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1 import sys
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2 def readTab(infile): # read in txt file
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3 with open(infile, 'r') as input_file:
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4 # read in tab-delim text
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5 output = []
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6 for input_line in input_file:
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7 input_line = input_line.strip()
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8 temp = input_line.split('\t')
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9 output.append(temp)
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10 return output
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11 def network2JSON(nodes_att_file, edge_file):
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12 nodes = readTab(nodes_att_file)
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13 edges = readTab(edge_file)
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14
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15 start = """{"nodes": ["""
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16 node_numbers = {}
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17 cnt=0
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18 for i in nodes[1:]:
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19 node_numbers[i[0]] = cnt
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20 cnt+=1
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21 start = start + '{"id":'+'"'+i[0]+'", "size":'+str(float(i[2])*1)+', "score":'+i[1]+',"type":"circle"},'
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22 start = start[:-1]
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23 start = start+"""], "links": ["""
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24 for i in edges:
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25 start = start + """{"source":"""+str(node_numbers[i[0]])+""","target":"""+str(node_numbers[i[1]])+"""},"""
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26 start = start[:-1]
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27 start = start + """]}"""
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28 return start
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29
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30
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31 output = """<!DOCTYPE html>
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32 <meta charset="utf-8">
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33 <style>
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34 body {
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35 overflow:hidden;
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36 margin:0;
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37 }
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38
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39 text {
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40 font-family: sans-serif;
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41 pointer-events: none;
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42 }
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43
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44 </style>
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45 <body>
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46 <script src="http://d3js.org/d3.v3.min.js"></script>
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47 <script>
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48 jsondata='"""
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49
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50 output = output + network2JSON(sys.argv[1],sys.argv[2]) + "'\n"
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51
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52 output = output + """var w = window.innerWidth;
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53 var h = window.innerHeight;
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54
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55 var keyc = true, keys = true, keyt = true, keyr = true, keyx = true, keyd = true, keyl = true, keym = true, keyh = true, key1 = true, key2 = true, key3 = true, key0 = true
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56
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57 var focus_node = null, highlight_node = null;
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58
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59 var text_center = false;
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60 var outline = false;
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61
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62 var min_score = 0;
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63 var max_score = 1;
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64
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65 var color = d3.scale.category20()
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66 .range(["green", "orange", "red","black","steelblue","purple","gray","blue","yellow","lime"]);
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67
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68 var highlight_color = "red";
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69 var highlight_trans = 0.1;
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70
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71 var size = d3.scale.pow().exponent(1)
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72 .domain([1,100])
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73 .range([8,24]);
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74
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75 var force = d3.layout.force()
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76 .linkDistance(60)
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77 .charge(-500)
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78 .size([w,h]);
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79
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80 var default_node_color = "#000";
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81 //var default_node_color = "rgb(3,190,100)";
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82 var default_link_color = "#888";
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83 var nominal_base_node_size = 8;
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84 var nominal_text_size = 10;
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85 var max_text_size = 24;
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86 var nominal_stroke = 1.5;
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87 var max_stroke = 4.5;
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88 var max_base_node_size = 36;
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89 var min_zoom = 0.1;
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90 var max_zoom = 7;
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91 var svg = d3.select("body").append("svg");
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92 var zoom = d3.behavior.zoom().scaleExtent([min_zoom,max_zoom])
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93 var g = svg.append("g");
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94 svg.style("cursor","move");
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95
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96 var data = JSON.parse(jsondata);
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97 function plot_graph(graph) {
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98
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99 var linkedByIndex = {};
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100 graph.links.forEach(function(d) {
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101 linkedByIndex[d.source + "," + d.target] = true;
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102 });
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103
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104 function isConnected(a, b) {
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105 return linkedByIndex[a.index + "," + b.index] || linkedByIndex[b.index + "," + a.index] || a.index == b.index;
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106 }
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107
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108 function hasConnections(a) {
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109 for (var property in linkedByIndex) {
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110 s = property.split(",");
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111 if ((s[0] == a.index || s[1] == a.index) && linkedByIndex[property]) return true;
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112 }
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113 return false;
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114 }
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115
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116 force
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117 .nodes(graph.nodes)
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118 .links(graph.links)
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119 .start();
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120
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121 var link = g.selectAll(".link")
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122 .data(graph.links)
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123 .enter().append("line")
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124 .attr("class", "link")
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125 .style("stroke-width",nominal_stroke)
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126 .style("stroke", function(d) {
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127 if (isNumber(d.score) && d.score>=0) return color(d.score);
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128 else return default_link_color; })
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129
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130
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131 var node = g.selectAll(".node")
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132 .data(graph.nodes)
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133 .enter().append("g")
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134 .attr("class", "node")
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135
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136 .call(force.drag)
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137
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138
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139 node.on("dblclick.zoom", function(d) { d3.event.stopPropagation();
