1 | # Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
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2 | # Supports files generated by Framsticks experiments.
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3 |
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4 | import json
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5 | import random
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6 | import math
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7 | import argparse
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8 |
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9 | TIME = "" # BIRTHS / GENERATIONAL / REAL
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10 | BALANCE = "" # MIN / DENSITY
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11 |
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12 | DOT_STYLE = "" # NONE / NORMAL / CLEAR
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13 |
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14 | JITTER = "" #
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15 |
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16 | # ------SVG---------
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17 | svg_file = 0
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18 |
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19 | svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.7"'
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20 | svg_mutation_line_style = 'stroke-width="1"'
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21 | svg_crossover_line_style = 'stroke-width="1"'
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22 | svg_spine_line_style = 'stroke="rgb(0%,90%,40%)" stroke-width="2" stroke-opacity="1"'
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23 | svg_scale_line_style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
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24 |
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25 | svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
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26 | svg_clear_dot_style = 'r="2" stroke="black" stroke-width="0.4" fill="none"'
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27 | svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
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28 |
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29 | svg_scale_text_style = 'style="font-family: Arial; font-size: 12; fill: #000000;"'
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30 |
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31 | def hex_to_style(hex):
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32 | default_style = ' stroke="black" stroke-opacity="0.5" '
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33 |
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34 | if hex[0] == "#":
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35 | hex = hex[1:]
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36 |
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37 | if len(hex) == 6 or len(hex) == 8:
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38 | try:
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39 | int(hex, 16)
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40 | except:
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41 | print("Invalid characters in the color's hex #" + hex + "! Assuming black.")
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42 | return default_style
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43 | red = 100*int(hex[0:2], 16)/255
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44 | green = 100*int(hex[2:4], 16)/255
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45 | blue = 100*int(hex[4:6], 16)/255
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46 | opacity = 0.5
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47 | if len(hex) == 8:
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48 | opacity = int(hex[6:8], 16)/255
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49 | return ' stroke="rgb(' +str(red)+ '%,' +str(green)+ '%,' +str(blue)+ '%)" stroke-opacity="' +str(opacity)+ '" '
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50 | else:
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51 | print("Invalid number of digits in the color's hex #" + hex + "! Assuming black.")
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52 | return default_style
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53 |
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54 | def svg_add_line(from_pos, to_pos, style=svg_line_style):
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55 | svg_file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) +
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56 | '" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" fill="none"/>')
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57 |
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58 | def svg_add_text(text, pos, anchor, style=svg_scale_text_style):
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59 | svg_file.write('<text ' + style + ' text-anchor="' + anchor + '" x="' + str(pos[0]) + '" y="' + str(pos[1]) + '" >' + text + '</text>')
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60 |
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61 | def svg_add_dot(pos, style=svg_dot_style):
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62 | svg_file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
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63 |
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64 | def svg_generate_line_style(percent):
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65 | # hotdog
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66 | from_col = [100, 70, 0]
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67 | to_col = [60, 0, 0]
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68 | # lava
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69 | # from_col = [100, 80, 0]
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70 | # to_col = [100, 0, 0]
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71 | # neon
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72 | # from_col = [30, 200, 255]
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73 | # to_col = [240, 0, 220]
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74 |
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75 | from_opa = 0.2
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76 | to_opa = 1.0
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77 | from_stroke = 1
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78 | to_stroke = 3
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79 |
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80 | opa = from_opa*(1-percent) + to_opa*percent
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81 | stroke = from_stroke*(1-percent) + to_stroke*percent
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82 |
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83 | percent = 1 - ((1-percent)**20)
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84 |
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85 | return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
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86 | + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
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87 | + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="' + str(stroke) + '" stroke-opacity="' + str(opa) + '"'
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88 |
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89 | def svg_generate_dot_style(kind):
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90 | kinds = ["red", "lawngreen", "royalblue", "magenta", "yellow", "cyan", "white", "black"]
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91 |
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92 | r = min(2500/len(nodes), 10)
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93 |
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94 | return 'fill="' + kinds[kind] + '" r="' + str(r) + '" stroke="black" stroke-width="' + str(r/10) + '" fill-opacity="1.0" ' \
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95 | 'stroke-opacity="1.0"'
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96 |
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97 | # -------------------
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98 |
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99 | def load_data(dir):
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100 | global firstnode, nodes, inv_nodes, time
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101 | f = open(dir)
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102 | for line in f:
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103 | sline = line.split(' ', 1)
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104 | if len(sline) == 2:
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105 | if sline[0] == "[OFFSPRING]":
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106 | creature = json.loads(sline[1])
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107 | #print("B" +str(creature))
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108 | if "FromIDs" in creature:
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109 | if not creature["ID"] in nodes:
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110 | nodes[creature["ID"]] = {}
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111 | # we assign to each parent its contribution to the genotype of the child
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112 | for i in range(0, len(creature["FromIDs"])):
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113 | inherited = 1 #(creature["Inherited"][i] if 'Inherited' in creature else 1) #ONLY FOR NOW
