let speed = 0.2; // needs to depend on the spacing too.

​

​

class DNA {

  constructor(lengths) {

    this.lengths = lengths;

    this.allelles = [

      [0,0,1,'a'],

      [0,0,5,'B'],

      [0,0,6,'c'],

      [0,1,3,'D'],

      [1,0,1,'A'],

      [1,0,5,'b'],

      [1,0,6,'C'],

      [1,1,3,'d'],

    ]

  }

​

  setAllelles() {

    for (let a of this.allelles) {

      this.chromosomes[a[0]][a[1]].genes[a[2]].allelle = a[3];

    }

  }  

  meiosis() {

    speed = .2;

    this.createChromosomes();

    setTimeout(()=>this.calibrateChromosomes(),0);

    setTimeout(()=>this.split(),delay*1);

    setTimeout(()=>this.cross(),delay*2);

    setTimeout(()=>this.swap(),delay*3); 

    setTimeout(()=>this.collapse(),delay*4);

  }

  createChromosomes() {

    this.chromosomes = [[],[]];

    for (let len of this.lengths) {

      let c1 = new Chromosome(color(0,215,225),len);

      let c2 = new Chromosome(color(225,225,0),len);

      this.chromosomes[0].push(c1);

      this.chromosomes[1].push(c2);

    }

    this.geneSize = 0;

    this.setAllelles();

  }

  calibrateChromosomes() {

    let w = -1;

    for (let i=0;i<this.chromosomes[0].length;i++){

      w+= this.chromosomes[0][i].genes.length +1;

    }

    let ratio = 1 - 1/w;

    this.geneSizeTarget = width*ratio/w;

    let startingPos=[];

    let relPos = 0;

    for (let i=0;i<this.chromosomes[0].length;i++) {

      let c = this.chromosomes[0][i];

      startingPos.push(width*(1-ratio)+relPos*this.geneSizeTarget);

      relPos += c.genes.length+1;

    }

    for (let i=0;i<this.chromosomes.length;i++) {

      for (let j=0;j<this.chromosomes[i].length;j++) {

        let c = this.chromosomes[i][j];

        let v = createVector(startingPos[j],100+i*100);

        c.glideTo(v,this.geneSizeTarget);

      }

    }

  }

​

  split() {

    let copies=[];

    for (let i in this.chromosomes) {

      copies[i] = [];

      for (let c of this.chromosomes[i]) {

        let newC = new Chromosome(c.color,c.genes.length);

        for (let j in c.genes) {

          let change = createVector(0,.6*this.geneSize);

          // let g = c.genes[j];

          // let ng = newC.genes[j];

          newC.genes[j]=c.genes[j].copy();

          newC.genes[j].glideTo(newC.genes[j].pos.copy().sub(change));

          c.genes[j].glideTo(c.genes[j].pos.copy().add(change));

          // ng.glideTo(ng.pos.copy().add(change));

          // g.glideTo(g.pos.copy().sub(change));

          //print(ng.pos,g.pos);

        }

        copies[i].push(newC);

      }

    }

    for (let copy of copies) {

      this.chromosomes.push(copy);

    }

  }

  cross() {

    //choose a point for the swap

    for (let i=0;i<2;i++) { // loop through the original chromatids

      for (let j=0;j<this.chromosomes[i].length;j++) {

        // for now just cross each one

        let len = this.chromosomes[i][j].genes.length;

        let pos = int(random(len))

        //print(i,j,pos,len);

        let crossIndex = 3-i;

        // define the range depending on whether it goes up or down

        if (pos < (len-1)/2) {

          // loop from 0 to pos 

          for (let k=0;k<=pos;k++) {

            let ga = this.chromosomes[i][j].genes[k];

            let gb = this.chromosomes[3-i][j].genes[k];

            this.chromosomes[i][j].genes[k] = gb.copy();

            this.chromosomes[3-i][j].genes[k] = ga.copy(); 

            this.chromosomes[i][j].genes[k].glideTo(ga.pos.copy());

            this.chromosomes[3-i][j].genes[k].glideTo(gb.pos.copy());  

          }          

        } else {

          // loop from pos to end

          for (let k=pos;k<len;k++) {

            let ga = this.chromosomes[i][j].genes[k];

            let gb = this.chromosomes[3-i][j].genes[k];

            this.chromosomes[i][j].genes[k] = gb.copy();

            this.chromosomes[3-i][j].genes[k] = ga.copy();

            this.chromosomes[i][j].genes[k].glideTo(ga.pos.copy());

            this.chromosomes[3-i][j].genes[k].glideTo(gb.pos.copy());       

          }

        }      

      }

    }

  }

  swap() {

    for (let i=0;i<this.chromosomes[0].length;i++) {

      if (random() < 0.5) {

        // do the swap.

        for (let j=0;j<this.chromosomes[0][i].genes.length;j++) {

            let ga = this.chromosomes[0][i].genes[j];

            let gb = this.chromosomes[3][i].genes[j];

            this.chromosomes[0][i].genes[j] = gb.copy();

            this.chromosomes[3][i].genes[j] = ga.copy();

            this.chromosomes[0][i].genes[j].glideTo(ga.pos.copy());

            this.chromosomes[3][i].genes[j].glideTo(gb.pos.copy());  

            ga = this.chromosomes[1][i].genes[j];

            gb = this.chromosomes[2][i].genes[j];

            this.chromosomes[1][i].genes[j] = gb.copy();

            this.chromosomes[2][i].genes[j] = ga.copy();

            this.chromosomes[1][i].genes[j].glideTo(ga.pos.copy());

            this.chromosomes[2][i].genes[j].glideTo(gb.pos.copy());           

        }

      }

    }

  }

  collapse() {

    speed = speed/2;

    for (let i=0;i<this.chromosomes.length;i++) {

      let geneSeq = new Chromosome(color(0),0);

      for (let c of this.chromosomes[i]) {

        for (let g of c.genes) {

          if (g.allelle) {

            geneSeq.genes.push(g);    

          }   

        }

      }

      let adj = (geneSeq.genes.length-1)*this.geneSize/2;

      let pos = createVector(width/2-adj,this.chromosomes[i][0].genes[0].pos.y);

      this.chromosomes[i] = [geneSeq];

      geneSeq.positionGenes(pos)

    } 

  }

  update() {

    for (let chromes of this.chromosomes) {

      chromes.forEach((c)=>c.update());

    }

    if (this.geneSizeTarget) {

      this.geneSize += (this.geneSizeTarget - this.geneSize)*0.05;

      if (this.geneSizeTarget == this.geneSize) delete this.geneSizeTarget;

    }

  }

  show() {

    for (let chromes of this.chromosomes) {

      chromes.forEach((c)=>c.show());

    }

  }

}

​

​

​

//   mousePressed() {

//     let pos = createVector(mouseX,mouseY);

//     this.chromosomes.forEach((c)=>c.mousePressed(pos));

//     // figure out how to create new Chromosome

//   }

//   mouseReleased() {

//     this.chromosomes.forEach((c)=>c.released());

//     this.calibrateChromosomes();

//   }