D3 Examples - Genome Viewer using GBK

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<!DOCTYPE html>
<!-- Check Out BioJS -->
​
<head>
  <meta charset="utf-8">
  <script type="text/javascript" src="https://cdn.jsdelivr.net/npm/d3@2.10.3/d3.v2.js"></script>
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
  <script src="//d3js.org/d3.v3.min.js" language="JavaScript"></script>
  <script src="https://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script>
  <style>
    body { 
        margin: ;
        position:fixed;
        top:0;
        right:0;
        bottom:0;
        left:2;
        background-image: linear-gradient(to bottom, #EFEFBB, #D4D3DD 100%); 
    }
  </style>
</head>
​
<body>
 
​
  <script>
    var svg = d3.select("body")
        .append("svg")
        .attr("height", 1000);
   
    d3.json("GBKtoJSONtest.json.txt", function(error, json) {
          if (error) return console.warn(error);
      svg.attr("width", function(d) {
        return d3.max(json, function(d) {
          return d.genomelength/10;
        })
      });
    
    
      var sequences = svg.selectAll(".genomes")
        .data(json)
        .enter()
        .append("g");
      sequences.attr("transform", function(d, i) { 
        return "translate(0," + (10 + (i*225)) + ")"; 
      });
      
      //Names of the Sequences 
      sequences.append("text")
        .attr({x:-500})
        .style({"font-family":"verdana","font-size":"18px","fill":"green"})
        .transition(1000).delay(3000).duration(1000).ease("bounce")
        .attr({x:10, y:20})
        .text(function(d) {
        return d.genomename;
      });
      
      //starting the ruler
      sequences.append("rect") 
        .attr({x: -500, y: 100, width: function(d) { 
          return d.genomelength/10; }, height: 30
              })
        .style({"stroke-width": "2px", "fill": "white", "stroke": "#9932CC",})
        .attr("stroke-opacity", 0)
        .transition(1000).duration(3000)
        .attr({x: 0})
        .attr("stroke-opacity", 1);
      
      //grouping the 3 tick groups and displaying them
        var group = sequences.selectAll(".a")
        .data(function (d) {
          ticks = [];
          genome_positions = d3.range(d.genomelength);
          genome_positions.forEach(function (currentValue, index, myArray) {
            if (currentValue % 1000 === 0) {
              ticks.push(currentValue);
            }
          });
          return ticks;
       })
      .enter()
        .append("g");
    group.append("rect")
        .style({"fill":"black"})
      //.attr({x: 0, y: 100, width: "1px", height: 30})
        .attr({x: -100})
            .transition().duration(3000)
        .attr({x: function (d) { return d/10; }, y: 100, width: "1px", height: 30})
        .attr({"fill-opacity": 1});
        //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
    //numbers @1000 ticks
    group.append("text")
        .attr("y", 112)
        .attr("x", function(d) { return (d/10) + 1 })
        .style({"font-size":"20px","fill":"red"})
        .transition().duration(2000).delay(2000)
        .style({"font-family":"verdana","font-size":"10px","fill":"green"})
      .text(function(d,i) { return i; })
        var group2 = sequences.selectAll(".b")
      .data(function(d) {
        ticks = [];
        genome_positions = d3.range(d.genomelength);
        genome_positions.forEach(function (currentValue, index, myArray) {
          if (currentValue % 500 === 0 & currentValue % 1000 !== 0) {
            ticks.push(currentValue);
          }
        })
        return ticks;
      })
      .enter()
        .append("g");
    group2.append("rect")
        .style({"fill": "black"})
      //.attr({x: 0, y: 100, width: "1px", height: 15})
        .attr({x:-100})
      .transition().duration(3000)
        .attr({x: function(d) {return d/10;}, y: 100, width: "1px", height: 15})
      //.attr("transform", function (d) {return "translate(" + d/10 + ",0)";});
        var group3 = sequences.selectAll(".onehundredticks")
      .data(function(d) {
        ticks = [];
        genome_positions = d3.range(d.genomelength);
        genome_positions.forEach(function (currentValue, index, myArray) {
          if (currentValue % 100 === 0 & currentValue % 500 !== 0 
              & currentValue % 1000 !== 0) {
            ticks.push(currentValue);
          }
        });
        return ticks;
      })
      .enter()
        .append("g");
    group3.append("rect")
        .style({"fill": "black"})
      //.attr({x: 0, y: 115, width: "1px", height: 15})
        .attr({x: -100})
      .transition().duration(3000)
        .attr({x: function (d) { return d/10; }, y: 115, width: "1px", height: 15})
      //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
    
        //Attaching the coming gene boxes to the graph w/the data 
      var genes = sequences.selectAll(".genes")
        .data(function(d) { return d.genes;})
          .enter()
        .append("g");
      
        var position = genes.selectAll(".location")
            .data(function (d) {return d.location;})
        .enter()
            .append("g");
​
         //The gene boxes attributes
         position.append("rect")
        .attr("x", function (d) {
             return (0 - ((d.end-d.start)/10)) - 2
            })
          .attr("y", function (d) { 
             if (((d.end-d.start)/10)%2==0) { 
               return 100;
           } else {
                return 160;
           }
     })
        .attr("height", function(d) { return 0; })
        .attr("width", function (d) { return (d.end-d.start)/10; })
        .style("fill", function(d) {
          if (d.start%3==0) { 
            return "009900"; 
          } else {
                return "009900";
            }
        })
        .style("stroke","black")
            .style({"stroke-width":"2px"})
            .transition().delay(2000).duration(2000)
            .attr("x", function (d) { 
          return d.start/10; 
        })
          .attr("y", function (d) { 
             if (d.start%3==0) { 
               return 140;
           } else {
                return 60;
           }
     })
        .attr("height", function (d) {return 30;})
        group.on("click", function() {
            console.log("rect");
        })
        //text in gene boxes
      genes.append("text") 
        .attr("x", function (d) { console.log(d);return ((d.location[0].start+d.location[0].end)/10)/2})
        .style("text-anchor","middle")
        .style({"font-family":"verdana","font-size":"18px","fill":"black"})
        .attr("y", 80)
        .text(function (d) {
            return d.gene;})
          //var c = 0;
          //var g = 0;
          //for (var i=0; i<=d.sequence.length; i++) {
           // if (d.sequence[i] === "C") {c++; }
           // else if (d.sequence[i] === "G") {g++;}
          //}
         // return (((c+g)/d.sequence.length)*100;})
        //.attr("fill-opacity",0)
        //.transition().duration(3000).delay(2000)
        //.attr("fill-opacity",1);
​
      // text above or below boxes
      position.append("text") 
        .attr("x", function(d) { return ((d.end - d.start)/2)/10;})
        .attr("y", 50)
        .style({"text-anchor":"middle","fill":"black","font-weight":"bold"})
        .attr("font-family","sans-serif")
        .text(function(d) {return d.start;})
        .attr("fill-opacity", 0)
        .transition().delay(4500).duration(1000)
        .attr("fill-opacity", 1);
​
 });
  </script>
  <button onclick="SNPs()" class="button">Show SNPs</button>
</body>
    