[193] | 1 | /* |
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| 2 | * f4_general.cpp - f4 genotype functions. |
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| 3 | * |
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| 4 | * f4genotype - f4 format genotype conversions for FramSticks |
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| 5 | * |
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| 6 | * Copyright (C) 1999,2000 Adam Rotaru-Varga (adam_rotaru@yahoo.com) |
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| 7 | * |
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| 8 | * This library is free software; you can redistribute it and/or |
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| 9 | * modify it under the terms of the GNU Lesser General Public |
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| 10 | * License as published by the Free Software Foundation; either |
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| 11 | * version 2.1 of the License, or (at your option) any later version. |
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| 12 | * |
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| 13 | * This library is distributed in the hope that it will be useful, |
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| 14 | * but WITHOUT ANY WARRANTY; without even the implied warranty of |
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| 15 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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| 16 | * Lesser General Public License for more details. |
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| 17 | * |
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| 18 | * You should have received a copy of the GNU Lesser General Public |
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| 19 | * License along with this library; if not, write to the Free Software |
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| 20 | * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA |
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| 21 | * |
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| 22 | */ |
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| 23 | |
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| 24 | #include "f4_general.h" |
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| 25 | #include "nonstd.h" |
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| 26 | #include "framsg.h" |
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| 27 | #include "model.h" // for min and max attributes |
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| 28 | #include "geno_fx.h" //for GENOPER_ constants |
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| 29 | #include <stdio.h> |
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| 30 | #include <math.h> |
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| 31 | |
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| 32 | #ifdef DMALLOC |
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| 33 | #include <dmalloc.h> |
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| 34 | #endif |
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| 35 | |
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| 36 | |
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| 37 | f4_Props::f4_Props() |
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| 38 | { |
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| 39 | len = 1.0; |
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| 40 | curv = 0.0; |
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| 41 | mass = 1.0; |
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| 42 | friction = 0.4; |
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| 43 | ruch = 0.25; // bio |
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| 44 | assim = 0.25; // bio |
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| 45 | odpor = 0.25; // bio |
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| 46 | ingest = 0.25; // bio |
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| 47 | twist = 0.0; |
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| 48 | energ = 1.0; |
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| 49 | normalizeBiol4(); |
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| 50 | } |
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| 51 | |
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| 52 | void f4_Props::normalizeBiol4() |
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| 53 | { |
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| 54 | // must sum to 1 |
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| 55 | double sum = ruch + assim + odpor + ingest; |
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| 56 | if (0 == sum) |
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| 57 | { |
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| 58 | ruch = assim = odpor = ingest = 0.25; |
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| 59 | } else { |
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| 60 | ruch /= sum; |
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| 61 | assim /= sum; |
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| 62 | odpor /= sum; |
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| 63 | ingest /= sum; |
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| 64 | } |
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| 65 | } |
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| 66 | |
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| 67 | void f4_Props::executeModifier(char modif) |
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| 68 | { |
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| 69 | switch (modif) |
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| 70 | { |
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| 71 | case 'L': len += (2.5 - len) * 0.3; |
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| 72 | len = min(len, Model::getMaxJoint().d.x); break; |
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| 73 | case 'l': len += (0.3 - len) * 0.3; |
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| 74 | len = max(len, Model::getMinJoint().d.x); break; |
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| 75 | case 'C': curv += ( 2.0 - curv) * 0.25; break; |
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| 76 | case 'c': curv += (-2.0 - curv) * 0.25; break; |
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| 77 | case 'Q': twist += ( 1.58 - twist) * 0.3; break; |
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| 78 | case 'q': twist += (-1.58 - twist) * 0.3; break; |
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| 79 | case 'A': assim += (1 - assim) * 0.8; normalizeBiol4(); break; |
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| 80 | case 'a': assim -= assim * 0.4; normalizeBiol4(); break; |
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| 81 | case 'I': ingest += (1 - ingest) * 0.8; normalizeBiol4(); break; |
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| 82 | case 'i': ingest -= ingest * 0.4; normalizeBiol4(); break; |
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| 83 | case 'S': odpor += (1 - odpor) * 0.8; normalizeBiol4(); break; |
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| 84 | case 's': odpor -= odpor * 0.4; normalizeBiol4(); break; |
