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