[562] | 1 | # Draws a genealogical tree (generates a SVG file) based on parent-child relationship information.
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| 2 |
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| 3 | import json
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| 4 | import random
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| 5 | import math
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| 6 | import argparse
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| 7 |
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[571] | 8 | TIME = "" # BIRTHS / GENERATIONAL / REAL
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| 9 | BALANCE = "" # MIN / DENSITY
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[562] | 10 |
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[571] | 11 | DOT_STYLE = "" # NONE / NORMAL / CLEAR
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| 12 |
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| 13 | JITTER = "" #
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| 14 |
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[562] | 15 | # ------SVG---------
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| 16 | svg_file = 0
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| 17 |
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[577] | 18 | svg_line_style = 'stroke="rgb(90%,10%,16%)" stroke-width="1" stroke-opacity="0.7"'
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[585] | 19 | svg_mutation_line_style = 'stroke-width="1"'
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| 20 | svg_crossover_line_style = 'stroke-width="1"'
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[577] | 21 | svg_spine_line_style = 'stroke="rgb(0%,90%,40%)" stroke-width="2" stroke-opacity="1"'
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| 22 | svg_scale_line_style = 'stroke="black" stroke-width="0.5" stroke-opacity="1" stroke-dasharray="5, 5"'
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| 23 |
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[562] | 24 | svg_dot_style = 'r="2" stroke="black" stroke-width="0.2" fill="red"'
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[571] | 25 | svg_clear_dot_style = 'r="2" stroke="black" stroke-width="0.4" fill="none"'
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[562] | 26 | svg_spine_dot_style = 'r="1" stroke="black" stroke-width="0.2" fill="rgb(50%,50%,100%)"'
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| 27 |
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[576] | 28 | svg_scale_text_style = 'style="font-family: Arial; font-size: 12; fill: #000000;"'
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| 29 |
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[585] | 30 | def hex_to_style(hex):
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| 31 | if hex[0] == "#":
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| 32 | hex = hex[1:]
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| 33 |
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| 34 | if len(hex) == 6 or len(hex) == 8:
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| 35 | try:
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| 36 | int(hex, 16)
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| 37 | except:
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| 38 | print("Wrong characters in the color's hex #" + hex + "! Assuming black.")
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| 39 | return ' stroke="black" stroke-opacity="0.5" '
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| 40 | red = 100*int(hex[0:2], 16)/255
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| 41 | green = 100*int(hex[2:4], 16)/255
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| 42 | blue = 100*int(hex[4:6], 16)/255
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| 43 | opacity = 0.5
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| 44 | if len(hex) == 8:
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| 45 | opacity = int(hex[6:8], 16)/255
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| 46 | return ' stroke="rgb(' +str(red)+ '%,' +str(green)+ '%,' +str(blue)+ '%)" stroke-opacity="' +str(opacity)+ '" '
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| 47 | else:
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| 48 | print("Wrong number of digits in the color's hex #" + hex + "! Assuming black.")
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| 49 | return ' stroke="black" stroke-opacity="0.5" '
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| 50 |
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[562] | 51 | def svg_add_line(from_pos, to_pos, style=svg_line_style):
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| 52 | svg_file.write('<line ' + style + ' x1="' + str(from_pos[0]) + '" x2="' + str(to_pos[0]) + '" y1="' + str(from_pos[1]) + '" y2="' + str(to_pos[1]) + '" />')
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| 53 |
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[576] | 54 | def svg_add_text(text, pos, anchor, style=svg_scale_text_style):
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| 55 | svg_file.write('<text ' + style + ' text-anchor="' + anchor + '" x="' + str(pos[0]) + '" y="' + str(pos[1]) + '" >' + text + '</text>')
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| 56 |
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[562] | 57 | def svg_add_dot(pos, style=svg_dot_style):
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| 58 | svg_file.write('<circle ' + style + ' cx="' + str(pos[0]) + '" cy="' + str(pos[1]) + '" />')
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| 59 |
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| 60 | def svg_generate_line_style(percent):
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[564] | 61 | # hotdog
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[562] | 62 | from_col = [100, 70, 0]
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[564] | 63 | to_col = [60, 0, 0]
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[585] | 64 | from_col = [0, 0, 0]
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| 65 | to_col = [80, 0, 80]
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[571] | 66 | # lava
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| 67 | # from_col = [100, 80, 0]
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| 68 | # to_col = [100, 0, 0]
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[564] | 69 | # neon
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| 70 | # from_col = [30, 200, 255]
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| 71 | # to_col = [240, 0, 220]
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[562] | 72 |
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[564] | 73 | from_opa = 0.2
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| 74 | to_opa = 1.0
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| 75 | from_stroke = 1
