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<!DOCTYPE html> |
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<head> |
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<meta charset="utf-8"> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"> |
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</script> |
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<script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.12.0.min.js"> |
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</script> |
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<script src="aminoacidseq.js" type="text/javascript"> |
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</script> |
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<!-- Latest compiled and minified CSS --> |
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<link crossorigin="anonymous" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap.min.css" integrity="sha384-1q8mTJOASx8j1Au+a5WDVnPi2lkFfwwEAa8hDDdjZlpLegxhjVME1fgjWPGmkzs7" rel="stylesheet"> |
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<!-- Optional theme --> |
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<link crossorigin="anonymous" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/css/bootstrap-theme.min.css" integrity="sha384-fLW2N01lMqjakBkx3l/M9EahuwpSfeNvV63J5ezn3uZzapT0u7EYsXMjQV+0En5r" rel="stylesheet"> |
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<!-- Latest compiled and minified JavaScript --> |
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<script src="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.6/js/bootstrap.min.js"> |
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</script> |
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<style> |
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#myModal { |
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font-family: arial; |
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font-size: 14px; |
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text-align: left; |
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vertical-align: middle; |
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word-wrap: break-word; |
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} |
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body{ |
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font-family:Arial; |
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} |
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</style> |
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<title></title> |
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</head> |
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<body> |
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<!-- Trigger the modal with a button --> |
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<!-- Modal --> |
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<div class="modal fade" id="myModal" role="dialog"> |
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<div class="modal-content" id="chicken"> |
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<!-- Modal content--> |
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<div class="modal-content"> |
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<div class="modal-header"> |
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<button class="close" data-dismiss="modal" type="button">×</button> |
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<h4 class="modal-title">Genome Information</h4> |
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</div> |
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<div class="modal-body">Sequence</div> |
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<div class="modal-body">G-C Content</div> |
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</div> |
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</div> |
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</div> |
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</body> |
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<head> |
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<meta charset="utf-8"> |
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<style> |
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svg { |
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font: 10px sans-serif; |
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} |
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path { |
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-webkit-transition: fill-opacity 250ms linear; |
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} |
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.selecting path { |
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fill-opacity: .2; |
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} |
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.selecting path.selected { |
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stroke: #f00; |
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stroke-width: 2px; |
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} |
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.axis path, .axis line { |
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fill: none; |
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stroke: #000; |
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shape-rendering: crispEdges; |
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} |
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.brush .extent { |
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stroke: #fff; |
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fill-opacity: .125; |
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shape-rendering: crispEdges; |
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} |
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.modal-body { |
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font-family: Courier; |
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} |
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</style> |
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<script src="//d3js.org/d3.v3.min.js"></script> |
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<script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script> |
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<script src="http://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script> |
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<style> |
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body { |
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margin:0; |
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position:fixed; |
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top:0; |
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right:0; |
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bottom:0; |
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left:0; |
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} |
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div.tooltip { |
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position: absolute; |
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text-align: center; |
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width: 60px; |
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height: 28px; |
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padding: 2px; |
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font: 12px sans-serif; |
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background: lightsteelblue; |
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border: 0px; |
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border-radius: 8px; |
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pointer-events: none; |
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} |
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.d3-tip { |
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line-height: 1; |
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font-weight: bold; |
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padding: 12px; |
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background: lightsteelblue; |
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color: #fff; |
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border-radius: 2px; |
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} |
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.d3-tip:after { |
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box-sizing: border-box; |
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display: inline; |
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font-size: 10px; |
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width: 100%; |
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line-height: 1; |
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color: rgba(0, 0, 0, 0.8); |
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content: "\25BC"; |
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position: absolute; |
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text-align: center; |
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} |
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.d3-tip.n:after { |
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margin: -1px 0 0 0; |
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top: 100%; |
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left: 0; |
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} |
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</style> |
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</head> |
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<body> |
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<script> |
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var margin = {top: 30, right: 10, bottom: 0, left: 10}, |
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width = 960 - margin.right - margin.left, |
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height = 500 - margin.top - margin.bottom; |
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var svg = d3.select("body").append("svg").attr("height", 1000) |
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.attr("width", width + margin.right + margin.left) |
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.attr("height", height + margin.top + margin.bottom) |