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| 85 | case 'M': ruch += (1 - ruch) * 0.8; normalizeBiol4(); break; |
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| 86 | case 'm': ruch -= ruch * 0.4; normalizeBiol4(); break; |
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| 87 | case 'F': friction += (4 - friction) * 0.2; break; |
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| 88 | case 'f': friction -= friction * 0.2; break; |
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| 89 | case 'W': mass += (2.0 - mass) * 0.3; break; |
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| 90 | case 'w': mass += (0.5 - mass) * 0.3; break; |
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| 91 | case 'E': energ += (10.0 - energ) * 0.1; break; |
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| 92 | case 'e': energ -= energ * 0.1; break; |
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| 93 | } |
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| 94 | } |
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| 95 | |
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| 96 | void f4_Props::adjust() |
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| 97 | { |
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| 98 | len = 0.5*len + 0.5*stdProps.len; |
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| 99 | curv = 0.66 * curv; |
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| 100 | twist = 0.66 * twist; |
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| 101 | } |
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| 102 | |
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| 103 | f4_Props stdProps; |
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| 104 | |
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| 105 | |
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| 106 | void rolling_dec(double * v) { |
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| 107 | *v -= 0.7853; // 0.7853981 45 degrees |
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| 108 | } |
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| 109 | void rolling_inc(double * v) { |
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| 110 | *v += 0.7853; // 0.7853981 45 degrees |
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| 111 | } |
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| 112 | |
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| 113 | |
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| 114 | int scanrec(const char * s, unsigned int slen, char stopchar) |
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| 115 | { |
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| 116 | unsigned int i = 0; |
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| 117 | //DB( printf(" scan('%s', '%c')\n", s, stopchar); ) |
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| 118 | while (1) |
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| 119 | { |
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| 120 | if (i >= slen) // ran out the string, should never happen with correct string |
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| 121 | return 1; |
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| 122 | if (stopchar == s[i]) // bumped into stopchar |
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| 123 | return i; |
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| 124 | if (i < slen-1) |
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| 125 | { // s[i] is not the last char |
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| 126 | if (s[i] == '(') |
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| 127 | { |
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| 128 | i += 2+scanrec(s+i+1, slen-i-1, ')'); |
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| 129 | continue; |
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| 130 | } |
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| 131 | if (s[i] == '<') |
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| 132 | { |
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| 133 | i += 2+scanrec(s+i+1, slen-i-1, '>'); |
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| 134 | continue; |
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| 135 | } |
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| 136 | if (s[i] == '#') |
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| 137 | { |
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| 138 | i += 2+scanrec(s+i+1, slen-i-1, '>'); |
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| 139 | continue; |
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| 140 | } |
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| 141 | } |
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| 142 | // s[i] a non-special character |
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| 143 | i++; |
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| 144 | } |
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| 145 | return i; |
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| 146 | } |
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| 147 | |
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| 148 | |
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| 149 | f4_Cell::f4_Cell(int nname, |
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| 150 | f4_Cell * ndad, int nangle, f4_Props newP) |
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| 151 | { |
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| 152 | name = nname; |
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| 153 | type = T_UNDIFF4; |
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| 154 | dadlink = ndad; |
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| 155 | org = NULL; |
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| 156 | genot = NULL; |
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| 157 | gcur = NULL; |
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| 158 | active = 1; |
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| 159 | repeat.null(); |
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| 160 | //genoRange.clear(); -- implicit |
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| 161 | |
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| 162 | anglepos = nangle; |
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| 163 | commacount = 0; |
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| 164 | childcount = 0; |
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| 165 | P = newP; |
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| 166 | rolling = 0; |
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| 167 | xrot = 0; |
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| 168 | zrot = 0; |
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| 169 | //OM = Orient_1; |
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| 170 | ctrl = 0; |
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| 171 | state = 0; |
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| 172 | inertia = 0.8; |
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| 173 | force = 0.04; |
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| 174 | sigmo = 2; |
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| 175 | nolink = 0; |