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114 | nodes[creature["ID"]][creature["FromIDs"][i]] = inherited
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115 | else:
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116 | print("Duplicated entry for " + creature["ID"])
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117 | quit()
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118 |
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119 | if not creature["FromIDs"][0] in nodes:
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120 | firstnode = creature["FromIDs"][0]
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121 |
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122 | if "Time" in creature:
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123 | time[creature["ID"]] = creature["Time"]
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124 |
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125 | if "Kind" in creature:
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126 | kind[creature["ID"]] = creature["Kind"]
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127 |
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128 | for k, v in sorted(nodes.items()):
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129 | for val in sorted(v):
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130 | inv_nodes[val] = inv_nodes.get(val, [])
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131 | inv_nodes[val].append(k)
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132 |
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133 |
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134 | def load_simple_data(dir):
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135 | global firstnode, nodes, inv_nodes
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136 | f = open(dir)
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137 | for line in f:
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138 | sline = line.split()
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139 | if len(sline) > 1:
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140 | #if int(sline[0]) > 15000:
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141 | # break
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142 | if sline[0] == firstnode:
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143 | continue
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144 | nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
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145 | else:
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146 | firstnode = sline[0]
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147 |
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148 | for k, v in sorted(nodes.items()):
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149 | inv_nodes[v] = inv_nodes.get(v, [])
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150 | inv_nodes[v].append(k)
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151 |
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152 | #print(str(inv_nodes))
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153 | #quit()
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154 |
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155 | def compute_depth(node):
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156 | my_depth = 0
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157 | if node in inv_nodes:
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158 | for c in inv_nodes[node]:
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159 | my_depth = max(my_depth, compute_depth(c)+1)
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160 | depth[node] = my_depth
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161 | return my_depth
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162 |
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163 | # ------------------------------------
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164 |
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165 | def xmin_crowd(x1, x2, y):
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166 | if BALANCE == "RANDOM":
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167 | return (x1 if random.randrange(2) == 0 else x2)
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168 | elif BALANCE == "MIN":
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169 | x1_closest = 999999
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170 | x2_closest = 999999
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171 | for pos in positions:
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172 | pos = positions[pos]
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173 | if pos[1] == y:
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174 | x1_closest = min(x1_closest, abs(x1-pos[0]))
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175 | x2_closest = min(x2_closest, abs(x2-pos[0]))
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176 | return (x1 if x1_closest > x2_closest else x2)
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177 | elif BALANCE == "DENSITY":
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178 | x1_dist = 0
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179 | x2_dist = 0
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180 | for pos in positions:
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181 | pos = positions[pos]
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182 | if pos[1] > y-10 or pos[1] < y+10:
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183 | dy = pos[1]-y
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184 | dx1 = pos[0]-x1
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185 | dx2 = pos[0]-x2
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186 |
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187 | x1_dist += math.sqrt(dy**2 + dx1**2)
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188 | x2_dist += math.sqrt(dy**2 + dx2**2)
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189 | return (x1 if x1_dist > x2_dist else x2)
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190 |
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191 | # ------------------------------------
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192 |
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193 | def prepos_children_reccurent(node):
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194 | global visited
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195 | for c in inv_nodes[node]:
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196 |
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197 | # we want to visit the node just once, after all of its parents
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198 | if not all_parents_visited(c):
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199 | continue
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200 | else:
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201 | visited[c] = True
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202 |
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203 | cy = 0
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204 | if TIME == "BIRTHS":
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205 | if c[0] == "c":
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206 | cy = int(c[1:])
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207 | else:
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208 | cy = int(c)
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209 | elif TIME == "GENERATIONAL":
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210 | cy = positions[node][1]+1
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211 | elif TIME == "REAL":
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212 | cy = time[c]
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213 |
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214 | if len(nodes[c]) == 1:
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215 | dissimilarity = 0
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216 | if JITTER == True:
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217 | dissimilarity = random.gauss(0,1)
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218 | else:
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219 | dissimilarity = 1
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220 | positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, cy), cy]
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221 | else:
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222 | vsum = sum([v for k, v in nodes[c].items()])
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223 | cx = sum([positions[k][0]*v/vsum for k, v in nodes[c].items()])
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224 |
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225 | if JITTER == True:
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226 | positions[c] = [cx + random.gauss(0, 0.1), cy]
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227 | else:
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228 | positions[c] = [cx, cy]
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229 |
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230 |
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231 | if c in inv_nodes:
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232 | prepos_children_reccurent(c)
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233 |
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234 | def prepos_children():
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235 | global max_height, max_width, min_width, visited
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236 |
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237 | if not bool(time):
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238 | print("REAL time requested, but no real time data provided. Assuming BIRTHS time instead.")
