public class DnaString {

  int opacity = 255;

  Nucleotide a = new Nucleotide("A");
  Nucleotide a2 = new Nucleotide("A2"); 

  Nucleotide c = new Nucleotide("C"); 
  Nucleotide c2 = new Nucleotide("C2");  
  Nucleotide g = new Nucleotide("G");  
  Nucleotide g2 = new Nucleotide("G2");  

  Nucleotide t = new Nucleotide("T");  
  Nucleotide t2 = new Nucleotide("T2"); 

  Scrollbar bar = new Scrollbar(20, 450, (width-20), 10, 0.0, (width-20));
  int x; //bar position

  Button buttonOst = new Button(485, 279, 100, 135);
  Button buttonFlam = new Button(595, 279, 60, 99);
  Button buttonTurkey = new Button(423, 319, 51, 93);
  Button buttonLoon = new Button(357, 319, 57, 93);
  Button buttonOwl = new Button(236, 319, 47, 93);
  Button buttonGull = new Button(300, 319, 57, 93);
  Button buttonWood = new Button(187, 319, 48, 93);

  int mode = 0;

  int xorigin;
  int yorigin;
  int zorigin;
  int size;
  char[] ost_basePairs = new char[0];
  char[] flam_basePairs = new char[0];
  char[] turk_basePairs = new char[0];
  char[] loon_basePairs = new char[0];
  char[] gull_basePairs = new char[0];
  char[] owl_basePairs = new char[0];
  char[] wood_basePairs = new char[0];

  int start_char = 79;
  int numBpairs_disp = 2; // to be multiplied by zoom factor for screen count and scroll increment  SD=2 HD=4
  int totalBpairs;
  int f; //zoom factor
  //int j[] = new int[]; // x coord value for scrolling text

  String ostrich_data = "struthio_camelus.fasta";
  String flamingo_data = "phoenicopterus_ruber(pink_flamingo).fasta"; 
  String turkey_data = "alectura_lathami(aust_turkey).fasta";
  String loon_data = "gavia_pacifica(loon).fasta"; 
  String gull_data = "Larus_dominicanus(gull).fasta"; 
  String owl_data = "ninox_novaeseelandiae(owl).fasta"; 
  String woodpecker_data = "dryocopus_pileatus(woodpecker).fasta"; 


  DnaString (int x, int y, int z){
    xorigin = x;
    yorigin = y;
    zorigin = z;
  }  

  void loadNucleotides() {
    a.loadAdenine();
    a2.loadAdenine();
    c.loadCytosine();
    c2.loadCytosine();
    g.loadGuanine();
    g2.loadGuanine();
    t.loadThymine();
    t2.loadThymine();
  }


