class BubbleChart
  constructor: (data) ->
    @data = data
    @width = 960
    @height = 600

    @tooltip = MyTooltip("my_tooltip", 190)

    @center = {x: @width / 2, y: @height / 2}
    @phase_centers = {
    "II" : {x : 3 * @width / 8, y : 7 * @height / 16},
    "III" : {x : @width / 2, y : 7 * @height / 16},
    "PostMkg" : {x : 5 * @width / 8, y : 7 * @height / 16}
    }
    @yearcat_centers = {
    "(1985,2005]" : {x : 3 * @width / 8, y : @height / 2},
    "(2005,2010]" : {x : @width / 2, y : @height / 2},
    "(2010,2014]" : {x : 5 * @width / 8, y : @height / 2}
    }
    @cmpd_centers = {
    "GA" : {x: 9 * @width / 40, y: 24 * @height / 80},
    "IFNβ-1b" : {x : 2 * @width / 5, y: 12 * @height / 40},
    "IFNβ-1a" : {x : 3 * @width / 5, y: 12 * @height / 40},
    "Fingolimod" : {x : 31 * @width / 40, y: 12 * @height / 40},
    "Laquinimod" : {x: 9 * @width / 40, y: 17 * @height / 40},
    "BG-12" : {x : 2 * @width / 5, y: 17 * @height / 40},
    "Teriflunomide" : {x : 3 * @width / 5, y: 35 * @height / 80},
    "Natalizumab" : {x : 31 * @width / 40, y: 69 * @height / 160},
    "Alemtuzumab" : {x: 17 * @width / 80, y: 23 * @height / 40},
    "Daclizumab" : {x : 2 * @width / 5, y: 45 * @height / 80},
    "Rituximab" : {x : 3 * @width / 5, y: 46 * @height / 80},
    "Mitoxantrone" : {x : 31 * @width / 40, y: 24 * @height / 40},
    "IVIg" : {x: 15 * @width / 80, y: 114 * @height / 160},
    "IFNA-2a" : {x : 2 * @width / 5, y: 28 * @height / 40},
    "MMF" : {x : 3 * @width / 5, y: 28 * @height / 40},
    "Other" : {x : 31 * @width / 40, y: 29 * @height / 40}
    }
    @funding_centers = {
    "Teva" : {x : @width / 5, y : 13 * @height / 40},
    "BiogenIdec" : {x : 2 * @width / 5, y : 53 * @height / 160},
    "EMDSerono" : {x : 3 * @width / 5, y : 13 * @height / 40},
    "Novartis" : {x : 4 * @width / 5, y : 13 * @height / 40},
    "BayerSchering" : {x : @width / 5, y : 3 * @height / 5},
    "GenzymeSanofi" : {x : 2 * @width / 5, y : 3 * @height / 5},
    "Roche" : {x : 3 * @width / 5, y : 3 * @height / 5},
    "Other" : {x : 4 * @width / 5, y : 25 * @height / 40}
    }
    @pop_centers = {
    "CIS" : {x : 3 * @width / 10, y : @height / 2},
    "RRMS" : {x : 9 * @width / 20, y : @height / 2},
    "SPMS" : {x : 6 * @width / 10, y : @height / 2},
    "PPMS" : {x : 7 * @width / 10, y : @height / 2}
    }
    @nbdoz_centers = {
    "1" : {x : 7 * @width / 24, y : @height / 2},
    "2" : {x : 10 * @width / 24, y : @height / 2},
    "3" : {x : 13 * @width / 24, y : @height / 2},
    "4" : {x : 15 * @width / 24, y : @height / 2},
    "5" : {x : 17 * @width / 24, y : @height / 2}
    }    

    @layout_gravity = -0.01
    @damper = 0.1

    @vis = null
    @nodes = []
    @force = null
    @circles = null

    @fill_color = d3.scale.ordinal()
      .domain(["Positive", "Negative", "No conclusion", "Ongoing", "Equivalence"])
      .range(["#5e93bc", "#ca8546", "#D9D9D9", "#D9D9D9", "#D9D9D9"])

    max_amount = d3.max(@data, (d) -> parseInt(d.N))
    @radius_scale = d3.scale.pow().exponent(0.5).domain([0, max_amount]).range([2, 45])
    
    this.create_nodes()
    this.create_vis()

  create_nodes: () =>
    @data.forEach (d) =>
      node = {
        id: d.Src
        radius: @radius_scale(parseInt(d.N))
        value: d.N
        name: d.Name
        cmpd: d.Cmpd
        outcome: d.Outcome
        phase: d.Phase
        yearcat: d.YearCat
        pop: d.Pop
        funding: d.Funding
        tdur: d.Tdur
        cmpddetails: d.CmpdDetails
        funddetails: d.FundDetails
        nbdoz: d.NbDoz
        year: d.Year
        x: Math.random() * 900
        y: Math.random() * 800
      }
      @nodes.push node