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| 76 | to_stroke = 3
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[562] | 77 |
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[564] | 78 | opa = from_opa*(1-percent) + to_opa*percent
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| 79 | stroke = from_stroke*(1-percent) + to_stroke*percent
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| 80 |
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| 81 | percent = 1 - ((1-percent)**20)
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| 82 |
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[562] | 83 | return 'stroke="rgb(' + str(from_col[0]*(1-percent) + to_col[0]*percent) + '%,' \
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| 84 | + str(from_col[1]*(1-percent) + to_col[1]*percent) + '%,' \
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[564] | 85 | + str(from_col[2]*(1-percent) + to_col[2]*percent) + '%)" stroke-width="' + str(stroke) + '" stroke-opacity="' + str(opa) + '"'
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[562] | 86 |
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[577] | 87 | def svg_generate_dot_style(kind):
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| 88 | kinds = ["red", "lawngreen", "royalblue", "magenta", "yellow", "cyan", "white", "black"]
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[562] | 89 |
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[577] | 90 | r = min(2500/len(nodes), 10)
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[562] | 91 |
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[577] | 92 | return 'fill="' + kinds[kind] + '" r="' + str(r) + '" stroke="black" stroke-width="' + str(r/10) + '" fill-opacity="1.0" ' \
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| 93 | 'stroke-opacity="1.0"'
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[564] | 94 |
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[562] | 95 | # -------------------
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| 96 |
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| 97 | def load_data(dir):
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[571] | 98 | global firstnode, nodes, inv_nodes, time
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[562] | 99 | f = open(dir)
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| 100 | for line in f:
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[571] | 101 | sline = line.split(' ', 1)
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| 102 | if len(sline) == 2:
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| 103 | if sline[0] == "[OFFSPRING]":
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| 104 | creature = json.loads(sline[1])
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[562] | 105 | #print("B" +str(creature))
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[563] | 106 | if "FromIDs" in creature:
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[572] | 107 | if not creature["ID"] in nodes:
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| 108 | nodes[creature["ID"]] = {}
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| 109 | # we assign to each parent its contribution to the genotype of the child
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| 110 | for i in range(0, len(creature["FromIDs"])):
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| 111 | inherited = 1 #(creature["Inherited"][i] if 'Inherited' in creature else 1) #ONLY FOR NOW
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| 112 | nodes[creature["ID"]][creature["FromIDs"][i]] = inherited
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| 113 | else:
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| 114 | print("Doubled entry for " + creature["ID"])
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| 115 | quit()
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| 116 |
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[563] | 117 | if not creature["FromIDs"][0] in nodes:
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| 118 | firstnode = creature["FromIDs"][0]
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[572] | 119 |
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[566] | 120 | if "Time" in creature:
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| 121 | time[creature["ID"]] = creature["Time"]
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[562] | 122 |
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[577] | 123 | if "Kind" in creature:
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| 124 | kind[creature["ID"]] = creature["Kind"]
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| 125 |
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[562] | 126 | for k, v in sorted(nodes.items()):
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[572] | 127 | for val in sorted(v):
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| 128 | inv_nodes[val] = inv_nodes.get(val, [])
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| 129 | inv_nodes[val].append(k)
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[562] | 130 |
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| 131 |
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| 132 | def load_simple_data(dir):
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| 133 | global firstnode, nodes, inv_nodes
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| 134 | f = open(dir)
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| 135 | for line in f:
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| 136 | sline = line.split()
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| 137 | if len(sline) > 1:
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| 138 | #if int(sline[0]) > 15000:
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| 139 | # break
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| 140 | if sline[0] == firstnode:
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| 141 | continue
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| 142 | nodes[sline[0]] = str(max(int(sline[1]), int(firstnode)))
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| 143 | else:
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| 144 | firstnode = sline[0]
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| 145 |
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| 146 | for k, v in sorted(nodes.items()):
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| 147 | inv_nodes[v] = inv_nodes.get(v, [])
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| 148 | inv_nodes[v].append(k)
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| 149 |
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| 150 | #print(str(inv_nodes))
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| 151 | #quit()
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| 152 |
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| 153 | def compute_depth(node):
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| 154 | my_depth = 0