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.append("g") |
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.attr("transform", "translate(" + margin.left + "," + margin.top + ")"); |
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d3.json("genes.json.txt", function(error, json) { |
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if (error) return console.warn(error); |
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//console.log(json); |
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svg.attr("width", function (d) { |
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return d3.max(json, function(d) { |
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return d.genomelength/10; |
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}) |
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}); |
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var x = d3.scale.ordinal() |
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.domain("height",1000) |
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.rangePoints([0, width], 1); |
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var brush = d3.svg.brush(); |
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svg.append("g") |
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.attr("class", "brush") |
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.call(brush.x(x) |
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.on("brushstart", brushstart) |
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.on("brush", brushmove) |
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.on("brushend", brushend)) |
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.selectAll("rect") |
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.attr("height", height); |
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function brushstart() { |
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svg.classed("selecting", true); |
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} |
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function brushmove() { |
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var s = d3.event.target.extent(); |
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} |
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function brushend() { |
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$('#myModal').modal('show'); |
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var modalbody = d3.select(".modal-body"); |
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var s = ""; |
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json.forEach(function(value, index, arr) { |
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s = s + value.sequence.slice(brush.extent()[0]*10, brush.extent()[1]*10) + "<br>" |
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}) |
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modalbody.html("<span>" + s + "</span>"); |
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console.log(json); |
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console.log("brush extent: ", brush.extent()); |
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//console.log(bbox.width); |
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var rect = svg.append("g") |
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//.attr("width", bbox.width) |
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// .attr("height", bbox.height) |
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svg.classed("selecting", !d3.event.target.empty()); |
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} |
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var tip = d3.tip() |
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.attr('class', 'd3-tip') |
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.offset(function (d) { |
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if (d.direction == "forward") { |
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return [-8, 0]; |
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} |
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else if (d.direction == "reverse") { |
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return [-8, 0]; |
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} |
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}) |
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.html(function(d) { |
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return "<b>GC Content:</b> <span style='color:white'>" |
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+ /*((((d.sequence.match(/G/gi).length)+(d.sequence.match(/C/gi).length))/(d.sequence.length))*100).toPrecision(3)+"%" |
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+ " ; " +*/ "Pham:" + d.pham +"</span>" |
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}) |
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//Clickable tip box attr |
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var hidden = d3.tip() |
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.attr('class', 'd3-hidden') |
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.offset(function (d) { |
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if (d.direction == "forward") { |
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return [50, 0]; |
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} |
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else if (d.direction == "reverse") { |
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return [50, 0]; |
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} |
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}) |
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//possible incert g/c content calculator |
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.html(function(d) { |
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return "<a style=color:black target=_blank href=http://blast.ncbi.nlm.nih.gov/Blast.cgi>BLAST:</a><span style='color:white'>" |
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+ " " + d.translation + "</span>"; |
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}) |
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//call the "tool-tips" |
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svg.call(tip); |
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svg.call(hidden); |
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var phage = svg.selectAll(".genomes") |
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.data(json) |
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.enter() |
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.append("g"); |
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phage.attr("transform", function(d, i) { return "translate(0," + (100 + (i*225)) + ")"; }); |
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phage.append("rect") // background for ruler |
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.attr({x: 0, y: 0, width: function(d) { return d.genomelength/10; }, height: 30}) |
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.style({"stroke-width": "2px", "fill": "white", "stroke": "black"}) |
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.attr("stroke-opacity", 0) |
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.transition().duration(1000) |
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.attr("stroke-opacity", 1) |
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var group = phage.selectAll(".thousandticks") |
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.data(function (d) { |
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ticks = []; |
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genome_positions = d3.range(d.genomelength); |
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genome_positions.forEach(function (currentValue, index, myArray) { |
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if (currentValue % 1000 === 0) { |
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ticks.push(currentValue); |
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} |
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}); |
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return ticks; |
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} |
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) |
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.enter() |
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.append("g"); |
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group.append("rect") |
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.style({"fill": "black"}) |
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//.attr({x: 0, y: 100, width: "1px", height: 30}) |
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.attr({x: function (d) { return d/10; }, y: 0, width: "1px", height: 30}) |
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.attr({"fill-opacity": 0}) |
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.transition().duration(1500) |
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.attr({"fill-opacity": 1}); |
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//.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; }); |
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group.append("text") // kbp label |
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.attr("x", function(d) {return (d/10) + 3;}) |
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.attr("y", 12) |
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.attr("font-family", "sans-serif") |
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.attr("font-size", "14px") |
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.attr("fill", "green") |
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.style("text-anchor", "start") |
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.text(function(d) { return d/1000; }) |
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.attr({"fill-opacity": 0}) |
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.transition().duration(1500) |
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.attr({"fill-opacity": 1}); |
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var group2 = phage.selectAll(".fivehundredticks") |
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.data(function (d) { |
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ticks = []; |
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genome_positions = d3.range(d.genomelength); |
