////////////////////////////////////////////////////////////
//////////////////////// Set-up ////////////////////////////
////////////////////////////////////////////////////////////

var screenWidth = $(window).innerWidth(), 
	mobileScreen = (screenWidth > 500 ? false : true);

var margin = {left: 50, top: 10, right: 50, bottom: 10},
	width = Math.min(screenWidth, 800) - margin.left - margin.right,
	height = (mobileScreen ? 300 : Math.min(screenWidth, 800)*5/6) - margin.top - margin.bottom;
		
var svg = d3.select("#chart").append("svg")
			.attr("width", (width + margin.left + margin.right))
			.attr("height", (height + margin.top + margin.bottom));
			
var wrapper = svg.append("g").attr("class", "chordWrapper")
			.attr("transform", "translate(" + (width / 2 + margin.left) + "," + (height / 1.75 + margin.top) + ")");;
			
var outerRadius = Math.min(width, height) / 2  - (mobileScreen ? 80 : 100),
	innerRadius = outerRadius * 0.95,
	opacityDefault = 0.7, //default opacity of chords
	opacityLow = 0.02; //hover opacity of those chords not hovered over
	
//How many pixels should the two halves be pulled apart
var pullOutSize = (mobileScreen? 20 : 50)

//////////////////////////////////////////////////////
//////////////////// Titles on top ///////////////////
//////////////////////////////////////////////////////

var titleWrapper = svg.append("g").attr("class", "chordTitleWrapper"),
	titleOffset = mobileScreen ? 15 : 40,
	titleSeparate = mobileScreen ? 30 : 0;

//Title	top left
titleWrapper.append("text")
	.attr("class","title left")
	.style("font-size", mobileScreen ? "12px" : "30px" )
	.attr("x", (width/2 + margin.left - outerRadius - titleSeparate))
	.attr("y", titleOffset)
	.text("Copepod");
titleWrapper.append("line")
	.attr("class","titleLine left")
	.attr("x1", (width/2 + margin.left - outerRadius - titleSeparate)*0.6)
	.attr("x2", (width/2 + margin.left - outerRadius - titleSeparate)*1.4)
	.attr("y1", titleOffset+8)
	.attr("y2", titleOffset+8);
//Title top right
titleWrapper.append("text")
	.attr("class","title right")
	.style("font-size", mobileScreen ? "12px" : "30px" )
	.attr("x", (width/2 + margin.left + outerRadius + titleSeparate))
	.attr("y", titleOffset)
	.text("Similarity");
titleWrapper.append("line")
	.attr("class","titleLine right")
	.attr("x1", (width/2 + margin.left - outerRadius - titleSeparate)*0.6 + 2*(outerRadius + titleSeparate))
	.attr("x2", (width/2 + margin.left - outerRadius - titleSeparate)*1.4 + 2*(outerRadius + titleSeparate))
	.attr("y1", titleOffset+8)
	.attr("y2", titleOffset+8);
	
////////////////////////////////////////////////////////////
/////////////////// Animated gradient //////////////////////
////////////////////////////////////////////////////////////

var defs = wrapper.append("defs");
var linearGradient = defs.append("linearGradient")
	.attr("id","animatedGradient")
	.attr("x1","0%")
	.attr("y1","0%")
	.attr("x2","100%")
	.attr("y2","0")
	.attr("spreadMethod", "reflect");

linearGradient.append("animate")
	.attr("attributeName","x1")
	.attr("values","0%;100%")
//	.attr("from","0%")
//	.attr("to","100%")
	.attr("dur","7s")
	.attr("repeatCount","indefinite");

linearGradient.append("animate")
	.attr("attributeName","x2")
	.attr("values","100%;200%")
//	.attr("from","100%")
//	.attr("to","200%")
	.attr("dur","7s")
	.attr("repeatCount","indefinite");

linearGradient.append("stop")
	.attr("offset","5%")
	.attr("stop-color","#a551ff");
linearGradient.append("stop")
	.attr("offset","45%")
	.attr("stop-color","#6d00c6");
linearGradient.append("stop")
	.attr("offset","55%")
	.attr("stop-color","#6d00c6");
linearGradient.append("stop")
	.attr("offset","95%")
	.attr("stop-color","#a551ff");


////////////////////////////////////////////////////////////
////////////////////////// Data ////////////////////////////
////////////////////////////////////////////////////////////
var Names = ["High","Moderate","Low","",          
"a62032;8:g129.t1","a181091;6:g176.t1",
             "a123900;7:g103.t1","a101529;8:g218.t1","a52440;9:g147.t1","a69769;9:g66.t1","a44833;11:g29.t1","a18604;33:g5.t1","a62666;11:g270.t1","a171373;7:g183.t1","a110923;7:g272.t1","a139729;7:g99.t1","a100325;8:g116.t1","a156879;7:g122.t1","a185333;7:g206.t1","a68619;8:g91.t1","a190650;6:g235.t1","a109509;7:g234.t1","a75038;8:g287.t1","a178293;6:g100.t1","a59106;10:g106.t1","a68702;9:g25.t1","a60722;8:g150.t1",""];