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| 155 | if node in inv_nodes:
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| 156 | for c in inv_nodes[node]:
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| 157 | my_depth = max(my_depth, compute_depth(c)+1)
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| 158 | depth[node] = my_depth
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| 159 | return my_depth
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| 160 |
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| 161 | # ------------------------------------
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| 162 |
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| 163 | def xmin_crowd(x1, x2, y):
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| 164 | if BALANCE == "RANDOM":
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| 165 | return (x1 if random.randrange(2) == 0 else x2)
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| 166 | elif BALANCE == "MIN":
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| 167 | x1_closest = 999999
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| 168 | x2_closest = 999999
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| 169 | for pos in positions:
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| 170 | pos = positions[pos]
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| 171 | if pos[1] == y:
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| 172 | x1_closest = min(x1_closest, abs(x1-pos[0]))
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| 173 | x2_closest = min(x2_closest, abs(x2-pos[0]))
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| 174 | return (x1 if x1_closest > x2_closest else x2)
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| 175 | elif BALANCE == "DENSITY":
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| 176 | x1_dist = 0
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| 177 | x2_dist = 0
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| 178 | for pos in positions:
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| 179 | pos = positions[pos]
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| 180 | if pos[1] > y-10 or pos[1] < y+10:
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| 181 | dy = pos[1]-y
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| 182 | dx1 = pos[0]-x1
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| 183 | dx2 = pos[0]-x2
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| 184 |
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| 185 | x1_dist += math.sqrt(dy**2 + dx1**2)
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| 186 | x2_dist += math.sqrt(dy**2 + dx2**2)
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| 187 | return (x1 if x1_dist > x2_dist else x2)
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| 188 |
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| 189 | # ------------------------------------
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| 190 |
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| 191 | def prepos_children_reccurent(node):
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[572] | 192 | global visited
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[562] | 193 | for c in inv_nodes[node]:
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[572] | 194 |
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| 195 | # we want to visit the node just once, after all of its parents
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| 196 | if not all_parents_visited(c):
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| 197 | continue
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[571] | 198 | else:
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[572] | 199 | visited[c] = True
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[571] | 200 |
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[572] | 201 | cy = 0
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[566] | 202 | if TIME == "BIRTHS":
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[562] | 203 | if c[0] == "c":
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[572] | 204 | cy = int(c[1:])
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[562] | 205 | else:
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[572] | 206 | cy = int(c)
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[562] | 207 | elif TIME == "GENERATIONAL":
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[572] | 208 | cy = positions[node][1]+1
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[566] | 209 | elif TIME == "REAL":
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[572] | 210 | cy = time[c]
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[562] | 211 |
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[572] | 212 | if len(nodes[c]) == 1:
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| 213 | dissimilarity = 0
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| 214 | if JITTER == True:
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| 215 | dissimilarity = random.gauss(0,1)
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| 216 | else:
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| 217 | dissimilarity = 1
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| 218 | positions[c] = [xmin_crowd(positions[node][0]-dissimilarity, positions[node][0]+dissimilarity, cy), cy]
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| 219 | else:
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| 220 | vsum = sum([v for k, v in nodes[c].items()])
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| 221 | cx = sum([positions[k][0]*v/vsum for k, v in nodes[c].items()])
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| 222 |
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| 223 | if JITTER == True:
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| 224 | positions[c] = [cx + random.gauss(0, 0.1), cy]
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| 225 | else:
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| 226 | positions[c] = [cx, cy]
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| 227 |
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| 228 |
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[562] | 229 | if c in inv_nodes:
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| 230 | prepos_children_reccurent(c)
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| 231 |
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| 232 | def prepos_children():
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[572] | 233 | global max_height, max_width, min_width, visited
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[562] | 234 |
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[566] | 235 | if not bool(time):
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| 236 | print("REAL time requested, but no real time data provided. Assuming BIRTHS time instead.")
