  if(e == 1){
+    thisZoomF = 1/ZOOM_F;
+  }else{
+    thisZoomF = ZOOM_F;
+  }
+  double worldX = mouseX/camS+camX;
+  double worldY = mouseY/camS+camY;
+  camX = (camX-worldX)/thisZoomF+worldX;
+  camY = (camY-worldY)/thisZoomF+worldY;
+  camS *= thisZoomF;
+}
+double euclidLength(double[] coor){
+  return Math.sqrt(Math.pow(coor[0]-coor[2],2)+Math.pow(coor[1]-coor[3],2));
+}
+void produceUGO(double[] coor){
+  if(getCellAt(coor,false) != null && getCellAt(coor,false).type == 0){
+    String genomeString = UGOcell.genome.getGenomeString();
+    Particle newUGO = new Particle(coor,2,genomeString,frameCount);
+    particles.get(2).add(newUGO);
+    newUGO.addToCellList();
+    lastEditTimeStamp = frameCount;
+  }
+}
+void drawBackground(){
+  background(255);
+}
+void drawArrow(double dx1, double dx2, double dy1, double dy2){
+  float x1 = (float)trueXtoAppX(dx1);
+  float y1 = (float)trueYtoAppY(dx2);
+  float x2 = (float)trueXtoAppX(dy1);
+  float y2 = (float)trueYtoAppY(dy2);
+  strokeWeight((float)(0.03*camS));
+  line(x1,y1,x2,y2);
+  float angle = atan2(y2-y1,x2-x1);
+  float head_size = (float)(0.2*camS);
+  float x3 = x2+head_size*cos(angle+PI*0.8);
+  float y3 = y2+head_size*sin(angle+PI*0.8);
+  line(x2,y2,x3,y3);
+  float x4 = x2+head_size*cos(angle-PI*0.8);
+  float y4 = y2+head_size*sin(angle-PI*0.8);
+  line(x2,y2,x4,y4);
+}
+String framesToTime(double f){
+  double ticks = f/GENE_TICK_TIME;
+  String timeStr = nf((float)ticks,0,1);
+  if(ticks >= 1000){
+    timeStr = (int)(Math.round(ticks))+"";
+  }
+  return timeStr+"t since";
+}
+String count(int count, String s){
+  if(count == 1){
+    return count+" "+s;
+  }else{
+    return count+" "+s+"s";
+  }
+}
+void drawUI(){
+  pushMatrix();
+  translate(W_H,0);
+  fill(0);
+  noStroke();
+  rect(0,0,W_W-W_H,W_H);
+  fill(255);
+  textFont(font,48);
+  textAlign(LEFT);
+  text(framesToTime(frameCount)+" start",25,60);
+  text(framesToTime(frameCount-lastEditTimeStamp)+" edit",25,108);
+  textFont(font,36);
+  text("Healthy: "+cellCounts[0]+" / "+START_LIVING_COUNT,360,50);
+  text("Tampered: "+cellCounts[1]+" / "+START_LIVING_COUNT,360,90);
+  text("Dead: "+cellCounts[2]+" / "+START_LIVING_COUNT,360,130);
+  if(selectedCell != null){
+    drawCellStats();
+  }
+  popMatrix();
+  drawUGObutton((selectedCell != UGOcell));
+}
+void drawUGObutton(boolean drawUGO){
+  fill(80);
+  noStroke();
+  rect(W_W-130,10,120,140);
+  fill(255);
+  textAlign(CENTER);
+  if(drawUGO){
+    textFont(font,48);
+    text("MAKE",W_W-70,70);
+    text("UGO",W_W-70,120);
+  }else{
+    textFont(font,36);
+    text("CANCEL",W_W-70,95);
+  }
+}
+void drawCellStats(){
+  boolean isUGO = (selectedCell.x == -1);
+  fill(80);
+  noStroke();
+  rect(10,160,530,W_H-170);
+  if(!isUGO){
+    rect(540,160,200,270);
+  }
+  fill(255);
+  textFont(font,96);
+  textAlign(LEFT);
+  text(selectedCell.getCellName(),25,255);
+  if(!isUGO){
+    textFont(font,32);
+    text("Inside this cell,",555,200);
+    text("there are:",555,232);
+    text(count(selectedCell.getParticleCount(-1),"particle"),555,296);
+    text("("+count(selectedCell.getParticleCount(0),"food")+")",555,328);
+    text("("+count(selectedCell.getParticleCount(1),"waste")+")",555,360);
+    text("("+count(selectedCell.getParticleCount(2),"UGO")+")",555,392);
+    drawBar(color(255,255,0),selectedCell.energy,"Energy",290);
+    drawBar(color(210,50,210),selectedCell.wallHealth,"Wall health",360);
+  }
+  drawGenomeAsList(selectedCell.genome,genomeListDims);
+  drawEditTable(editListDims);