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| 176 | |
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| 177 | // adjust firstend and OM if there is a stick dad |
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| 178 | if (ndad != NULL) |
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| 179 | { |
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| 180 | // make sure it is a stick (and not a stick f4_Cell!) |
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| 181 | if (T_STICK4 == ndad->type) |
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| 182 | { |
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| 183 | //firstend = ndad->lastend; |
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| 184 | //OM = ndad->OM; |
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| 185 | ndad->childcount++; |
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| 186 | } |
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| 187 | if (T_NEURON4 == ndad->type) |
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| 188 | { |
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| 189 | state = ndad->state; |
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| 190 | inertia = ndad->inertia; |
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| 191 | force = ndad->force; |
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| 192 | sigmo = ndad->sigmo; |
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| 193 | } |
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| 194 | } |
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| 195 | // adjust lastend |
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| 196 | //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len)); |
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| 197 | mz = 1; |
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| 198 | } |
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| 199 | |
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| 200 | |
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| 201 | f4_Cell::f4_Cell(f4_Cells * nO, int nname, f4_node * ngeno, f4_node * ngcur, |
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| 202 | f4_Cell * ndad, int nangle, f4_Props newP) |
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| 203 | { |
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| 204 | name = nname; |
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| 205 | type = T_UNDIFF4; |
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| 206 | dadlink = ndad; |
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| 207 | org = nO; |
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| 208 | genot = ngeno; |
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| 209 | gcur = ngcur; |
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| 210 | active = 1; |
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| 211 | repeat.null(); |
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| 212 | //genoRange.clear(); -- implicit |
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| 213 | // preserve geno range of parent cell |
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| 214 | if (NULL != ndad) |
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| 215 | genoRange.add( ndad->genoRange ); |
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| 216 | |
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| 217 | anglepos = nangle; |
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| 218 | commacount = 0; |
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| 219 | childcount = 0; |
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| 220 | P = newP; |
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| 221 | rolling = 0; |
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| 222 | xrot = 0; |
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| 223 | zrot = 0; |
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| 224 | //OM = Orient_1; |
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| 225 | ctrl = 0; |
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| 226 | state = 0; |
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| 227 | inertia = 0.8; |
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| 228 | force = 0.04; |
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| 229 | sigmo = 2; |
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| 230 | nolink = 0; |
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| 231 | |
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| 232 | // adjust firstend and OM if there is a stick dad |
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| 233 | if (ndad != NULL) |
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| 234 | { |
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| 235 | // make sure it is a stick (and not a stick f4_Cell!) |
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| 236 | if (T_STICK4 == ndad->type) { |
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| 237 | //firstend = ndad->lastend; |
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| 238 | //OM = ndad->OM; |
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| 239 | ndad->childcount++; |
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| 240 | } |
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| 241 | if (T_NEURON4 == ndad->type) |
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| 242 | { |
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| 243 | state = ndad->state; |
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| 244 | inertia = ndad->inertia; |
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| 245 | force = ndad->force; |
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| 246 | sigmo = ndad->sigmo; |
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| 247 | } |
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| 248 | } |
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| 249 | // adjust lastend |
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| 250 | //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len)); |
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| 251 | mz = 1; |
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| 252 | } |
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| 253 | |
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| 254 | |
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| 255 | f4_Cell::~f4_Cell() |
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| 256 | { |
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| 257 | // remove links |
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| 258 | if (nolink) |
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| 259 | { |
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| 260 | int i; |
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| 261 | for (i=nolink-1; i>=0; i--) |
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| 262 | delete links[i]; |
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| 263 | nolink=0; |
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| 264 | } |
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| 265 | } |
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| 266 | |
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| 267 | |
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| 268 | /* return codes: |