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genome_positions.forEach(function (currentValue, index, myArray) { |
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if (currentValue % 500 === 0 & currentValue % 1000 !== 0) { |
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ticks.push(currentValue); |
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} |
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}) |
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return ticks; |
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}) |
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.enter() |
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.append("g"); |
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group2.append("rect") |
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.on('mouseover', tip.show) |
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.style({"fill": "black"}) |
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.attr({x: function(d) {return d/10;}, y: 0, width: "1px", height: 15}) |
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.attr({"fill-opacity": 0}) |
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.transition().duration(1500) |
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.attr({"fill-opacity": 1}); |
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//.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; }); |
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var group3 = phage.selectAll(".onehundredticks") |
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.data(function (d) { |
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ticks = []; |
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genome_positions = d3.range(d.genomelength); |
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genome_positions.forEach(function (currentValue, index, myArray) { |
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if (currentValue % 100 === 0 & currentValue % 1000 !== 0 & currentValue % 500 !== 0) { |
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ticks.push(currentValue); |
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} |
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}) |
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return ticks; |
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}) |
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.enter() |
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.append("g"); |
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group3.append("rect") |
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.style({"fill": "black"}) |
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.attr({x: function (d) { return d/10; }, y: 15, width: "1px", height: 15}) |
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.attr("fill-opacity", 0) |
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.transition().duration(1500) |
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.attr("fill-opacity", 1); |
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gene = phage.selectAll(".genes") |
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.data(function(d, i) { console.log(i, d); return d.genes;}) |
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.enter() |
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.append("g"); |
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gene.append("rect") |
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.on('mouseover', tip.show) |
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.on('mouseout', tip.hide) |
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.on('click', hidden.show) |
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.on('dblclick', hidden.hide) |
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//.on("mouseup", function(d) {$('#myModal').modal('show')}) |
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.attr("y", function (d) { |
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if (d.direction == "forward") { |
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if (d.name % 2 === 0) { |
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return -70; |
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} |
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else { return -30;} |
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} |
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else if (d.direction == "reverse") { |
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if (d.name % 2 === 0) { |
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return 30; |
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} |
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else { return 60;} |
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} |
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}) |
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.attr("x", function (d) { |
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if (d.direction === "forward") { |
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return (0 - ((d.stop-d.start)/10)) - 2; |
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} |
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else if (d.direction === "reverse") { |
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w = d3.select("svg").style("width"); |
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return w; |
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} |
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}) |
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.attr("height", function (d) {return 30;}) |
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.attr("width", function (d) { return (d.stop-d.start)/10; }) |
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.style({"stroke":"black", "stroke-width": "2px"}) |
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.attr("fill", function (d) { |
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if (d.direction == "forward") { |
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return "green"; |
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} |
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else if (d.direction == "reverse") { |
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return "red"; |
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} |
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else { |
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return "black"; |
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} |
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}) |
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.transition().delay(1000).duration(1500) |
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.attr("x", function (d) { return d.start/10; }); |
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gene.append("text") // gene name |
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.attr("x", function(d) { return ((d.start + d.stop)/2)/10;}) |
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.attr("y", function (d) { |
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if (d.direction == "forward") { |
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if (d.name % 2 === 0) { // forward and even |
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return -50; |
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} |
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else { return -10;} // forward and odd |
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} |
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else if (d.direction == "reverse") { |
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if (d.name % 2 === 0) { // reverse and even |
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return 50; |
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} |
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else { return 80;} //reverse and odd |
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} |
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}) |
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.style({"text-anchor": "middle", "fill": "black"}) |
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.attr("font-family", "sans-serif") |
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.text(function(d) {return d.name}) |
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.attr("fill-opacity", 0) |
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.transition().delay(2000).duration(1500) |
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.attr("fill-opacity", 1); |
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gene.append("text") // pham name |
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.attr("x", function(d) { return ((d.start + d.stop)/2)/10;}) |
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.attr("y", function (d) { |
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if (d.direction == "forward") { |
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if (d.name % 2 === 0) { |
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return -80; |
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} |
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else { return -40;} |
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} |
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else if (d.direction == "reverse") { |
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if (d.name % 2 === 0) { |
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return 80; |
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} |
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else { return 110;} |
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} |
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}) |
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.style({"text-anchor": "middle", "fill": "blue"}) |
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.attr("font-family", "sans-serif") |
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.text(function(d) {return d.pham}) |
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.attr("fill-opacity", 0) |
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.transition().delay(3500).duration(1500) |
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.attr("fill-opacity", 1); |
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}); |
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</script> |
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</body> |