    @nodes.sort (a,b) -> b.value - a.value

  create_vis: () =>
    @vis = d3.select("#vis")
      .append("svg")
      .attr("width", @width)
      .attr("height", @height)
      .attr("id", "svg_vis")

    @circles = @vis.selectAll("circle")
      .data(@nodes, (d) -> d.Src)

    that = this

    @circles.enter().append("circle")
      .attr("r", 0)
      .attr("fill", (d) => @fill_color(d.outcome))
      .attr("stroke-width", 2)
      .attr("stroke", (d) => d3.rgb(@fill_color(d.outcome)).darker())
      .attr("id", (d) -> "bubble_#{d.src}")
      .on("mouseover", (d,i) -> that.show_details(d,i,this))
      .on("mouseout", (d,i) -> that.hide_details(d,i,this))

    @circles.transition().duration(2000).attr("r", (d) -> d.radius)

  charge: (d) ->
    -Math.pow(d.radius, 2.0) / 8

  start: () =>
    @force = d3.layout.force()
      .nodes(@nodes)
      .size([@width, @height])

  display_outcome_all: () =>
    @force.gravity(@layout_gravity)
      .charge(this.charge)
      .friction(0.9)
      .on "tick", (e) =>
        @circles.each(this.move_towards_center(e.alpha))
          .attr("cx", (d) -> d.x)
          .attr("cy", (d) -> d.y)
    @force.start()

    this.display_outcomes()
    this.display_outcomest()
    this.hide_phases()
    this.hide_yearcats()
    this.hide_cmpds()
    this.hide_cmpdst()
    this.hide_fundings()
    this.hide_pops()
    this.hide_nbdozs()
    this.hide_phasest()
    this.hide_yearcatst()
    this.hide_fundingst()
    this.hide_popst()
    this.hide_nbdozst()

  move_towards_center: (alpha) =>
    (d) =>
      d.x = d.x + (@center.x - d.x) * (@damper + 0.02) * alpha
      d.y = d.y + (@center.y - d.y) * (@damper + 0.02) * alpha

  display_outcomes: () =>
    outcomes_x = {"Positive": @width / 2, "Negative": @width / 2, "No conclusion": @width / 2, "Equivalent": @width / 2, "Ongoing": @width / 2 }
    outcomes_y = {"Positive": @height / 2, "Negative":  @height / 2, "No conclusion" : @height / 2, "Equivalent":  @height / 2, "Ongoing":  @height / 2 }    
    outcomes_data = d3.keys(outcomes_x, outcomes_y)
    outcomes = @vis.selectAll(".outcomes")
      .data(outcomes_data)

    outcomes.enter()
    .append("circle")
    .attr("class", "outcomes")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 475)
    .attr("fill", "#5e93bc")

    outcomes.enter()
    .append("circle")
    .attr("class", "outcomes")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 525)
    .attr("fill", "#D9D9D9")
    
    outcomes.enter()
    .append("circle")
    .attr("class", "outcomes")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 500)
    .attr("fill", "#ca8546")

  display_outcomest: () =>
    outcomest_x = {@width}
    outcomest_y = {@height}    
    outcomest_data = d3.keys(outcomest_x, outcomest_y)
    outcomest = @vis.selectAll(".outcomest")
      .data(outcomest_data)

    outcomest.enter()
    .append("text")
    .attr("class", "outcomest")
    .attr("id", "tout")
    .attr("y", 505)
    .attr("x", 75)
    .text( "Negative Outcome")

    outcomest.enter()
    .append("text")
    .attr("class", "outcomest")
    .attr("id", "tout")
    .attr("y", 530)
    .attr("x", 75)
    .text( "No conclusion, Ongoing, Equivalent")

    outcomest.enter()
    .append("text")
    .attr("class", "outcomest")
    .attr("id", "tout")
    .attr("y", 480)
    .attr("x", 75)
    .text( "Positive Outcome")

    outcomest.enter()
    .append("text")
    .attr("class", "outcomest")
    .attr("id", "tout")
    .attr("y", 60)
    .attr("x", 50)
    .text("106 clinical trials in MS including 44606 patients")

    
  hide_outcomest: () =>
    outcomest = @vis.selectAll(".outcomest").remove()

  hide_outcomes: () =>
    outcomes = @vis.selectAll(".outcomes").remove()
    
  display_by_phase: () =>
    @force.gravity(@layout_gravity)
      .charge(this.charge)
      .friction(0.9)
      .on "tick", (e) =>
        @circles.each(this.move_towards_phase(e.alpha))
          .attr("cx", (d) -> d.x)
          .attr("cy", (d) -> d.y)
    @force.start()

    this.display_phases()
    this.display_phasest()
    this.hide_yearcats()
    this.hide_cmpds()
    this.hide_fundings()
    this.hide_pops()
    this.hide_outcomes()
    this.hide_cmpdst()
    this.hide_nbdozs()
    this.hide_outcomest()
    this.hide_yearcatst()
    this.hide_fundingst()
    this.hide_popst()
    this.hide_nbdozst()