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239 | TIME = "BIRTHS"
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240 |
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241 | positions[firstnode] = [0, 0]
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242 |
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243 | visited = {}
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244 | visited[firstnode] = True
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245 | prepos_children_reccurent(firstnode)
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246 |
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247 | for pos in positions:
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248 | max_height = max(max_height, positions[pos][1])
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249 | max_width = max(max_width, positions[pos][0])
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250 | min_width = min(min_width, positions[pos][0])
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251 |
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252 | # ------------------------------------
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253 |
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254 | def all_parents_visited(node):
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255 | apv = True
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256 | for k, v in sorted(nodes[node].items()):
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257 | if not k in visited:
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258 | apv = False
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259 | break
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260 | return apv
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261 | # ------------------------------------
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262 |
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263 | def draw_children():
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264 | max_depth = 0
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265 | for k, v in depth.items():
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266 | max_depth = max(max_depth, v)
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267 |
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268 | nodes_to_visit = [firstnode]
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269 | while True:
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270 | current_node = nodes_to_visit[0]
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271 |
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272 | if current_node in inv_nodes:
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273 | for c in inv_nodes[current_node]: # inv_node => p->c
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274 |
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275 | if not c in nodes_to_visit:
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276 | nodes_to_visit.append(c)
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277 |
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278 | line_style = ""
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279 | if COLORING == "NONE":
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280 | line_style = svg_line_style
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281 | elif COLORING == "TYPE":
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282 | line_style = (svg_mutation_line_style if len(nodes[c]) == 1 else svg_crossover_line_style)
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283 | else: # IMPORTANCE, default
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284 | line_style = svg_generate_line_style(depth[c]/max_depth)
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285 |
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286 | svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
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287 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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288 |
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289 | # we want to draw the node just once
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290 | if DOT_STYLE == "NONE":
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291 | continue
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292 | elif DOT_STYLE == "TYPE":
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293 | dot_style = svg_generate_dot_style(kind[current_node] if current_node in kind else 0) #type
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294 | else: # NORMAL, default
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295 | dot_style = svg_clear_dot_style #svg_generate_dot_style(depth[c]/max_depth)
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296 | svg_add_dot( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height), dot_style)
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297 | #svg_add_text( str(depth[current_node]), (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width),
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298 | # h_margin+h_no_margs*positions[current_node][1]/max_height), "end")
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299 |
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300 | # we remove the current node from the list
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301 | nodes_to_visit = nodes_to_visit[1:]
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302 | # if none left, we can stop
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303 | if len(nodes_to_visit) == 0:
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304 | break
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305 |
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306 | def draw_spine():
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307 | nodes_to_visit = [firstnode]
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308 | while True:
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309 | current_node = nodes_to_visit[0]
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310 |
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311 | if current_node in inv_nodes:
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312 | for c in inv_nodes[current_node]: # inv_node => p->c
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313 | if depth[c] == depth[current_node] - 1:
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314 | if not c in nodes_to_visit:
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315 | nodes_to_visit.append(c)
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316 | line_style = svg_spine_line_style
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317 | svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
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318 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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319 |
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320 | # we remove the current node from the list
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321 | nodes_to_visit = nodes_to_visit[1:]
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322 | # if none left, we can stop