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| 237 | TIME = "BIRTHS"
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| 238 |
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[562] | 239 | positions[firstnode] = [0, 0]
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| 240 |
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[572] | 241 | visited = {}
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| 242 | visited[firstnode] = True
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[562] | 243 | prepos_children_reccurent(firstnode)
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| 244 |
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| 245 | for pos in positions:
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| 246 | max_height = max(max_height, positions[pos][1])
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| 247 | max_width = max(max_width, positions[pos][0])
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| 248 | min_width = min(min_width, positions[pos][0])
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| 249 |
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| 250 | # ------------------------------------
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| 251 |
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[572] | 252 | def all_parents_visited(node):
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| 253 | apv = True
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| 254 | for k, v in sorted(nodes[node].items()):
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| 255 | if not k in visited:
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| 256 | apv = False
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| 257 | break
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| 258 | return apv
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| 259 | # ------------------------------------
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| 260 |
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[562] | 261 | def draw_children_recurrent(node, max_depth):
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[572] | 262 | global visited
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| 263 |
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[562] | 264 | for c in inv_nodes[node]:
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[572] | 265 |
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| 266 | # we want to draw the node just once
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| 267 | if not all_parents_visited(c):
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| 268 | continue
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| 269 | else:
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| 270 | visited[c] = True
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| 271 |
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[562] | 272 | if c in inv_nodes:
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| 273 | draw_children_recurrent(c, max_depth)
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[564] | 274 |
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[577] | 275 | line_style = ""
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| 276 | if COLORING == "NONE":
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| 277 | line_style = svg_line_style
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| 278 | elif COLORING == "TYPE":
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| 279 | line_style = (svg_mutation_line_style if len(nodes[c]) == 1 else svg_crossover_line_style)
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| 280 | else: # IMPORTANCE, default
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| 281 | line_style = svg_generate_line_style(depth[c]/max_depth)
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| 282 |
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[572] | 283 | for k, v in sorted(nodes[c].items()):
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| 284 | svg_add_line( (w_margin+w_no_margs*(positions[k][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[k][1]/max_height),
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| 285 | (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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[571] | 286 |
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| 287 | if DOT_STYLE == "NONE":
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| 288 | continue
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[585] | 289 | elif DOT_STYLE == "TYPE":
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[577] | 290 | dot_style = svg_generate_dot_style(kind[c] if c in kind else 0) #type
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[571] | 291 | else: # NORMAL, default
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[577] | 292 | dot_style = svg_clear_dot_style #svg_generate_dot_style(depth[c]/max_depth)
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[564] | 293 | svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), dot_style)
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[562] | 294 | def draw_children():
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[572] | 295 | global visited
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| 296 | visited = {}
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| 297 | visited[firstnode] = True
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| 298 |
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[562] | 299 | max_depth = 0
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| 300 | for k, v in depth.items():
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| 301 | max_depth = max(max_depth, v)
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| 302 | draw_children_recurrent(firstnode, max_depth)
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[571] | 303 |
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| 304 | if DOT_STYLE == "NONE":
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| 305 | return
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[585] | 306 | elif DOT_STYLE == "TYPE":
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[577] | 307 | dot_style = svg_generate_dot_style(kind[firstnode] if firstnode in kind else 0)
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[571] | 308 | else: # NORMAL, default
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[577] | 309 | dot_style = svg_clear_dot_style #svg_generate_dot_style(depth[c]/max_depth)
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[564] | 310 | svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), dot_style)
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[562] | 311 |
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| 312 | def draw_spine_recurrent(node):
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| 313 | for c in inv_nodes[node]:
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| 314 | if depth[c] == depth[node] - 1:
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| 315 | if c in inv_nodes:
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| 316 | draw_spine_recurrent(c)
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[564] | 317 |
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| 318 | line_style = svg_spine_line_style
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[562] | 319 | svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
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[564] | 320 | (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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[562] | 321 | #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height), svg_spine_dot_style)
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| 322 | def draw_spine():
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| 323 | draw_spine_recurrent(firstnode)
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| 324 | #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height), svg_spine_dot_style)
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| 325 |
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| 326 | def draw_skeleton_reccurent(node, max_depth):
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| 327 | for c in inv_nodes[node]:
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| 328 | if depth[c] >= min_skeleton_depth or depth[c] == max([depth[q] for q in inv_nodes[node]]):
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| 329 | if c in inv_nodes:
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| 330 | draw_skeleton_reccurent(c, max_depth)
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[564] | 331 |
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| 332 | line_style = svg_spine_line_style
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[562] | 333 | svg_add_line( (w_margin+w_no_margs*(positions[node][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[node][1]/max_height),
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[564] | 334 | (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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[562] | 335 | #svg_add_dot( (w_margin+w_no_margs*(positions[c][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[c][1]/max_height),
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| 336 | # svg_spine_dot_style)
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| 337 | def draw_skeleton():
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| 338 | max_depth = 0
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| 339 | for k, v in depth.items():
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| 340 | max_depth = max(max_depth, v)
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| 341 |
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| 342 | draw_skeleton_reccurent(firstnode, max_depth)
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| 343 | #svg_add_dot( (w_margin+w_no_margs*(positions[firstnode][0]-min_width)/(max_width-min_width), h_margin+h_no_margs*positions[firstnode][1]/max_height),
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| 344 | # svg_spine_dot_style)
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| 345 |
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[576] | 346 | # ------------------------------------
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[562] | 347 |
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[576] | 348 | def draw_scale(filename ,type):
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[562] | 349 |
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[576] | 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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[577] | 370 | svg_add_text( end_text, (w, h-h_margin + 15), "end")
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[576] | 371 |
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| 372 |
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[562] | 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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[576] | 379 | h_margin = 20
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[562] | 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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[572] | 394 | visited= {}
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[562] | 395 | depth = {}
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[566] | 396 | time = {}
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[577] | 397 | kind = {}
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[562] | 398 |
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| 399 | def main():
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[585] | 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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[562] | 403 |
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| 404 | parser = argparse.ArgumentParser(description='Process some integers.')