  move_towards_phase: (alpha) =>
    (d) =>
      target = @phase_centers[d.phase]
      d.x = d.x + (target.x - d.x) * (@damper + 0.02) * alpha * 1.1
      d.y = d.y + (target.y - d.y) * (@damper + 0.02) * alpha * 1.1

  display_phases: () =>
    phases_x = {"II": 8 * @width / 32, "(N=8612, 58 trials)": 8 * @width / 32, "III": @width / 2, "(N=26067, 32 trials)": @width / 2, "PostMkg": 24 * @width / 32, "(N=9927, 16 trials)": 24 * @width / 32 }
    phases_y = {"II": 2 * @height / 32, "(N=8612, 58 trials)": 3 * @height / 32, "III":  2 * @height / 32, "(N=26067, 32 trials)": 3 * @height / 32, "PostMkg" : 2 * @height / 32, "(N=9927, 16 trials)": 3 * @height / 32 }    
    phases_data = d3.keys(phases_x, phases_y)
    phases = @vis.selectAll(".phases")
      .data(phases_data)

    phases.enter().append("text")
      .attr("class", "phases")
      .attr("x", (d) => phases_x[d] )
      .attr("y", (d) => phases_y[d] )
      .attr("text-anchor", "middle")
      .text((d) -> d)

  display_phasest: () =>
    phasest_x = {@width}
    phasest_y = {@height}    
    phasest_data = d3.keys(phasest_x, phasest_y)
    phasest = @vis.selectAll(".phasest")
      .data(phasest_data)

    phasest.enter()
    .append("text")
    .attr("class", "phasest")
    .attr("id", "tpha")
    .attr("y", 560)
    .attr("x", 0)
    .text( "As expected, the number of reported trials in Phase II (n=58) is larger than the one in Phase III (n=32), and their sample size is smaller.")

    phasest.enter()
    .append("text")
    .attr("class", "phasest")
    .attr("id", "tpha")
    .attr("y", 578)
    .attr("x", 0)
    .text( "The proportion of Phase II trials with negative outcome, 22%, is probably underestimated due to the 'publication bias'.")

    phasest.enter()
    .append("text")
    .attr("class", "phasest")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 65)
    .text( "Positive Outcome")

    phasest.enter()
    .append("circle")
    .attr("class", "phasest")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 515)
    .attr("fill", "#5e93bc")

    phasest.enter()
    .append("text")
    .attr("class", "phasest")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 215)
    .text( "Negative Outcome")

    phasest.enter()
    .append("circle")
    .attr("class", "phasest")
    .attr("r", 10)
    .attr("cx", 200)
    .attr("cy", 515)
    .attr("fill", "#ca8546")

    phasest.enter()
    .append("text")
    .attr("class", "phasest")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 365)
    .text( "No conclusion, Ongoing, Equivalent")

    phasest.enter()
    .append("circle")
    .attr("class", "phasest")
    .attr("r", 10)
    .attr("cx", 350)
    .attr("cy", 515)
    .attr("fill", "#D9D9D9")

  hide_phasest: () =>
    phasest = @vis.selectAll(".phasest").remove()

  hide_phases: () =>
    phases = @vis.selectAll(".phases").remove()

  display_by_yearcat: () =>
    @force.gravity(@layout_gravity)
      .charge(this.charge)
      .friction(0.9)
      .on "tick", (e) =>
        @circles.each(this.move_towards_yearcat(e.alpha))
          .attr("cx", (d) -> d.x)
          .attr("cy", (d) -> d.y)
    @force.start()

    this.display_yearcats()
    this.display_yearcatst()
    this.hide_phases()
    this.hide_cmpds()
    this.hide_cmpdst()
    this.hide_fundings()
    this.hide_pops()
    this.hide_outcomes()
    this.hide_nbdozs()
    this.hide_outcomest()
    this.hide_phasest()
    this.hide_fundingst()
    this.hide_popst()
    this.hide_nbdozst()

  move_towards_yearcat: (alpha) =>
    (d) =>
      target = @yearcat_centers[d.yearcat]
      d.x = d.x + (target.x - d.x) * (@damper + 0.02) * alpha * 1.1
      d.y = d.y + (target.y - d.y) * (@damper + 0.02) * alpha * 1.1

  display_yearcats: () =>
    yearcats_x = {"(1985,2005]":5 * @width / 20, "(N=8513, 34 trials)":5 * @width / 20, "(2005,2010]": 19 * @width / 40, "(N=16710, 39 trials)": 19 * @width / 40, "(2010,2014]": 14 * @width / 20, "(N=19383, 33 trials)": 14 * @width / 20 }
    yearcats_y = {"(1985,2005]": 4 * @height / 32, "(N=8513, 34 trials)": 5 * @height / 32, "(2005,2010]": 4 * @height / 32, "(N=16710, 39 trials)": 5 * @height / 32, "(2010,2014]" : 4 * @height / 32,"(N=19383, 33 trials)": 5 * @height / 32 }  
    yearcats_data = d3.keys(yearcats_x, yearcats_y)
    yearcats = @vis.selectAll(".yearcats")
      .data(yearcats_data)