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323 | if len(nodes_to_visit) == 0:
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324 | break
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325 |
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326 | def draw_skeleton():
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327 | nodes_to_visit = [firstnode]
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328 | while True:
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329 | current_node = nodes_to_visit[0]
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330 |
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331 | if current_node in inv_nodes:
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332 | for c in inv_nodes[current_node]: # inv_node => p->c
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333 | if depth[c] >= min_skeleton_depth:
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334 | if not c in nodes_to_visit:
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335 | nodes_to_visit.append(c)
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336 | line_style = svg_spine_line_style
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337 | svg_add_line( (w_margin+w_no_margs*(positions[current_node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[current_node][1]/max_height),
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338 | (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), line_style)
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339 |
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340 | # we remove the current node from the list
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341 | nodes_to_visit = nodes_to_visit[1:]
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342 | # if none left, we can stop
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343 | if len(nodes_to_visit) == 0:
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344 | break
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345 |
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346 | # ------------------------------------
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347 |
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348 | def draw_scale(filename ,type):
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349 |
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350 | svg_add_text("Generated from " + filename.split("\\")[-1], (5, 15), "start")
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351 |
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352 | svg_add_line( (w*0.7, h_margin), (w, h_margin), svg_scale_line_style)
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353 | start_text = ""
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354 | if TIME == "BIRTHS":
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355 | start_text = "Birth #" + str(min([int(k[1:]) for k, v in nodes.items()]))
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356 | if TIME == "REAL":
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357 | start_text = "Time " + str(min([v for k, v in time.items()]))
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358 | if TIME == "GENERATIONAL":
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359 | start_text = "Depth " + str(min([v for k, v in depth.items()]))
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360 | svg_add_text( start_text, (w, h_margin + 15), "end")
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361 |
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362 | svg_add_line( (w*0.7, h-h_margin), (w, h-h_margin), svg_scale_line_style)
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363 | end_text = ""
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364 | if TIME == "BIRTHS":
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365 | end_text = "Birth #" + str(max([int(k[1:]) for k, v in nodes.items()]))
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366 | if TIME == "REAL":
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367 | end_text = "Time " + str(max([v for k, v in time.items()]))
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368 | if TIME == "GENERATIONAL":
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369 | end_text = "Depth " + str(max([v for k, v in depth.items()]))
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370 | svg_add_text( end_text, (w, h-h_margin + 15), "end")
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371 |
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372 |
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373 | ##################################################### main #####################################################
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374 |
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375 | args = 0
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376 |
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377 | h = 800
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378 | w = 600
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379 | h_margin = 20
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380 | w_margin = 10
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381 | h_no_margs = h - 2* h_margin
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382 | w_no_margs = w - 2* w_margin
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383 |
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384 | max_height = 0
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385 | max_width = 0
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386 | min_width = 9999999999
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387 |
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388 | min_skeleton_depth = 0
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389 |
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390 | firstnode = ""
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391 | nodes = {}
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392 | inv_nodes = {}
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393 | positions = {}
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394 | visited= {}
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395 | depth = {}
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396 | time = {}
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397 | kind = {}
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398 |
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399 | def main():
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400 | global svg_file, min_skeleton_depth, args, \
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401 | TIME, BALANCE, DOT_STYLE, COLORING, JITTER, \
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402 | svg_mutation_line_style, svg_crossover_line_style
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403 |
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404 | parser = argparse.ArgumentParser(description='Draws a genealogical tree (generates a SVG file) based on parent-child relationship information from a text file. Supports files generated by Framsticks experiments.')