+  if(!isUGO){
+    textFont(font,32);
+    textAlign(LEFT);
+    text("Memory: "+getMemory(selectedCell),25,940);
+  }
+}
+String getMemory(Cell c){
+  if(c.memory.length() == 0){
+    return "[NOTHING]";
+  }else{
+    return "\""+c.memory+"\"";
+  }
+}
+void drawGenomeAsList(Genome g, double[] dims){
+  double x = dims[0];
+  double y = dims[1];
+  double w = dims[2];
+  double h = dims[3];
+  int GENOME_LENGTH = g.codons.size();
+  double appCodonHeight = h/GENOME_LENGTH;
+  double appW = w*0.5-margin;
+  textFont(font,30);
+  textAlign(CENTER);
+  pushMatrix();
+  dTranslate(x,y);
+  pushMatrix();
+  dTranslate(0,appCodonHeight*(g.appRO+0.5));
+  if(selectedCell != UGOcell){
+    drawGenomeArrows(w,appCodonHeight);
+  }
+  popMatrix();
+  for(int i = 0; i < GENOME_LENGTH; i++){
+    double appY = appCodonHeight*i;
+    Codon codon = g.codons.get(i);
+    for(int p = 0; p < 2; p++){
+      double extraX = (w*0.5-margin)*p;
+      color fillColor = codon.getColor(p);
+      color textColor = codon.getTextColor(p);
+      fill(0);
+      dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
+      if(codon.hasSubstance()){
+        fill(fillColor);
+        double trueW = appW*codon.codonHealth;
+        double trueX = extraX+margin;
+        if(p == 0){
+          trueX += appW*(1-codon.codonHealth);
+        }
+        dRect(trueX,appY+margin,trueW,appCodonHeight-margin*2);
+      }
+      fill(textColor);
+      dText(codon.getText(p),extraX+w*0.25,appY+appCodonHeight/2+11);
+      
+      if(p == codonToEdit[0] && i == codonToEdit[1]){
+        double highlightFac = 0.5+0.5*sin(frameCount*0.25);
+        fill(255,255,255,(float)(highlightFac*140));
+        dRect(extraX+margin,appY+margin,appW,appCodonHeight-margin*2);
+      }
+    }
+  }
+  if(selectedCell == UGOcell){
+    fill(255);
+    textFont(font,60);
+    double avgY = (h+height-y)/2;
+    dText("( - )",w*0.25,avgY+11);
+    dText("( + )",w*0.75-margin,avgY+11);
+  }
+  popMatrix();
+}
+void drawEditTable(double[] dims){
+  double x = dims[0];
+  double y = dims[1];
+  double w = dims[2];
+  double h = dims[3];
+  
+  double appW = w-margin*2;
+  textFont(font,30);
+  textAlign(CENTER);
+  
+  int p = codonToEdit[0];
+  int s = codonToEdit[2];
+  int e = codonToEdit[3];
+  if(p >= 0){
+    pushMatrix();
+    dTranslate(x,y);
+    int choiceCount = CodonInfo.getOptionSize(codonToEdit[0]);
+    double appChoiceHeight = h/choiceCount;
+    for(int i = 0; i < choiceCount; i++){
+      double appY = appChoiceHeight*i;
+      color fillColor = intToColor(CodonInfo.getColor(p,i));
+      color textColor = intToColor(CodonInfo.getTextColor(p,i));
+      fill(fillColor);
+      dRect(margin,appY+margin,appW,appChoiceHeight-margin*2);
+      fill(textColor);
+      dText(CodonInfo.getTextSimple(p, i, s, e),w*0.5,appY+appChoiceHeight/2+11);
+    }
+    popMatrix();
+  }
+}
+color colorInterp(color a, color b, double x){
+  float newR = (float)(red(a)+(red(b)-red(a))*x);
+  float newG = (float)(green(a)+(green(b)-green(a))*x);
+  float newB = (float)(blue(a)+(blue(b)-blue(a))*x);
+  return color(newR, newG, newB);
+}
+void drawGenomeArrows(double dw, double dh){
+  float w = (float)dw;
+  float h = (float)dh;
+  fill(255);
+  beginShape();
+  vertex(-5,0);
+  vertex(-45,-40);
+  vertex(-45,40);
+  endShape(CLOSE);
+  beginShape();
+  vertex(w+5,0);
+  vertex(w+45,-40);
+  vertex(w+45,40);
+  endShape(CLOSE);
+  noStroke();
+  rect(0,-h/2,w,h);
+}
+void dRect(double x, double y, double w, double h){
+  noStroke();