var Nematodes =[ "AgB14_g001_t01","AgE05_g008_t17","AgE04_g004_t05","AgE77_g001_t01","AgE54_g003_t03","AgE09_g003_t02","AgE47_g005_t02","AgB03_g007_t04","AgB04_g462_t03","AgE11_g008_t06","AgE09_g002_t06","AgE66_g002_t01","AgE07_g013_t01","AgE02_g006_t11","AgE13_g008_t01","AgE05_g005_t04","AgE76_g001_t11","AgB19_g001_t04","AgB29_g009_t10","AgE49_g002_t01","AgB21_g006_t03","AgE22_g001_t03","AgE14_g010_t04","AgE46_g003_t05","AgB28X_g018_t01","AgE10_g003_t13","AgE01_g016_t01","AgE06_g024_t02","AgE01_g026_t01","AgE01_g027_t07","AgB28X_g013_t01","AgE02_g014_t04","AgB03_g007_t04","AgE52_g004_t02","AgB23_g079_t04","AgB28X_g023_t08","AgE01_g004_t02","AgE14_g014_t06","AgB17_g092_t02","AgE19_g001_t02","AgE85_g001_t01","AgB31X_g003_t01","AgE02_g034_t08","AgE01_g027_t07","AgE03_g025_t01","AgE06_g022_t01","AgE03_g022_t01","AgB24_g004_t05","AgB23_g072_t01","AgE11_g006_t01","AgE01_g047_t02","AgE44_g001_t02","AgE22_g001_t03","AgB31X_g004_t01","AgE07_g004_t04","AgE01_g054_t02","AgB24_g005_t05","AgE02_g034_t08","AgE25_g003_t04","AgE03_g018_t01","AgE42_g003_t02","AgE01_g016_t01","AgB34_g004_t01","AgE54_g001_t01","AgE01_g037_t02","AgE06_g023_t02","AgE70_g002_t04","AgE06_g007_t07","AgE04_g007_t14"
];

var respondents = 3290.3, //Total number of respondents (i.e. the number that make up the total group
	emptyPerc = 0.45, //What % of the circle should become empty
	emptyStroke = Math.round(respondents*emptyPerc); 
var matrix = [
  [0,0,0,0,88.9,87.6,85.7,85.7,80,80,80,80,80,70,70,70,71.4,71.4,72.7,72.7,75,75,75,75,75,77.8,77.8,0],  [0,0,0,0,63.6,87.5,77.8,50,40,66.7,45,47.8,47,66.7,46.2,50,60,45,52.9,60,37,58.4,40,46.7,53.8,35.3,37.5,0], [0,0,0,0,50,26.3,42,43.8,30.8,66.6,34.9,32.3,46.1,61.5,38.1,49.4,50,43.7,38.5,50,36,58.3,33.3,34.8,36.3,35,21.9,0],
[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,emptyStroke],
[88.9,63.6,50,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [87.6,87.5,26.3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [85.7,77.8,42,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [85.7,50,43.8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [80,40,30.8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [80,66.7,66.6,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [80,45,34.9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [80,47.8,32.3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [80,47,46.1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [70,66.7,61.5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [70,46.2,38.1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [70,50,49.4,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [71.4,60,50,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [71.4,45,43.7,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],       [72.7,52.9,38.5,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [72.7,60,50,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [75,37,36,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [75,58.4,58.3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [75,40,33.3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [75,46.7,34.8,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [75,53.8,36.3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [77.8,35.3,35,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],  [77.8,37.5,21.9,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],
 [0,0,0,emptyStroke,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0]
];
//Calculate how far the Chord Diagram needs to be rotated clockwise to make the dummy
//invisible chord center vertically
var offset = (2 * Math.PI) * (emptyStroke/(respondents + emptyStroke))/7.5;

//Custom sort function of the chords to keep them in the original order
var chord = customChordLayout() //d3.layout.chord()
	.padding(.02)
	.sortChords(d3.descending) //which chord should be shown on top when chords cross. Now the biggest chord is at the bottom
	.matrix(matrix);

var arc = d3.svg.arc()
	.innerRadius(innerRadius)
	.outerRadius(outerRadius)
	.startAngle(startAngle) //startAngle and endAngle now include the offset in degrees
	.endAngle(endAngle);

var path = stretchedChord() //Call the stretched chord function 
	.radius(innerRadius)
	.startAngle(startAngle)
	.endAngle(endAngle)
	.pullOutSize(pullOutSize);

////////////////////////////////////////////////////////////
//////////////////// Draw outer Arcs ///////////////////////
////////////////////////////////////////////////////////////

var g = wrapper.selectAll("g.group")
	.data(chord.groups)
	.enter().append("g")
	.attr("class", "group")
	.on("mouseover", fade(opacityLow))
	.on("mouseout", fade(opacityDefault));

g.append("path")
	.style("stroke", function(d,i) { return (Names[i] === "" ? "none" : "#fff605"); })
	.style("fill", function(d,i) { return (Names[i] === "" ? "none" : "#fff605"); })
	.style("pointer-events", function(d,i) { return (Names[i] === "" ? "none" : "auto"); })
	.attr("d", arc)
	.attr("transform", function(d, i) { //Pull the two slices apart
				d.pullOutSize = pullOutSize * ( d.startAngle + 0.001 > Math.PI ? -1 : 1);
				return "translate(" + d.pullOutSize + ',' + 0 + ")";
	});