  void loadTextfile() 
  { 
    if (mode == 1) {
      
      byte[] ost_bytes;
      ost_bytes = loadBytes(ostrich_data);
      println("there are " + ost_bytes.length + "bytes");
      for (int i=0; i < ost_bytes.length; i++) {
        char x = char(ost_bytes[i]);
        if (x != '\t' && x != '\r' && x != '\f' && x != '\n' && x != ' '){
          ost_basePairs = (char[])append(ost_basePairs, x);
        }
      }
      println(ost_basePairs.length + "bpairs");
    } 
    else if (mode == 2) {
      byte[] flam_bytes;
      flam_bytes = loadBytes(flamingo_data);
      println("there are " + flam_bytes.length + "bytes");
      for (int i=0; i < flam_bytes.length; i++) {
        char x = char(flam_bytes[i]);
        if (x != '\t' && x != '\r' && x != '\f' && x != '\n' && x != ' '){
          flam_basePairs = (char[])append(flam_basePairs, x);
        }
      }
      println(flam_basePairs.length + "bpairs");
    } 
    else if (mode == 3) {
      byte[] turk_bytes;
      turk_bytes = loadBytes(turkey_data);
      println("there are " + turk_bytes.length + "bytes");
      for (int i=0; i < turk_bytes.length; i++) {
        char x = char(turk_bytes[i]);
        if (x != '\t' && x != '\r' && x != '\f' && x != '\n' && x != ' '){
          turk_basePairs = (char[])append(turk_basePairs, x);
        }
      }
      println(turk_basePairs.length + "bpairs");
    } 
    else if (mode == 4) {
      byte[] loon_bytes;
      loon_bytes = loadBytes(loon_data);
      println("there are " + loon_bytes.length + "bytes");
      for (int i=0; i < loon_bytes.length; i++) {
        char x = char(loon_bytes[i]);
        if (x != '\t' && x != '\r' && x != '\f' && x != '\n' && x != ' '){
          loon_basePairs = (char[])append(loon_basePairs, x);
        }
      }
      println(loon_basePairs.length + "bpairs");
    } 
    else if (mode == 5) {
      byte[] gull_bytes;
      gull_bytes = loadBytes(gull_data);
      println("there are " + gull_bytes.length + "bytes");
      for (int i=0; i < gull_bytes.length; i++) {
        char x = char(gull_bytes[i]);
        if (x != '\t' && x != '\r' && x != '\f' && x != '\n' && x != ' '){
          gull_basePairs = (char[])append(gull_basePairs, x);
        }
      }
      println(gull_basePairs.length + "bpairs");
    } 
    else if (mode == 6) {
      byte[] owl_bytes;
      owl_bytes = loadBytes(owl_data);
      println("there are " + owl_bytes.length + "bytes");
      for (int i=0; i < owl_bytes.length; i++) {
        char x = char(owl_bytes[i]);
        if (x != '\t' && x != '\r' && x != '\f' && x != '\n' && x != ' '){
          owl_basePairs = (char[])append(owl_basePairs, x);
        }
      }
      println(owl_basePairs.length + "bpairs");
    } 
    else if (mode == 7) {
      byte[] wood_bytes;
      wood_bytes = loadBytes(woodpecker_data);
      println("there are " + wood_bytes.length + "bytes");
      for (int i=0; i < wood_bytes.length; i++) {
        char x = char(wood_bytes[i]);
        if (x != '\t' && x != '\r' && x != '\f' && x != '\n' && x != ' '){
          wood_basePairs = (char[])append(wood_basePairs, x);
        }
      }
      println(wood_basePairs.length + "bpairs");
    } 
    //    else {
    //      bytes = loadBytes(ostrich_data);
    //    }

  }

  void renderText(){
    if (mode == 1) {
      fill(0);
      text("Struthio camelus", 22, 357);
      text("Ostrich", 22, 377);
      text("of " + ost_basePairs.length + " base pairs", 102, 407);
      text((x*f) + " - " + ((x*f) + (f*numBpairs_disp)), 22, 407); 
    } 
    else if (mode == 2) {
      fill(0);
      text("Phoenicopterus ruber", 22, 357);
      text("American Flamingo", 22, 377);
      text("of " + flam_basePairs.length + " base pairs", 102, 407);
      text((x*f) + " - " + ((x*f) + (f*numBpairs_disp)), 22, 407); 
    } 
    else if (mode == 3) {
      fill(0);
      text("Meleagris gallopavo", 22, 357);
      text("Wild Turkey", 22, 377);
      text("of " + turk_basePairs.length + " base pairs", 102, 407);
      text((x*f) + " - " + ((x*f) + (f*numBpairs_disp)), 22, 407); 
    } 
    else if (mode == 4) {
      fill(0);
      text("Gavia pacifica", 22, 357);
      text("Pacific Loon", 22, 377);
      text("of " + loon_basePairs.length + " base pairs", 102, 407);
      text((x*f) + " - " + ((x*f) + (f*numBpairs_disp)), 22, 407); 
    } 
    else if (mode == 5) {
      fill(0);
      text("Larus canus", 22, 357);
      text("Common Gull", 22, 377);
      text("of " + gull_basePairs.length + " base pairs", 102, 407);
      text((x*f) + " - " + ((x*f) + (f*numBpairs_disp)), 22, 407); 
    } 
    else if (mode == 6) {
      fill(0);
      text("Lophostrix cristata", 22, 357);
      text("Crested Owl", 22, 377);
      text("of " + owl_basePairs.length + " base pairs", 102, 407);
      text((x*f) + " - " + ((x*f) + (f*numBpairs_disp)), 22, 407); 
    } 
    else if (mode == 7) {
      fill(0);
      text("Dryocopus pileatus", 22, 357);
      text("Pileated Woodpecker", 22, 377);
      text("of " + wood_basePairs.length + " base pairs", 102, 407);
      text((x*f) + " - " + ((x*f) + (f*numBpairs_disp)), 22, 407); 
    }
  }

  void renderButtons() {
    buttonOst.update();
    buttonOst.display("ostrich");
    buttonFlam.update();
    buttonFlam.display("flamingo");
    buttonTurkey.update();
    buttonTurkey.display("turkey");
    buttonLoon.update();
    buttonLoon.display("loon");
    buttonGull.update();
    buttonGull.display("gull");
    buttonOwl.update();
    buttonOwl.display("owl");
    buttonWood.update();
    buttonWood.display("wood");
  }
  