    yearcats.enter()
    .append("text")
    .attr("class", "yearcats")
    .attr("x", (d) => yearcats_x[d] )
    .attr("y", (d) => yearcats_y[d] )
    .attr("text-anchor", "middle")
    .text((d) -> d)

  display_yearcatst: () =>
    yearcatst_x = {@width}
    yearcatst_y = {@height}   
    yearcatst_data = d3.keys(yearcatst_x, yearcatst_y)
    yearcatst = @vis.selectAll(".yearcatst")
      .data(yearcatst_data)

    yearcatst.enter()
    .append("text")
    .attr("class", "yearcatst")
    .attr("id", "tyea")
    .attr("y", 560)
    .attr("x", 0)
    .text( "'Year' refers to the date of publication of the clinical results.")

    yearcatst.enter()
    .append("text")
    .attr("class", "yearcatst")
    .attr("id", "tyea")
    .attr("y", 578)
    .attr("x", 0)
    .text( "Since the first reported trial in 1987, the number and size of clinical trials in MS have been steadily growing.")

    yearcatst.enter()
    .append("text")
    .attr("class", "yearcatst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 65)
    .text( "Positive Outcome")

    yearcatst.enter()
    .append("circle")
    .attr("class", "yearcatst")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 515)
    .attr("fill", "#5e93bc")

    yearcatst.enter()
    .append("text")
    .attr("class", "yearcatst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 215)
    .text( "Negative Outcome")

    yearcatst.enter()
    .append("circle")
    .attr("class", "yearcatst")
    .attr("r", 10)
    .attr("cx", 200)
    .attr("cy", 515)
    .attr("fill", "#ca8546")

    yearcatst.enter()
    .append("text")
    .attr("class", "yearcatst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 365)
    .text( "No conclusion, Ongoing, Equivalent")

    yearcatst.enter()
    .append("circle")
    .attr("class", "yearcatst")
    .attr("r", 10)
    .attr("cx", 350)
    .attr("cy", 515)
    .attr("fill", "#D9D9D9")

  hide_yearcatst: () =>
    yearcatst = @vis.selectAll(".yearcatst").remove()

  hide_yearcats: () =>
    yearcats = @vis.selectAll(".yearcats").remove()

  display_by_cmpd: () =>
    @force.gravity(@layout_gravity)
      .charge(this.charge)
      .friction(0.9)
      .on "tick", (e) =>
        @circles.each(this.move_towards_cmpd(e.alpha))
          .attr("cx", (d) -> d.x)
          .attr("cy", (d) -> d.y)
    @force.start()

    this.display_cmpds()
    this.display_cmpdst()
    this.hide_yearcats()
    this.hide_phases()
    this.hide_fundings()
    this.hide_pops()
    this.hide_outcomes()
    this.hide_nbdozs()
    this.hide_outcomest()
    this.hide_phasest()
    this.hide_yearcatst()
    this.hide_fundingst()
    this.hide_popst()
    this.hide_nbdozst()

  move_towards_cmpd: (alpha) =>
    (d) =>
      target = @cmpd_centers[d.cmpd]
      d.x = d.x + (target.x - d.x) * (@damper + 0.02) * alpha * 1.1
      d.y = d.y + (target.y - d.y) * (@damper + 0.02) * alpha * 1.1

  display_cmpds: () =>
    cmpds_x = {"GA (N=6318)" : @width / 8, "IFNB-1b (N=5425)" : 3 * @width / 8, "IFNB-1a (N=5130)" : 5 * @width / 8, "Fingolimod (N=5068)" : 7 * @width / 8,"Laquinimod (N=2952)" : @width / 8, "BG-12 (N=2924)" : 3 * @width / 8, "Teriflunomide (N=2878)" : 5 * @width / 8, "Natalizumab (N=2628)" : 7 * @width / 8,"Alemtuzumab (N=1755)" : @width / 8, "Daclizumab (N=854)" : 3 * @width / 8, "Rituximab (N=599)" : 24 * @width / 40, "Mitoxantrone (N=436)" : 34 * @width / 40,"IVIg (N=392)" : 9 * @width / 80, "IFNA-2a (N=147)" : 3 * @width / 8, "MMF (N=89)" : 24 * @width / 40, "Other (N=7011)" : 33 * @width / 40 }