////////////////////////////////////////////////////////////
////////////////////// Append Names ////////////////////////
////////////////////////////////////////////////////////////

//The text also needs to be displaced in the horizontal directions
//And also rotated with the offset in the clockwise direction
g.append("text")
	.each(function(d) { d.angle = ((d.startAngle + d.endAngle) / 2) + offset;})
	.attr("dy", ".35em")
	.attr("class", "titles")
	.style("font-size", mobileScreen ? "8px" : "8px" )
	.attr("text-anchor", function(d) { return d.angle > Math.PI ? "end" : null; })
	.attr("transform", function(d,i) { 
		var c = arc.centroid(d);
		return "translate(" + (c[0] + d.pullOutSize) + "," + c[1] + ")"
		+ "rotate(" + (d.angle * 180 / Math.PI - 90) + ")"
		+ "translate(" + 20 + ",0)"
		+ (d.angle > Math.PI ? "rotate(180)" : "")
	})
  .text(function(d,i) { return Names[i]; })
  .call(wrapChord, 100);

////////////////////////////////////////////////////////////
//////////////////// Draw inner chords /////////////////////
////////////////////////////////////////////////////////////
 
wrapper.selectAll("path.chord")
	.data(chord.chords)
	.enter().append("path")
	.attr("class", "chord")
	.style("stroke", "none")
	.style("fill", "url(#animatedGradient)") //An SVG Gradient to give the impression of a flow from left to right
	.style("opacity", function(d) { return (Names[d.source.index] === "" ? 0 : opacityDefault); }) //Make the dummy strokes have a zero opacity (invisible)
	.style("pointer-events", function(d,i) { return (Names[d.source.index] === "" ? "none" : "auto"); }) //Remove pointer events from dummy strokes
	.attr("d", path)
	.on("mouseover", fadeOnChord)
	.on("mouseout", fade(opacityDefault))
  
  .append("title")
	.text(function(d, i) {
  	console.log("i:", i);
  console.log(Names.length, Nematodes.length);
  	if (d.source.index === "High") {
    	return [Math.round(d.source.value), "% Identity between ", Names[d.target.index], " and ", Nematodes[((i-4)*3)]].join(""); 
    }
  	else if (d.source.index === "Moderate") {
      		return [Math.round(d.source.value), "% Identity between ", Names[d.target.index], " and ", Nematodes[((i-4)*3)+1]].join(""); 
    }
  	else {
      		return [Math.round(d.source.value), "% Identity between ", Names[d.target.index], " and ", Nematodes[((i-4)*3)+2]].join(""); 
    }
		//return [Math.round(d.source.value), "% Identity between ", Names[d.target.index], " and ", Nematodes[d.source.index]].join(""); 
	});


////////////////////////////////////////////////////////////
////////////////// Extra Functions /////////////////////////
////////////////////////////////////////////////////////////

//Include the offset in de start and end angle to rotate the Chord diagram clockwise
function startAngle(d) { return d.startAngle + offset; }
function endAngle(d) { return d.endAngle + offset; }

// Returns an event handler for fading a given chord group
function fade(opacity) {
  return function(d, i) {
	wrapper.selectAll("path.chord")
		.filter(function(d) { return d.source.index !== i && d.target.index !== i && Names[d.source.index] !== ""; })
		.transition()
		.style("opacity", opacity);
  };
}//fade

// Fade function when hovering over chord
function fadeOnChord(d) {
	var chosen = d;
	wrapper.selectAll("path.chord")
		.transition()
		.style("opacity", function(d) {
			return d.source.index === chosen.source.index && d.target.index === chosen.target.index ? opacityDefault : opacityLow;
		});
}//fadeOnChord

/*Taken from http://bl.ocks.org/mbostock/7555321
//Wraps SVG text*/
function wrapChord(text, width) {
  text.each(function() {
	var text = d3.select(this),
		words = text.text().split(/\s+/).reverse(),
		word,
		line = [],
		lineNumber = 0,
		lineHeight = 1.1, // ems
		y = 0,
		x = 0,
		dy = parseFloat(text.attr("dy")),
		tspan = text.text(null).append("tspan").attr("x", x).attr("y", y).attr("dy", dy + "em");

	while (word = words.pop()) {
	  line.push(word);
	  tspan.text(line.join(" "));
	  if (tspan.node().getComputedTextLength() > width) {
		line.pop();
		tspan.text(line.join(" "));
		line = [word];
		tspan = text.append("tspan").attr("x", x).attr("y", y).attr("dy", ++lineNumber * lineHeight + dy + "em").text(word);
	  }
	}
  });
}//wrapChord