  void renderBar() {  
    x = int(bar.getPos());
    bar.update(mouseX, mouseY);
    bar.display();
    //println(x);
  }



  void renderMolecules_ost(){
    int xcoord = this.xorigin;
    int ycoord = this.yorigin;
    int zcoord = this.zorigin;
    float inc_rotation = 0;
    int gap = 80;

    f = int(ost_basePairs.length/bar.sw);
    x = x * f;
    println(f);

    for (int i = x; i < (x + (f*numBpairs_disp)); i++) { 
      xcoord += 0;
      ycoord += 50;
      zcoord += 0;
      inc_rotation += 0.3;
      
      
      switch(ost_basePairs[i]){
      case 'A':
        pushMatrix();
        rotateY(inc_rotation);
        a.AdenineDisplay(xcoord, ycoord, zcoord, radians(260), radians(10), radians(-27), gap); 
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        t2.ThymineDisplay((xcoord), ycoord, zcoord, (radians(-150)), radians(210), gap);
        popMatrix();
        break;
      case 'C':
        pushMatrix();
        rotateY(inc_rotation);
        c.CytosineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), radians(0), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        g2.GuanineDisplay((xcoord), ycoord, zcoord, -(radians(90)), (radians(190)),  radians(-30), gap);
        popMatrix();
        break;
      case 'G':
        pushMatrix();
        rotateY(inc_rotation);
        g.GuanineDisplay(xcoord, ycoord, zcoord, radians(-90), radians(10), radians(-30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        c2.CytosineDisplay((xcoord), ycoord, zcoord, (radians(30)-radians(180)), radians(210), (radians(0)), gap);
        text("C", (xcoord), ycoord, 10+zcoord);
        popMatrix();
        break;
      case 'T':
        pushMatrix();
        rotateY(inc_rotation);
        t.ThymineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        a2.AdenineDisplay((xcoord), ycoord, zcoord, (radians(-80)), -(radians(170)), (radians(-30)), gap);
        popMatrix();
        break;
      }  
    }
  }
  
 void renderMolecules_flam(){
    int xcoord = this.xorigin;
    int ycoord = this.yorigin;
    int zcoord = this.zorigin;
    float inc_rotation = 0;
    int gap = 80;

    f = int(ost_basePairs.length/bar.sw);
    x = x * f;

    for (int i = x; i < (x + (f*numBpairs_disp)); i++) { 
      xcoord += 0;
      ycoord += 50;
      zcoord += 0;
      inc_rotation += 0.3;

      switch(flam_basePairs[i]){
      case 'A':
        pushMatrix();
        rotateY(inc_rotation);
        a.AdenineDisplay(xcoord, ycoord, zcoord, radians(260), radians(10), radians(-27), gap); 
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        t2.ThymineDisplay((xcoord), ycoord, zcoord, (radians(-150)), radians(210), gap);
        popMatrix();
        break;
      case 'C':
        pushMatrix();
        rotateY(inc_rotation);
        c.CytosineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), radians(0), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        g2.GuanineDisplay((xcoord), ycoord, zcoord, -(radians(90)), (radians(190)),  radians(-30), gap);
        popMatrix();
        break;
      case 'G':
        pushMatrix();
        rotateY(inc_rotation);
        g.GuanineDisplay(xcoord, ycoord, zcoord, radians(-90), radians(10), radians(-30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        c2.CytosineDisplay((xcoord), ycoord, zcoord, (radians(30)-radians(180)), radians(210), (radians(0)), gap);
        text("C", (xcoord), ycoord, 10+zcoord);
        popMatrix();
        break;
      case 'T':
        pushMatrix();
        rotateY(inc_rotation);
        t.ThymineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        a2.AdenineDisplay((xcoord), ycoord, zcoord, (radians(-80)), -(radians(170)), (radians(-30)), gap);
        popMatrix();
        break;
      }  
    }
  }
   void renderMolecules_turk(){
    int xcoord = this.xorigin;
    int ycoord = this.yorigin;
    int zcoord = this.zorigin;
    float inc_rotation = 0;
    int gap = 80;

    f = int(turk_basePairs.length/bar.sw);
    x = x * f;

    for (int i = x; i < (x + (f*numBpairs_disp)); i++) { 
      xcoord += 0;
      ycoord += 50;
      zcoord += 0;
      inc_rotation += 0.3;