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140 var dcx = (window.innerWidth/2-d.x*zoom.scale());
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141 var dcy = (window.innerHeight/2-d.y*zoom.scale());
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142 zoom.translate([dcx,dcy]);
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143 g.attr("transform", "translate("+ dcx + "," + dcy + ")scale(" + zoom.scale() + ")");
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144
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145
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146 });
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147
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148
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149
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150
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151 var tocolor = "fill";
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152 var towhite = "stroke";
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153 if (outline) {
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154 tocolor = "stroke"
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155 towhite = "fill"
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156 }
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157
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158
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159
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160 var circle = node.append("path")
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161
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162
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163 .attr("d", d3.svg.symbol()
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164 .size(function(d) { return Math.PI*Math.pow(size(d.size)||nominal_base_node_size,2); })
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165 .type(function(d) { return d.type; }))
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166
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167 .style(tocolor, function(d) {
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168 if (isNumber(d.score) && d.score>=0) return color(d.score);
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169 else return default_node_color; })
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170 //.attr("r", function(d) { return size(d.size)||nominal_base_node_size; })
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171 .style("stroke-width", nominal_stroke)
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172 .style(towhite, "white");
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173
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174
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175 var text = g.selectAll(".text")
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176 .data(graph.nodes)
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177 .enter().append("text")
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178 .attr("dy", ".35em")
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179 .style("font-size", nominal_text_size + "px")
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180
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181 if (text_center)
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182 text.text(function(d) { return d.id; })
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183 .style("text-anchor", "middle");
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184 else
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185 text.attr("dx", function(d) {return (size(d.size)||nominal_base_node_size);})
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186 .text(function(d) { return '\u2002'+d.id; });
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187
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188 node.on("mouseover", function(d) {
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189 set_highlight(d);
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190 })
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191 .on("mousedown", function(d) { d3.event.stopPropagation();
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192 focus_node = d;
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193 set_focus(d)
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194 if (highlight_node === null) set_highlight(d)
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195
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196 } ).on("mouseout", function(d) {
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197 exit_highlight();
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198
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199 } );
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200
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201 d3.select(window).on("mouseup",
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202 function() {
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203 if (focus_node!==null)
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204 {
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205 focus_node = null;
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206 if (highlight_trans<1)
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207 {
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208
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209 circle.style("opacity", 1);
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210 text.style("opacity", 1);
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211 link.style("opacity", 1);
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212 }
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213 }
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214
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215 if (highlight_node === null) exit_highlight();
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216 });
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217
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218 function exit_highlight()
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219 {
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220 highlight_node = null;
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221 if (focus_node===null)
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222 {
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223 svg.style("cursor","move");
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224 if (highlight_color!="white")
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225 {
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226 circle.style(towhite, "white");
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227 text.style("font-weight", "normal");
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228 link.style("stroke", function(o) {return (isNumber(o.score) && o.score>=0)?color(o.score):default_link_color});
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229 }
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230
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231 }
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232 }
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233
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234 function set_focus(d)
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235 {
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236 if (highlight_trans<1) {
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237 circle.style("opacity", function(o) {
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238 return isConnected(d, o) ? 1 : highlight_trans;
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239 });
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240
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241 text.style("opacity", function(o) {
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242 return isConnected(d, o) ? 1 : highlight_trans;
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243 });
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244
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245 link.style("opacity", function(o) {
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246 return o.source.index == d.index || o.target.index == d.index ? 1 : highlight_trans;
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247 });
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248 }
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249 }
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250
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251
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252 function set_highlight(d)
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253 {
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254 svg.style("cursor","pointer");
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255 if (focus_node!==null) d = focus_node;
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256 highlight_node = d;
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257
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258 if (highlight_color!="white")
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259 {
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260 circle.style(towhite, function(o) {
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261 return isConnected(d, o) ? highlight_color : "white";});
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262 text.style("font-weight", function(o) {
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263 return isConnected(d, o) ? "bold" : "normal";});
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264 link.style("stroke", function(o) {
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265 return o.source.index == d.index || o.target.index == d.index ? highlight_color : ((isNumber(o.score) && o.score>=0)?color(o.score):default_link_color);
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266
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267 });
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268 }
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269 }
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270
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271
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272 zoom.on("zoom", function() {
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273
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274 var stroke = nominal_stroke;
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275 if (nominal_stroke*zoom.scale()>max_stroke) stroke = max_stroke/zoom.scale();
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276 link.style("stroke-width",stroke);
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277 circle.style("stroke-width",stroke);
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278
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279 var base_radius = nominal_base_node_size;
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280 if (nominal_base_node_size*zoom.scale()>max_base_node_size) base_radius = max_base_node_size/zoom.scale();