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[576] | 405 | parser.add_argument('-i', '--in', dest='input', required=True, help='input file with stuctured evolutionary data')
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| 406 | parser.add_argument('-o', '--out', dest='output', required=True, help='output file for the evolutionary tree')
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[562] | 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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[585] | 420 | parser.add_argument('-t', '--time', default='GENERATIONAL', dest='time', help='values on vertical axis (BIRTHS/GENERATIONAL/REAL); '
|
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[571] | 421 | 'BIRTHS: time measured as the number of births since the beggining; '
|
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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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[585] | 424 | parser.add_argument('-b', '--balance', default='DENSITY', dest='balance', help='method of placing node in the tree (RANDOM/MIN/DENSITY)')
|
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[577] | 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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[585] | 427 | parser.add_argument('-d', '--dots', default='TYPE', dest='dots', help='method of drawing dots (individuals) (NONE/NORMAL/TYPE)')
|
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[571] | 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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[585] | 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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[562] | 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')
|
---|
| 434 | parser.add_argument('--seed', type=int, dest='seed', help='seed for the random number generator (-1 for random)')
|
---|
| 435 |
|
---|
| 436 | parser.add_argument('--simple-data', type=bool, dest='simple_data', help='input data are given in a simple format (#child #parent)')
|
---|
| 437 |
|
---|
| 438 | parser.set_defaults(draw_tree=True)
|
---|
| 439 | parser.set_defaults(draw_skeleton=False)
|
---|
| 440 | parser.set_defaults(draw_spine=False)
|
---|
| 441 |
|
---|
| 442 | parser.set_defaults(seed=-1)
|
---|
| 443 |
|
---|
| 444 | args = parser.parse_args()
|
---|
| 445 |
|
---|
| 446 | TIME = args.time
|
---|
| 447 | BALANCE = args.balance
|
---|
[571] | 448 | DOT_STYLE = args.dots
|
---|
[577] | 449 | COLORING = args.coloring
|
---|
[571] | 450 | JITTER = args.jitter
|
---|
[562] | 451 |
|
---|
[585] | 452 | svg_mutation_line_style += hex_to_style(args.color_mut)
|
---|
| 453 | svg_crossover_line_style += hex_to_style(args.color_cross)
|
---|
| 454 |
|
---|
[562] | 455 | dir = args.input
|
---|
| 456 | min_skeleton_depth = args.min_skeleton_depth
|
---|
| 457 | seed = args.seed
|
---|
| 458 | if seed == -1:
|
---|
| 459 | seed = random.randint(0, 10000)
|
---|
| 460 | random.seed(seed)
|
---|
| 461 | print("seed:", seed)
|
---|
| 462 |
|
---|
| 463 | if args.simple_data:
|
---|
| 464 | load_simple_data(dir)
|
---|
| 465 | else:
|
---|
| 466 | load_data(dir)
|
---|
| 467 |
|
---|
| 468 | compute_depth(firstnode)
|
---|
| 469 |
|
---|
| 470 | svg_file = open(args.output, "w")
|
---|
| 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" '
|
---|
| 472 | 'width="' + str(w) + '" height="' + str(h) + '">')
|
---|
| 473 |
|
---|
| 474 | prepos_children()
|
---|
| 475 |
|
---|
| 476 | if args.draw_tree:
|
---|
| 477 | draw_children()
|
---|
| 478 | if args.draw_skeleton:
|
---|
| 479 | draw_skeleton()
|
---|
| 480 | if args.draw_spine:
|
---|
| 481 | draw_spine()
|
---|
| 482 |
|
---|
[576] | 483 | draw_scale(dir, args.scale)
|
---|
| 484 |
|
---|
[562] | 485 | svg_file.write("</svg>")
|
---|
| 486 | svg_file.close()
|
---|
| 487 |
|
---|
| 488 | main()
|
---|
| 489 |
|
---|