      switch(turk_basePairs[i]){
      case 'A':
        pushMatrix();
        rotateY(inc_rotation);
        a.AdenineDisplay(xcoord, ycoord, zcoord, radians(260), radians(10), radians(-27), gap); 
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        t2.ThymineDisplay((xcoord), ycoord, zcoord, (radians(-150)), radians(210), gap);
        popMatrix();
        break;
      case 'C':
        pushMatrix();
        rotateY(inc_rotation);
        c.CytosineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), radians(0), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        g2.GuanineDisplay((xcoord), ycoord, zcoord, -(radians(90)), (radians(190)),  radians(-30), gap);
        popMatrix();
        break;
      case 'G':
        pushMatrix();
        rotateY(inc_rotation);
        g.GuanineDisplay(xcoord, ycoord, zcoord, radians(-90), radians(10), radians(-30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        c2.CytosineDisplay((xcoord), ycoord, zcoord, (radians(30)-radians(180)), radians(210), (radians(0)), gap);
        text("C", (xcoord), ycoord, 10+zcoord);
        popMatrix();
        break;
      case 'T':
        pushMatrix();
        rotateY(inc_rotation);
        t.ThymineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        a2.AdenineDisplay((xcoord), ycoord, zcoord, (radians(-80)), -(radians(170)), (radians(-30)), gap);
        popMatrix();
        break;
      }  
    }
  } 
  void renderMolecules_loon(){
    int xcoord = this.xorigin;
    int ycoord = this.yorigin;
    int zcoord = this.zorigin;
    float inc_rotation = 0;
    int gap = 80;

    f = int(loon_basePairs.length/bar.sw);
    x = x * f;

    for (int i = x; i < (x + (f*numBpairs_disp)); i++) { 
      xcoord += 0;
      ycoord += 50;
      zcoord += 0;
      inc_rotation += 0.3;

      switch(loon_basePairs[i]){
      case 'A':
        pushMatrix();
        rotateY(inc_rotation);
        a.AdenineDisplay(xcoord, ycoord, zcoord, radians(260), radians(10), radians(-27), gap); 
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        t2.ThymineDisplay((xcoord), ycoord, zcoord, (radians(-150)), radians(210), gap);
        popMatrix();
        break;
      case 'C':
        pushMatrix();
        rotateY(inc_rotation);
        c.CytosineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), radians(0), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        g2.GuanineDisplay((xcoord), ycoord, zcoord, -(radians(90)), (radians(190)),  radians(-30), gap);
        popMatrix();
        break;
      case 'G':
        pushMatrix();
        rotateY(inc_rotation);
        g.GuanineDisplay(xcoord, ycoord, zcoord, radians(-90), radians(10), radians(-30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        c2.CytosineDisplay((xcoord), ycoord, zcoord, (radians(30)-radians(180)), radians(210), (radians(0)), gap);
        text("C", (xcoord), ycoord, 10+zcoord);
        popMatrix();
        break;
      case 'T':
        pushMatrix();
        rotateY(inc_rotation);
        t.ThymineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        a2.AdenineDisplay((xcoord), ycoord, zcoord, (radians(-80)), -(radians(170)), (radians(-30)), gap);
        popMatrix();
        break;
      }  
    }
  }
   void renderMolecules_gull(){
    int xcoord = this.xorigin;
    int ycoord = this.yorigin;
    int zcoord = this.zorigin;
    float inc_rotation = 0;
    int gap = 80;

    f = int(gull_basePairs.length/bar.sw);
    x = x * f;

    for (int i = x; i < (x + (f*numBpairs_disp)); i++) { 
      xcoord += 0;
      ycoord += 50;
      zcoord += 0;
      inc_rotation += 0.3;