    cmpds_y = {"GA (N=6318)" : 2 * @height / 40, "IFNB-1b (N=5425)" : 2 * @height / 40, "IFNB-1a (N=5130)" : 2 * @height / 40, "Fingolimod (N=5068)" : 2 * @height / 40,"Laquinimod (N=2952)" : 60 * @height / 160, "BG-12 (N=2924)" : 3 * @height / 8, "Teriflunomide (N=2878)" : 3 * @height / 8, "Natalizumab (N=2628)" : 28 * @height / 80,"Alemtuzumab (N=1755)" : 97 * @height / 160, "Daclizumab (N=854)" : 5 * @height / 8, "Rituximab (N=599)" : 99 * @height / 160, "Mitoxantrone (N=436)" : 23 * @height / 40,"IVIg (N=392)" : 63 * @height / 80, "IFNA-2a (N=147)" : 32 * @height / 40, "MMF (N=89)" : 32 * @height / 40, "Other (N=7011)" : 28 * @height / 40 }

    cmpds_data = d3.keys(cmpds_x, cmpds_y)
    cmpds = @vis.selectAll(".cmpds")
      .data(cmpds_data)

    cmpds.enter()
    .append("text")
    .attr("class", "cmpds")
    .attr("x", (d) => cmpds_x[d] )
    .attr("y", (d) => cmpds_y[d] )
    .attr("text-anchor", "middle")
    .text((d) -> d)

  display_cmpdst: () =>
    cmpdst_x = {@width}
    cmpdst_y = {@height}    
    cmpdst_data = d3.keys(cmpdst_x, cmpdst_y)
    cmpdst = @vis.selectAll(".cmpdst")
      .data(cmpdst_data)

    cmpdst.enter()
    .append("text")
    .attr("class", "cmpdst")
    .attr("id", "tout")
    .attr("y", 580)
    .attr("x", 65)
    .text( "Positive Outcome")

    cmpdst.enter()
    .append("circle")
    .attr("class", "cmpdst")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 575)
    .attr("fill", "#5e93bc")

    cmpdst.enter()
    .append("text")
    .attr("class", "cmpdst")
    .attr("id", "tout")
    .attr("y", 580)
    .attr("x", 215)
    .text( "Negative Outcome")

    cmpdst.enter()
    .append("circle")
    .attr("class", "cmpdst")
    .attr("r", 10)
    .attr("cx", 200)
    .attr("cy", 575)
    .attr("fill", "#ca8546")

    cmpdst.enter()
    .append("text")
    .attr("class", "cmpdst")
    .attr("id", "tout")
    .attr("y", 580)
    .attr("x", 365)
    .text( "No conclusion, Ongoing, Equivalent")

    cmpdst.enter()
    .append("circle")
    .attr("class", "cmpdst")
    .attr("r", 10)
    .attr("cx", 350)
    .attr("cy", 575)
    .attr("fill", "#D9D9D9")
 
  hide_cmpdst: () =>
    cmpdst = @vis.selectAll(".cmpdst").remove()

  hide_cmpds: () =>
    cmpds = @vis.selectAll(".cmpds").remove()

  display_by_funding: () =>
    @force.gravity(@layout_gravity)
      .charge(this.charge)
      .friction(0.9)
      .on "tick", (e) =>
        @circles.each(this.move_towards_funding(e.alpha))
          .attr("cx", (d) -> d.x)
          .attr("cy", (d) -> d.y)
    @force.start()

    this.display_fundings()
    this.display_fundingst()
    this.hide_yearcats()
    this.hide_phases()
    this.hide_cmpds()
    this.hide_cmpdst()
    this.hide_pops()
    this.hide_outcomes()
    this.hide_nbdozs()
    this.hide_outcomest()
    this.hide_phasest()
    this.hide_yearcatst()
    this.hide_popst()
    this.hide_nbdozst()

  move_towards_funding: (alpha) =>
    (d) =>
      target = @funding_centers[d.funding]
      d.x = d.x + (target.x - d.x) * (@damper + 0.02) * alpha * 1.1
      d.y = d.y + (target.y - d.y) * (@damper + 0.02) * alpha * 1.1

  display_fundings: () =>
    fundings_x = {"Teva": 7 * @width / 64, "(N=9310, 16 trials)": 7 * @width / 64, "BiogenIdec": 25 * @width / 64, "(N=8535, 21 trials)": 25 * @width / 64, "EMDSerono": 41 * @width / 64, "(N=5568, 12 trials)": 41 * @width / 64, "Novartis": 57 * @width / 64, "(N=5438, 8 trials)": 57 * @width / 64, "BayerSchering": @width / 8, "(N=5334, 13 trials)": @width / 8, "GenzymeSanofi": 25 * @width / 64, "(N=4633, 8 trials)": 25 * @width / 64, "Roche": 81 * @width / 128, "(N=535, 5 trials)": 81 * @width / 128, "Other": 7 * @width / 8, "(N=5253, 23 trials)": 7 * @width / 8 }
    fundings_y = {"Teva": @height / 36, "(N=9310, 16 trials)": @height / 18, "BiogenIdec": @height / 36, "(N=8535, 21 trials)": @height / 18, "EMDSerono": @height / 36, "(N=5568, 12 trials)": @height / 18, "Novartis": @height / 36, "(N=5438, 8 trials)": @height / 18, "BayerSchering": 19 * @height / 36, "(N=5334, 13 trials)": 20 * @height / 36, "GenzymeSanofi": 19 * @height / 36, "(N=4633, 8 trials)": 20 * @height / 36, "Roche": 19 * @height / 36, "(N=535, 5 trials)": 20 * @height / 36, "Other": 19 * @height / 36, "(N=5253, 23 trials)": 20 * @height / 36 }    
    fundings_data = d3.keys(fundings_x, fundings_y)
    fundings = @vis.selectAll(".fundings")
      .data(fundings_data)