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| 269 | >1 error at pos |
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| 270 | 0 halt development for a cycle |
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| 271 | -1 development finished OK |
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| 272 | */ |
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| 273 | int f4_Cell::onestep() |
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| 274 | { |
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| 275 | int i, j, k, relfrom, t; |
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| 276 | double w; |
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| 277 | f4_Cell * tmp; |
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| 278 | f4_Cell * tneu; |
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| 279 | if (gcur == NULL) |
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| 280 | { |
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| 281 | active = 0; |
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| 282 | return 0; // stop |
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| 283 | } |
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| 284 | while ( NULL != gcur ) |
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| 285 | { |
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| 286 | //DB( printf(" %d (%d) executing '%c' %d\n", name, type, gcur->name, gcur->pos); ) |
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| 287 | // currently this is the last one processed |
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| 288 | // the current genotype code is processed |
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| 289 | genoRange.add( gcur->pos ); |
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| 290 | switch (gcur->name) |
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| 291 | { |
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| 292 | case '<': |
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| 293 | // cell division! |
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| 294 | //DB( printf(" div! %d\n", name); ) |
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| 295 | |
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| 296 | // error: sticks cannot divide |
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| 297 | if (T_STICK4 == type) { |
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| 298 | // cannot fix |
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| 299 | org->setError(gcur->pos); |
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| 300 | return 1; // stop |
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| 301 | } |
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| 302 | |
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| 303 | // undiff divides |
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| 304 | if (T_UNDIFF4 == type) { |
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| 305 | // commacount is set only when daughter turns into X |
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| 306 | // daughter cell |
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| 307 | // adjust new len |
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| 308 | f4_Props newP = P; |
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| 309 | newP.adjust(); |
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| 310 | tmp = new f4_Cell(org, org->nc, genot, gcur->child2, |
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| 311 | this, commacount, newP); |
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| 312 | tmp->repeat = repeat; |
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| 313 | repeat.null(); |
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| 314 | org->addCell( tmp ); |
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| 315 | } |
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| 316 | // a neuron divides: create a new, duplicate links |
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| 317 | if (T_NEURON4 == type) { |
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| 318 | // daughter cell |
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| 319 | tmp = new f4_Cell(org, org->nc, genot, gcur->child2, |
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| 320 | // has the same dadlink |
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| 321 | this->dadlink, commacount, P); |
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| 322 | tmp->repeat = repeat; |
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| 323 | repeat.null(); |
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| 324 | // it is a neuron from start |
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| 325 | tmp->type = T_NEURON4; |
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| 326 | // duplicate links |
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| 327 | f4_CellLink * ll; |
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| 328 | for (i=0; i<nolink; i++) { |
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| 329 | ll = links[i]; |
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| 330 | tmp->addlink(ll->from, ll->w, ll->t); |
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| 331 | } |
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| 332 | org->addCell( tmp ); |
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| 333 | } |
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| 334 | // adjustments for this cell |
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| 335 | gcur = gcur->child; |
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| 336 | // halt development |
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| 337 | return 0; |
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| 338 | |
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| 339 | case '>': |
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| 340 | // finish |
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| 341 | // see if there is a repet count |
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| 342 | if (repeat.top > 0) |
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| 343 | { // there is a repeat counter |
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| 344 | if (!repeat.first()->isNull()) |
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| 345 | { // repeat counter is not null |
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| 346 | repeat.first()->dec(); |
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| 347 | if (repeat.first()->count > 0) |
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| 348 | { |
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| 349 | // return to repeat |
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| 350 | gcur = repeat.first()->node->child; |
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| 351 | } else { |
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| 352 | // continue |
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| 353 | gcur = repeat.first()->node->child2; |
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| 354 | repeat.pop(); |
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| 355 | } |
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| 356 | break; |
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| 357 | } else { |