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281 circle.attr("d", d3.svg.symbol()
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282 .size(function(d) { return Math.PI*Math.pow(size(d.size)*base_radius/nominal_base_node_size||base_radius,2); })
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283 .type(function(d) { return d.type; }))
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284
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285 //circle.attr("r", function(d) { return (size(d.size)*base_radius/nominal_base_node_size||base_radius); })
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286 if (!text_center) text.attr("dx", function(d) { return (size(d.size)*base_radius/nominal_base_node_size||base_radius); });
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287
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288 var text_size = nominal_text_size;
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289 if (nominal_text_size*zoom.scale()>max_text_size) text_size = max_text_size/zoom.scale();
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290 text.style("font-size",text_size + "px");
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291
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292 g.attr("transform", "translate(" + d3.event.translate + ")scale(" + d3.event.scale + ")");
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293 });
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294
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295 svg.call(zoom);
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296
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297 resize();
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298 //window.focus();
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299 d3.select(window).on("resize", resize).on("keydown", keydown);
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300
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301 force.on("tick", function() {
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302
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303 node.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
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304 text.attr("transform", function(d) { return "translate(" + d.x + "," + d.y + ")"; });
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305
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306 link.attr("x1", function(d) { return d.source.x; })
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307 .attr("y1", function(d) { return d.source.y; })
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308 .attr("x2", function(d) { return d.target.x; })
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309 .attr("y2", function(d) { return d.target.y; });
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310
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311 node.attr("cx", function(d) { return d.x; })
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312 .attr("cy", function(d) { return d.y; });
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313 });
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314
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315 function resize() {
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316 var width = window.innerWidth, height = window.innerHeight;
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317 svg.attr("width", width).attr("height", height);
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318
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319 force.size([force.size()[0]+(width-w)/zoom.scale(),force.size()[1]+(height-h)/zoom.scale()]).resume();
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320 w = width;
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321 h = height;
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322 }
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323
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324 function keydown() {
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325 if (d3.event.keyCode==32) { force.stop();}
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326 else if (d3.event.keyCode>=48 && d3.event.keyCode<=90 && !d3.event.ctrlKey && !d3.event.altKey && !d3.event.metaKey)
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327 {
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328 switch (String.fromCharCode(d3.event.keyCode)) {
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329 case "C": keyc = !keyc; break;
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330 case "S": keys = !keys; break;
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331 case "T": keyt = !keyt; break;
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332 case "R": keyr = !keyr; break;
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333 case "X": keyx = !keyx; break;
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334 case "D": keyd = !keyd; break;
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335 case "L": keyl = !keyl; break;
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336 case "M": keym = !keym; break;
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337 case "H": keyh = !keyh; break;
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338 case "1": key1 = !key1; break;
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339 case "2": key2 = !key2; break;
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340 case "3": key3 = !key3; break;
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341 case "0": key0 = !key0; break;
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342 }
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343
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344 link.style("display", function(d) {
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345 var flag = vis_by_type(d.source.type)&&vis_by_type(d.target.type)&&vis_by_node_score(d.source.score)&&vis_by_node_score(d.target.score)&&vis_by_link_score(d.score);
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346 linkedByIndex[d.source.index + "," + d.target.index] = flag;
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347 return flag?"inline":"none";});
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348 node.style("display", function(d) {
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349 return (key0||hasConnections(d))&&vis_by_type(d.type)&&vis_by_node_score(d.score)?"inline":"none";});
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350 text.style("display", function(d) {
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351 return (key0||hasConnections(d))&&vis_by_type(d.type)&&vis_by_node_score(d.score)?"inline":"none";});
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352
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353 if (highlight_node !== null)
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354 {
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355 if ((key0||hasConnections(highlight_node))&&vis_by_type(highlight_node.type)&&vis_by_node_score(highlight_node.score)) {
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356 if (focus_node!==null) set_focus(focus_node);
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357 set_highlight(highlight_node);
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358 }
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359 else {exit_highlight();}
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360 }
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361
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362 }
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363 }
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364
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365 };
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366
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367 function vis_by_type(type)
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368 {
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369 switch (type) {
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370 case "circle": return keyc;
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371 case "circle": return keys;
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372 case "triangle-up": return keyt;
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373 case "diamond": return keyr;
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374 case "cross": return keyx;
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375 case "triangle-down": return keyd;
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376 default: return true;
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377 }
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378 }
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379 function vis_by_node_score(score)
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380 {
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381 if (isNumber(score))
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382 {
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383 if (score>=0.666) return keyh;
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384 else if (score>=0.333) return keym;
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385 else if (score>=0) return keyl;
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386 }
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387 return true;
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388 }
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389
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390 function vis_by_link_score(score)
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391 {
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392 if (isNumber(score))
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393 {
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394 if (score>=0.666) return key3;
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395 else if (score>=0.333) return key2;
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396 else if (score>=0) return key1;
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397 }
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398 return true;
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399 }
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400
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401 function isNumber(n) {
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402 return !isNaN(parseFloat(n)) && isFinite(n);
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403 }
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404 plot_graph(data)
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405
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406 </script>"""
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407
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408 with open(sys.argv[3],"w") as x:
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409 x.write(output)
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