      switch(gull_basePairs[i]){
      case 'A':
        pushMatrix();
        rotateY(inc_rotation);
        a.AdenineDisplay(xcoord, ycoord, zcoord, radians(260), radians(10), radians(-27), gap); 
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        t2.ThymineDisplay((xcoord), ycoord, zcoord, (radians(-150)), radians(210), gap);
        popMatrix();
        break;
      case 'C':
        pushMatrix();
        rotateY(inc_rotation);
        c.CytosineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), radians(0), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        g2.GuanineDisplay((xcoord), ycoord, zcoord, -(radians(90)), (radians(190)),  radians(-30), gap);
        popMatrix();
        break;
      case 'G':
        pushMatrix();
        rotateY(inc_rotation);
        g.GuanineDisplay(xcoord, ycoord, zcoord, radians(-90), radians(10), radians(-30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        c2.CytosineDisplay((xcoord), ycoord, zcoord, (radians(30)-radians(180)), radians(210), (radians(0)), gap);
        text("C", (xcoord), ycoord, 10+zcoord);
        popMatrix();
        break;
      case 'T':
        pushMatrix();
        rotateY(inc_rotation);
        t.ThymineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        a2.AdenineDisplay((xcoord), ycoord, zcoord, (radians(-80)), -(radians(170)), (radians(-30)), gap);
        popMatrix();
        break;
      }  
    }
  }
 void renderMolecules_owl(){
    int xcoord = this.xorigin;
    int ycoord = this.yorigin;
    int zcoord = this.zorigin;
    float inc_rotation = 0;
    int gap = 80;

    f = int(owl_basePairs.length/bar.sw);
    x = x * f;

    for (int i = x; i < (x + (f*numBpairs_disp)); i++) { 
      xcoord += 0;
      ycoord += 50;
      zcoord += 0;
      inc_rotation += 0.3;

      switch(owl_basePairs[i]){
      case 'A':
        pushMatrix();
        rotateY(inc_rotation);
        a.AdenineDisplay(xcoord, ycoord, zcoord, radians(260), radians(10), radians(-27), gap); 
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        t2.ThymineDisplay((xcoord), ycoord, zcoord, (radians(-150)), radians(210), gap);
        popMatrix();
        break;
      case 'C':
        pushMatrix();
        rotateY(inc_rotation);
        c.CytosineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), radians(0), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        g2.GuanineDisplay((xcoord), ycoord, zcoord, -(radians(90)), (radians(190)),  radians(-30), gap);
        popMatrix();
        break;
      case 'G':
        pushMatrix();
        rotateY(inc_rotation);
        g.GuanineDisplay(xcoord, ycoord, zcoord, radians(-90), radians(10), radians(-30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        c2.CytosineDisplay((xcoord), ycoord, zcoord, (radians(30)-radians(180)), radians(210), (radians(0)), gap);
        text("C", (xcoord), ycoord, 10+zcoord);
        popMatrix();
        break;
      case 'T':
        pushMatrix();
        rotateY(inc_rotation);
        t.ThymineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        a2.AdenineDisplay((xcoord), ycoord, zcoord, (radians(-80)), -(radians(170)), (radians(-30)), gap);
        popMatrix();
        break;
      }  
    }
  }
 void renderMolecules_wood(){
    int xcoord = this.xorigin;
    int ycoord = this.yorigin;
    int zcoord = this.zorigin;
    float inc_rotation = 0;
    int gap = 80;

    f = int(wood_basePairs.length/bar.sw);
    x = x * f;

    for (int i = x; i < (x + (f*numBpairs_disp)); i++) { 
      xcoord += 0;
      ycoord += 50;
      zcoord += 0;
      inc_rotation += 0.3;

      switch(wood_basePairs[i]){
      case 'A':
        pushMatrix();
        rotateY(inc_rotation);
        a.AdenineDisplay(xcoord, ycoord, zcoord, radians(260), radians(10), radians(-27), gap); 
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        t2.ThymineDisplay((xcoord), ycoord, zcoord, (radians(-150)), radians(210), gap);
        popMatrix();
        break;
      case 'C':
        pushMatrix();
        rotateY(inc_rotation);
        c.CytosineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), radians(0), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        g2.GuanineDisplay((xcoord), ycoord, zcoord, -(radians(90)), (radians(190)),  radians(-30), gap);
        popMatrix();
        break;
      case 'G':
        pushMatrix();
        rotateY(inc_rotation);
        g.GuanineDisplay(xcoord, ycoord, zcoord, radians(-90), radians(10), radians(-30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        c2.CytosineDisplay((xcoord), ycoord, zcoord, (radians(30)-radians(180)), radians(210), (radians(0)), gap);
        text("C", (xcoord), ycoord, 10+zcoord);
        popMatrix();
        break;
      case 'T':
        pushMatrix();
        rotateY(inc_rotation);
        t.ThymineDisplay(xcoord, ycoord, zcoord, radians(-30), radians(30), gap);
        popMatrix();
        pushMatrix();
        rotateY(inc_rotation);
        a2.AdenineDisplay((xcoord), ycoord, zcoord, (radians(-80)), -(radians(170)), (radians(-30)), gap);
        popMatrix();
        break;
      }  
    }
  }


}