    fundings.enter()
    .append("text")
    .attr("class", "fundings")
    .attr("x", (d) => fundings_x[d] )
    .attr("y", (d) => fundings_y[d] )
    .attr("text-anchor", "middle")
    .text((d) -> d)

  display_fundingst: () =>
    fundingst_x = {@width}
    fundingst_y = {@height}    
    fundingst_data = d3.keys(fundingst_x, fundingst_y)
    fundingst = @vis.selectAll(".fundingst")
      .data(fundingst_data)

    fundingst.enter()
    .append("text")
    .attr("class", "fundingst")
    .attr("id", "tfun")
    .attr("y", 560)
    .attr("x", 0)
    .text( "The most active pharmaceutical companies in MS are Teva, Biogen-Idec and EMD-Serono;")

    fundingst.enter()
    .append("text")
    .attr("class", "fundingst")
    .attr("id", "tfun")
    .attr("y", 578)
    .attr("x", 0)
    .text( "none of these are among the top 10 largest pharma companies in the world.")

    fundingst.enter()
    .append("text")
    .attr("class", "fundingst")
    .attr("id", "tout")
    .attr("y", 530)
    .attr("x", 65)
    .text( "Positive Outcome")

    fundingst.enter()
    .append("circle")
    .attr("class", "fundingst")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 525)
    .attr("fill", "#5e93bc")

    fundingst.enter()
    .append("text")
    .attr("class", "fundingst")
    .attr("id", "tout")
    .attr("y", 530)
    .attr("x", 215)
    .text( "Negative Outcome")

    fundingst.enter()
    .append("circle")
    .attr("class", "fundingst")
    .attr("r", 10)
    .attr("cx", 200)
    .attr("cy", 525)
    .attr("fill", "#ca8546")

    fundingst.enter()
    .append("text")
    .attr("class", "fundingst")
    .attr("id", "tout")
    .attr("y", 530)
    .attr("x", 365)
    .text( "No conclusion, Ongoing, Equivalent")

    fundingst.enter()
    .append("circle")
    .attr("class", "fundingst")
    .attr("r", 10)
    .attr("cx", 350)
    .attr("cy", 525)
    .attr("fill", "#D9D9D9")

  hide_fundingst: () =>
    fundingst = @vis.selectAll(".fundingst").remove()

  hide_fundings: () =>
    fundings = @vis.selectAll(".fundings").remove()

  display_by_pop: () =>
    @force.gravity(@layout_gravity)
      .charge(this.charge)
      .friction(0.9)
      .on "tick", (e) =>
        @circles.each(this.move_towards_pop(e.alpha))
          .attr("cx", (d) -> d.x)
          .attr("cy", (d) -> d.y)
    @force.start()

    this.display_pops()
    this.display_popst()
    this.hide_fundings()
    this.hide_yearcats()
    this.hide_phases()
    this.hide_cmpds()
    this.hide_cmpdst()
    this.hide_outcomes()
    this.hide_nbdozs()
    this.hide_outcomest()
    this.hide_phasest()
    this.hide_yearcatst()
    this.hide_fundingst()
    this.hide_nbdozst()

  move_towards_pop: (alpha) =>
    (d) =>
      target = @pop_centers[d.pop]
      d.x = d.x + (target.x - d.x) * (@damper + 0.02) * alpha * 1.1
      d.y = d.y + (target.y - d.y) * (@damper + 0.02) * alpha * 1.1

  display_pops: () =>
    pops_x = {"CIS": 5 * @width / 32, "(N=1849, 4 trials)": 5 * @width / 32, "RRMS": 7 * @width / 16, "(N=37852, 93 trials)": 7 * @width / 16, "SPMS": 28 * @width / 40, "(N=2469, 4 trials)": 28 * @width / 40, "PPMS": 36 * @width / 40, "(N=2436, 5 trials)": 36 * @width / 40 }
    pops_y = {"CIS": 3 * @height / 32, "(N=1849, 4 trials)": 4 * @height / 32, "RRMS": 3 * @height / 32, "(N=37852, 93 trials)": 4 * @height / 32, "SPMS": 3 * @height / 32, "(N=2469, 4 trials)": 4 * @height / 32, "PPMS": 3 * @height / 32, "(N=2436, 5 trials)": 4 * @height / 32 }    
    pops_data = d3.keys(pops_x, pops_y)
    pops = @vis.selectAll(".pops")
      .data(pops_data)