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| 358 | repeat.pop(); |
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| 359 | } |
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| 360 | } else { |
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| 361 | // error: still undiff |
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| 362 | if (T_UNDIFF4 == type) |
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| 363 | { |
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| 364 | // fix it: insert an 'X' |
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| 365 | f4_node * insertnode = new f4_node('X', NULL, gcur->pos); |
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| 366 | if (org->setRepairInsert(gcur->pos, gcur, insertnode)) |
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| 367 | // not in repair mode, release |
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| 368 | delete insertnode; |
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| 369 | return 1; |
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| 370 | } |
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| 371 | repeat.null(); |
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| 372 | active = 0; // stop |
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| 373 | // eat up rest |
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| 374 | gcur = NULL; |
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| 375 | return 0; |
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| 376 | } |
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| 377 | |
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| 378 | case '#': |
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| 379 | // repetition marker |
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| 380 | if (repeat.top >= repeat_stack::stackSize) |
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| 381 | { |
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| 382 | // repepeat pointer stack is full, cannot remember this one. |
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| 383 | // fix: delete it |
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| 384 | org->setRepairRemove(gcur->pos, gcur); |
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| 385 | return 1; // stop |
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| 386 | } |
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| 387 | repeat.push( repeat_ptr(gcur, gcur->i1) ); |
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| 388 | gcur = gcur->child; |
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| 389 | break; |
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| 390 | |
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| 391 | case ',': |
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| 392 | commacount++; |
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| 393 | gcur = gcur->child; |
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| 394 | break; |
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| 395 | |
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| 396 | case 'r': case 'R': |
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| 397 | // error: if neuron |
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| 398 | if (T_NEURON4 == type) { |
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| 399 | // fix: delete it |
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| 400 | org->setRepairRemove(gcur->pos, gcur); |
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| 401 | return 1; // stop |
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| 402 | } |
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| 403 | switch (gcur->name) { |
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| 404 | case 'r': rolling_dec( &rolling ); break; |
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| 405 | case 'R': rolling_inc( &rolling ); break; |
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| 406 | } |
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| 407 | gcur = gcur->child; |
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| 408 | break; |
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| 409 | |
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| 410 | case 'l': case 'L': |
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| 411 | case 'c': case 'C': |
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| 412 | case 'q': case 'Q': |
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| 413 | case 'a': case 'A': |
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| 414 | case 'i': case 'I': |
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| 415 | case 's': case 'S': |
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| 416 | case 'm': case 'M': |
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| 417 | case 'f': case 'F': |
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| 418 | case 'w': case 'W': |
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| 419 | case 'e': case 'E': |
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| 420 | // error: if neuron |
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| 421 | if (T_NEURON4 == type) { |
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| 422 | // fix: delete it |
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| 423 | org->setRepairRemove(gcur->pos, gcur); |
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| 424 | return 1; // stop |
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| 425 | } |
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| 426 | P.executeModifier(gcur->name); |
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| 427 | gcur = gcur->child; |
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| 428 | break; |
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| 429 | |
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| 430 | case 'X': |
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| 431 | // turn undiff. cell into a stick |
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| 432 | // error: already differentiated |
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| 433 | if (T_UNDIFF4 != type) { |
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| 434 | // fix: delete this node |
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| 435 | org->setRepairRemove(gcur->pos, gcur); |
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| 436 | return 1; // stop |
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| 437 | } |
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| 438 | type = T_STICK4; |
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| 439 | // fix dad commacount and own anglepos |
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| 440 | if (NULL != dadlink) { |
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| 441 | dadlink->commacount++; |
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| 442 | anglepos = dadlink->commacount; |
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| 443 | } |
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| 444 | // change of type halts developments, see comment at 'N' |
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| 445 | gcur = gcur->child; |
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| 446 | return 0; |
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| 447 | |
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| 448 | case 'N': |