+  rect((float)x, (float)y, (float)w, (float)h);
+}
+void dText(String s, double x, double y){
+  text(s, (float)x, (float)y);
+}
+void dTranslate(double x, double y){
+  translate((float)x, (float)y);
+}
+void daLine(double[] a, double[] b){
+  float x1 = (float)trueXtoAppX(a[0]);
+  float y1 = (float)trueYtoAppY(a[1]);
+  float x2 = (float)trueXtoAppX(b[0]);
+  float y2 = (float)trueYtoAppY(b[1]);
+  strokeWeight((float)(0.03*camS));
+  line(x1,y1,x2,y2);
+}
+void drawBar(color col, double stat, String s, double y){
+  fill(150);
+  rect(25,(float)y,500,60);
+  fill(col);
+  rect(25,(float)y,(float)(stat*500),60);
+  fill(0);
+  textFont(font,48);
+  textAlign(LEFT);
+  text(s+": "+nf((float)(stat*100),0,1)+"%",35,(float)y+47);
+}
+void drawCells(){
+  for(int y = 0; y < WORLD_SIZE; y++){
+    for(int x = 0; x < WORLD_SIZE; x++){
+      cells[y][x].drawCell(trueXtoAppX(x),trueYtoAppY(y),trueStoAppS(1));
+    }
+  }
+}
+double trueXtoAppX(double x){
+  return (x-camX)*camS;
+}
+double trueYtoAppY(double y){
+  return (y-camY)*camS;
+}
+double appXtoTrueX(double x){
+  return x/camS+camX;
+}
+double appYtoTrueY(double y){
+  return y/camS+camY;
+}
+double trueStoAppS(double s){
+  return s*camS;
+}
+int getCellTypeAt(double x, double y, boolean allowLoop){
+  int ix = (int)x;
+  int iy = (int)y;
+  if(allowLoop){
+    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
+    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
+  }else{
+    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
+      return 0;
+    }
+  }
+  return cells[iy][ix].type;
+}
+int getCellTypeAt(double[] coor, boolean allowLoop){
+  return getCellTypeAt(coor[0],coor[1],allowLoop);
+}
+Cell getCellAt(double x, double y, boolean allowLoop){
+  int ix = (int)x;
+  int iy = (int)y;
+  if(allowLoop){
+    ix = (ix+WORLD_SIZE)%WORLD_SIZE;
+    iy = (iy+WORLD_SIZE)%WORLD_SIZE;
+  }else{
+    if(ix < 0 || ix >= WORLD_SIZE || iy < 0 || iy >= WORLD_SIZE){
+      return null;
+    }
+  }
+  return cells[iy][ix];
+}
+Cell getCellAt(double[] coor, boolean allowLoop){
+  return getCellAt(coor[0],coor[1],allowLoop);
+}
+boolean cellTransfer(double x1, double y1, double x2, double y2){
+  int ix1 = (int)Math.floor(x1);
+  int iy1 = (int)Math.floor(y1);
+  int ix2 = (int)Math.floor(x2);
+  int iy2 = (int)Math.floor(y2);
+  return (ix1 != ix2 || iy1 != iy2);
+}
+boolean cellTransfer(double[] coor1, double[] coor2){
+  return cellTransfer(coor1[0], coor1[1], coor2[0], coor2[1]);
+}
+double loopIt(double x, double len, boolean evenSplit){
+  if(evenSplit){
+    while(x >= len*0.5){
+      x -= len;
+    }
+    while(x < -len*0.5){
+      x += len;
+    }
+  }else{
+    while(x > len-0.5){
+      x -= len;
+    }
+    while(x < -0.5){
+      x += len;
+    }
+  }
+  return x;
+}
+int loopItInt(int x, int len){
+  return (x+len*10)%len;
+}
+color intToColor(int[] c){
+  return color(c[0],c[1],c[2]);
+}
+color transperize(color col, double trans){
+  float alpha = (float)(trans*255);
+  return color(red(col),green(col),blue(col),alpha);
+}
+String infoToString(int[] info){
+  String result = info[0]+""+info[1];
+  if(info[1] == 7){
+    result += codonValToChar(info[2])+""+codonValToChar(info[3]);
+  }
+  return result;
+}
+int[] stringToInfo(String str){
+  int[] info = new int[4];
+  for(int i = 0; i < 2; i++){
+    info[i] = Integer.parseInt(str.substring(i,i+1));
+  }
+  if(info[1] == 7){
+    for(int i = 2; i < 4; i++){
+      char c = str.charAt(i);
+      info[i] = codonCharToVal(c);
+    }
+  }
+  return info;
+}