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405 | parser.add_argument('-i', '--in', dest='input', required=True, help='input file name with stuctured evolutionary data')
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406 | parser.add_argument('-o', '--out', dest='output', required=True, help='output file name for the evolutionary tree (SVG format)')
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407 | draw_tree_parser = parser.add_mutually_exclusive_group(required=False)
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408 | draw_tree_parser.add_argument('--draw-tree', dest='draw_tree', action='store_true', help='whether drawing the full tree should be skipped')
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409 | draw_tree_parser.add_argument('--no-draw-tree', dest='draw_tree', action='store_false')
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410 |
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411 | draw_skeleton_parser = parser.add_mutually_exclusive_group(required=False)
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412 | draw_skeleton_parser.add_argument('--draw-skeleton', dest='draw_skeleton', action='store_true', help='whether the skeleton of the tree should be drawn')
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413 | draw_skeleton_parser.add_argument('--no-draw-skeleton', dest='draw_skeleton', action='store_false')
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414 |
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415 | draw_spine_parser = parser.add_mutually_exclusive_group(required=False)
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416 | draw_spine_parser.add_argument('--draw-spine', dest='draw_spine', action='store_true', help='whether the spine of the tree should be drawn')
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417 | draw_spine_parser.add_argument('--no-draw-spine', dest='draw_spine', action='store_false')
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418 |
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419 | #TODO: better names for those parameters
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420 | parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL/REAL); '
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421 | 'BIRTHS: time measured as the number of births since the beginning; '
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422 | 'GENERATIONAL: time measured as number of ancestors; '
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423 | 'REAL: real time of the simulation')
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424 | parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing nodes in the tree (RANDOM/MIN/DENSITY)')
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425 | parser.add_argument('-s', '--scale', default='NONE', dest='scale', help='type of timescale added to the tree (NONE/SIMPLE)')
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426 | parser.add_argument('-c', '--coloring', default='IMPORTANCE', dest="coloring", help='method of coloring the tree (NONE/IMPORTANCE/TYPE)')
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427 | parser.add_argument('-d', '--dots', default='TYPE', dest='dots', help='method of drawing dots (individuals) (NONE/NORMAL/TYPE)')
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428 | parser.add_argument('-j', '--jitter', dest="jitter", action='store_true', help='draw horizontal positions of children from the normal distribution')
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429 |
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430 | parser.add_argument('--color-mut', default="#000000", dest="color_mut", help='color of clone/mutation lines in rgba (e.g. #FF60B240) for TYPE coloring')
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431 | parser.add_argument('--color-cross', default="#660198", dest="color_cross", help='color of crossover lines in rgba (e.g. #FF60B240) for TYPE coloring')
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432 |
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433 | parser.add_argument('--min-skeleton-depth', type=int, default=2, dest='min_skeleton_depth', help='minimal distance from the leafs for the nodes in the skeleton')
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434 | parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
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435 |
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436 | parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
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437 |
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438 | parser.set_defaults(draw_tree=True)
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439 | parser.set_defaults(draw_skeleton=False)
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440 | parser.set_defaults(draw_spine=False)
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441 |
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442 | parser.set_defaults(seed=-1)
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443 |
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444 | args = parser.parse_args()
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445 |
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446 | TIME = args.time
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447 | BALANCE = args.balance
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448 | DOT_STYLE = args.dots
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449 | COLORING = args.coloring
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450 | JITTER = args.jitter
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451 |
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452 | svg_mutation_line_style += hex_to_style(args.color_mut)
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453 | svg_crossover_line_style += hex_to_style(args.color_cross)
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454 |
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455 | dir = args.input
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456 | min_skeleton_depth = args.min_skeleton_depth
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457 | seed = args.seed
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458 | if seed == -1:
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459 | seed = random.randint(0, 10000)
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460 | random.seed(seed)
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461 | print("seed:", seed)
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462 |
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463 | if args.simple_data:
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464 | load_simple_data(dir)
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465 | else:
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466 | load_data(dir)
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467 |
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468 | compute_depth(firstnode)
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469 |
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470 | svg_file = open(args.output, "w")
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471 | svg_file.write('<svg xmlns:svg="http://www.w3.org/2000/svg" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.0" '
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472 | 'width="' + str(w) + '" height="' + str(h) + '">')
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473 |
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474 | prepos_children()
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475 |
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476 | if args.draw_tree:
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477 | draw_children()
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478 | if args.draw_skeleton:
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479 | draw_skeleton()
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480 | if args.draw_spine:
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481 | draw_spine()
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482 |
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483 | draw_scale(dir, args.scale)
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484 |
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485 | svg_file.write("</svg>")
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486 | svg_file.close()
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487 |
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488 | main()
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