    pops.enter()
    .append("text")
    .attr("class", "pops")
    .attr("x", (d) => pops_x[d] )
    .attr("y", (d) => pops_y[d] )
    .attr("text-anchor", "middle")
    .text((d) -> d)

  display_popst: () =>
    popst_x = {@width}
    popst_y = {@height}    
    popst_data = d3.keys(popst_x, popst_y)
    popst = @vis.selectAll(".popst")
      .data(popst_data)

    popst.enter()
    .append("text")
    .attr("class", "popst")
    .attr("id", "tpop")
    .attr("y", 560)
    .attr("x", 0)
    .text( "About 85% of all initial MS diagnoses are RRMS; hence the large proportion of trials in this population.")

    popst.enter()
    .append("text")
    .attr("class", "popst")
    .attr("id", "tpop")
    .attr("y", 578)
    .attr("x", 0)
    .text( "Few trials have also been run in early form (CIS) or, at the opposite, in more severe forms of MS (PPMS, SPMS).")

    popst.enter()
    .append("text")
    .attr("class", "popst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 65)
    .text( "Positive Outcome")

    popst.enter()
    .append("circle")
    .attr("class", "popst")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 515)
    .attr("fill", "#5e93bc")

    popst.enter()
    .append("text")
    .attr("class", "popst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 215)
    .text( "Negative Outcome")

    popst.enter()
    .append("circle")
    .attr("class", "popst")
    .attr("r", 10)
    .attr("cx", 200)
    .attr("cy", 515)
    .attr("fill", "#ca8546")

    popst.enter()
    .append("text")
    .attr("class", "popst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 365)
    .text( "No conclusion, Ongoing, Equivalent")

    popst.enter()
    .append("circle")
    .attr("class", "popst")
    .attr("r", 10)
    .attr("cx", 350)
    .attr("cy", 515)
    .attr("fill", "#D9D9D9")

  hide_popst: () =>
    popst = @vis.selectAll(".popst").remove()

  hide_pops: () =>
    pops = @vis.selectAll(".pops").remove()

  display_by_nbdoz: () =>
    @force.gravity(@layout_gravity)
      .charge(this.charge)
      .friction(0.9)
      .on "tick", (e) =>
        @circles.each(this.move_towards_nbdoz(e.alpha))
          .attr("cx", (d) -> d.x)
          .attr("cy", (d) -> d.y)
    @force.start()

    this.display_nbdozs()
    this.display_nbdozst()
    this.hide_yearcats()
    this.hide_cmpds()
    this.hide_cmpdst()
    this.hide_fundings()
    this.hide_pops()
    this.hide_outcomes()
    this.hide_phases()
    this.hide_outcomest()
    this.hide_phasest()
    this.hide_yearcatst()
    this.hide_fundingst()
    this.hide_popst()

  move_towards_nbdoz: (alpha) =>
    (d) =>
      target = @nbdoz_centers[d.nbdoz]
      d.x = d.x + (target.x - d.x) * (@damper + 0.02) * alpha * 1.1
      d.y = d.y + (target.y - d.y) * (@damper + 0.02) * alpha * 1.1

  display_nbdozs: () =>
    nbdozs_x = {"1 Dose Level": 5 * @width / 24,"(N=16154, 52 trials)": 5 * @width / 24, "2 Dose Levels": 9 * @width / 20, "(N=25773, 45 trials)": 9 * @width / 20, "3 Dose Levels": 31 * @width / 48, "(N=1760, 5 trials)": 31 * @width / 48, "4 Dose Levels": 37 * @width / 48, "(N=622, 3 trials)": 37 * @width / 48, "5 Dose Levels": 85 * @width /96, "(N=297, 1 trial)": 85 * @width /96 }
    nbdozs_y = {"1 Dose Level": 4 * @height / 32, "(N=16154, 52 trials)": 5 * @height / 32, "2 Dose Levels": 4 * @height / 32, "(N=25773, 45 trials)": 5 * @height / 32, "3 Dose Levels" : 4 * @height / 32, "(N=1760, 5 trials)": 5 * @height / 32, "4 Dose Levels" : 4 * @height / 32, "(N=622, 3 trials)": 5 * @height / 32, "5 Dose Levels" : 4 * @height / 32, "(N=297, 1 trial)": 5 * @height / 32 }    
    nbdozs_data = d3.keys(nbdozs_x, nbdozs_y)
    nbdozs = @vis.selectAll(".nbdozs")
      .data(nbdozs_data)

    nbdozs.enter().append("text")
    .attr("class", "nbdozs")
    .attr("x", (d) => nbdozs_x[d] )
    .attr("y", (d) => nbdozs_y[d] )
    .attr("text-anchor", "middle")
    .text((d) -> d)

  display_nbdozst: () =>
    nbdozst_x = {@width}
    nbdozst_y = {@height}    
    nbdozst_data = d3.keys(nbdozst_x, nbdozst_y)
    nbdozst = @vis.selectAll(".nbdozst")
      .data(nbdozst_data)

    nbdozst.enter()
    .append("text")
    .attr("class", "nbdozst")
    .attr("id", "tnbd")
    .attr("y", 550)
    .attr("x", 0)
    .text( "A medication is, before anything, a 'correct' dose for an active ingredient, i.e. a dose providing a relevant therapeutical benefit and limited side-effects.")

    nbdozst.enter()
    .append("text")
    .attr("class", "nbdozst")
    .attr("id", "tnbd")
    .attr("y", 568)
    .attr("x", 0)
    .text( "It is critical to test various dose levels (at least 3 ideally), usually in Phase II to identify such a 'correct' dose level.")

    nbdozst.enter()
    .append("text")
    .attr("class", "nbdozst")
    .attr("id", "tnbd")
    .attr("y", 586)
    .attr("x", 0)
    .text( "In MS, rare are the trials which have investigated more than 2 dose levels.")

    nbdozst.enter()
    .append("text")
    .attr("class", "nbdozst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 65)
    .text( "Positive Outcome")

    nbdozst.enter()
    .append("circle")
    .attr("class", "nbdozst")
    .attr("r", 10)
    .attr("cx", 50)
    .attr("cy", 515)
    .attr("fill", "#5e93bc")

    nbdozst.enter()
    .append("text")
    .attr("class", "nbdozst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 215)
    .text( "Negative Outcome")

    nbdozst.enter()
    .append("circle")
    .attr("class", "nbdozst")
    .attr("r", 10)
    .attr("cx", 200)
    .attr("cy", 515)
    .attr("fill", "#ca8546")

    nbdozst.enter()
    .append("text")
    .attr("class", "nbdozst")
    .attr("id", "tout")
    .attr("y", 520)
    .attr("x", 365)
    .text( "No conclusion, Ongoing, Equivalent")

    nbdozst.enter()
    .append("circle")
    .attr("class", "nbdozst")
    .attr("r", 10)
    .attr("cx", 350)
    .attr("cy", 515)
    .attr("fill", "#D9D9D9")

  hide_nbdozst: () =>
    nbdozst = @vis.selectAll(".nbdozst").remove()

  hide_nbdozs: () =>
    nbdozs = @vis.selectAll(".nbdozs").remove()
  


  show_details: (data, i, element) =>
    d3.select(element).attr("stroke", "black")
    content = "<span class=\"name\">Trial:</span><span class=\"value\"> #{data.name}</span><br/>"
    content +="<span class=\"name\">Compound:</span><span class=\"value\"> #{data.cmpddetails}</span><br/>"
    content +="<span class=\"name\">Phase:</span><span class=\"value\"> #{data.phase}</span>
      <span class=\"name\"> (N=</span><span class=\"value\"> #{data.value}</span>)<br/>"    
    content +="<span class=\"name\">Population:</span><span class=\"value\"> #{data.pop}</span><br/>"
    content +="<span class=\"name\">Number of Dose:</span><span class=\"value\"> #{data.nbdoz}</span><br/>"
    content +="<span class=\"name\">Trial Duration (y):</span><span class=\"value\"> #{data.tdur}</span><br/>"
    content +="<span class=\"name\">Year:</span><span class=\"value\"> #{data.year}</span><br/>"
    content +="<span class=\"name\">Funding:</span><span class=\"value\"> #{data.funddetails}</span><br/>"
    @tooltip.showTooltip(content,d3.event)


  hide_details: (data, i, element) =>
    d3.select(element).attr("stroke", (d) => d3.rgb(@fill_color(d.outcome)).darker())
    @tooltip.hideTooltip()


root = exports ? this

$ ->
  chart = null

  render_vis = (csv) ->
    chart = new BubbleChart csv
    chart.start()
    root.display_all()
  root.display_all = () =>
    chart.display_outcome_all()
  root.display_phase = () =>
    chart.display_by_phase()
  root.display_yearcat = () =>
    chart.display_by_yearcat()
  root.display_cmpd = () =>
    chart.display_by_cmpd()
  root.display_funding = () =>
    chart.display_by_funding()
  root.display_pop = () =>
    chart.display_by_pop()
  root.display_nbdoz = () =>
    chart.display_by_nbdoz()
  root.toggle_view = (view_type) =>
   if view_type == 'phase'
      root.display_phase()
   else if view_type == 'yearcat'
      root.display_yearcat()
   else if view_type == 'cmpd'
      root.display_cmpd()
   else if view_type == 'funding'
      root.display_funding()
   else if view_type == 'pop'
      root.display_pop()
   else if view_type == 'nbdoz'
      root.display_nbdoz()
    else
      root.display_all()

  d3.csv "/sites/all/themes/msdf/MStrials/MStrials2014.csv", render_vis