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| 449 | // turn undiff. cell into a neuron |
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| 450 | // error: already differentiated |
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| 451 | if (T_UNDIFF4 != type) { |
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| 452 | // fix: delete this node |
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| 453 | org->setRepairRemove(gcur->pos, gcur); |
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| 454 | return 1; // stop |
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| 455 | } |
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| 456 | // error: if no previous |
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| 457 | if (NULL == dadlink) { |
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| 458 | // fix: delete it |
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| 459 | org->setRepairRemove(gcur->pos, gcur); |
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| 460 | return 1; // stop |
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| 461 | } |
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| 462 | type = T_NEURON4; |
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| 463 | // change of type also halts development, to give other |
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| 464 | // cells a chance for adjustment. Namely, it is important |
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| 465 | // to wait for other cells to turn N before adding links |
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| 466 | gcur = gcur->child; |
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| 467 | return 0; |
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| 468 | |
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| 469 | case '@': |
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| 470 | case '|': |
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| 471 | // neuron rotating / bending |
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| 472 | j = 1; |
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| 473 | if ('@' == gcur->name) j = 1; // rot |
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| 474 | if ('|' == gcur->name) j = 2; // bend |
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| 475 | // error: not a neuron (undiff) |
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| 476 | if (T_UNDIFF4 == type) { |
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| 477 | // fix: delete it |
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| 478 | org->setRepairRemove(gcur->pos, gcur); |
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| 479 | return 1; // stop |
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| 480 | } |
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| 481 | // error: not a neuron (stick) |
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| 482 | if (T_NEURON4 != type) { |
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| 483 | // fix: delete it |
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| 484 | org->setRepairRemove(gcur->pos, gcur); |
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| 485 | return 1; // stop |
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| 486 | } |
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| 487 | // error: already has control |
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| 488 | if (ctrl != 0) { |
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| 489 | // fix: delete it |
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| 490 | org->setRepairRemove(gcur->pos, gcur); |
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| 491 | return 1; // stop |
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| 492 | } |
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| 493 | // make neuron ctrl = 1 or 2 |
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| 494 | ctrl = j; |
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| 495 | gcur = gcur->child; |
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| 496 | break; |
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| 497 | |
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| 498 | case '[': |
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| 499 | // link to neuron |
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| 500 | // error: not a neuron |
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| 501 | if (T_NEURON4 != type) { |
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| 502 | // fix: delete it |
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| 503 | org->setRepairRemove(gcur->pos, gcur); |
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| 504 | return 1; // stop |
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| 505 | } |
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| 506 | // input ('*', 'G', 'T', 'S', or %d) |
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| 507 | t = gcur->i1; |
---|
| 508 | relfrom = gcur->l1; |
---|
| 509 | w = gcur->f1; |
---|
| 510 | if (t>0) { |
---|
| 511 | // * or G |
---|
| 512 | tneu = NULL; |
---|
| 513 | } else { |
---|
| 514 | // input from other neuron |
---|
| 515 | // find neuron at relative i |
---|
| 516 | // find own index |
---|
| 517 | j = 0; k = 0; |
---|
| 518 | for(i=0; i<org->nc; i++) { |
---|
| 519 | if (org->C[i]->type == T_NEURON4) k++; |
---|
| 520 | if (org->C[i] == this) {j=k-1; break;} |
---|
| 521 | } |
---|
| 522 | // find index of incoming |
---|
| 523 | j = j + relfrom; |
---|
| 524 | if (j<0) goto wait_link; |
---|
| 525 | if (j>=org->nc) goto wait_link; |
---|
| 526 | // find that neuron |
---|
| 527 | k = 0; |
---|
| 528 | for(i=0; i<org->nc; i++) { |
---|
| 529 | if (org->C[i]->type == T_NEURON4) k++; |
---|
| 530 | if (j == (k-1)) break; |
---|
| 531 | } |
---|
| 532 | if (i>=org->nc) goto wait_link; |
---|
| 533 | tneu = org->C[i]; |
---|
| 534 | } |
---|
| 535 | // add link |
---|
| 536 | // error: could not add link (too many?) |
---|
| 537 | if (addlink(tneu, w, t)) { |
---|
| 538 | // cannot fix |
---|
| 539 | org->setError(gcur->pos); |
---|
| 540 | return 1; // stop |
---|
| 541 | } |
---|
| 542 | gcur = gcur->child; |
---|
| 543 | break; |
---|
| 544 | wait_link: |
---|
| 545 | // wait for other neurons to develop |
---|
| 546 | // if there are others still active |
---|
| 547 | active = 0; |
---|
| 548 | j = 0; |
---|
| 549 | for(i=0; i<org->nc; i++) { |
---|
| 550 | if (org->C[i]->active) j++; |
---|
| 551 | } |
---|
| 552 | if (j>0) |
---|
| 553 | return 0; // there is other active, halt, try again |
---|
| 554 | // no more actives, cannot add link, ignore, but treat not as an error |
---|
| 555 | gcur = gcur->child; |
---|
| 556 | break; |
---|
| 557 | |
---|
| 558 | case ':': |
---|
| 559 | // neuron parameter |
---|
| 560 | // error: not a neuron |
---|
| 561 | if (T_NEURON4 != type) { |
---|
| 562 | // fix: delete it |
---|
| 563 | org->setRepairRemove(gcur->pos, gcur); |
---|
| 564 | return 1; // stop |
---|
| 565 | } |
---|
| 566 | j = (int)gcur->l1; |
---|
| 567 | switch ((char)gcur->i1) { |
---|
| 568 | case '!': |
---|
| 569 | if (j) force += (1.0 - force) * 0.2; |
---|
| 570 | else force -= force * 0.2; break; |
---|
| 571 | case '=': |
---|
| 572 | if (j) inertia += (1.0 - inertia) * 0.2; |
---|
| 573 | else inertia -= inertia * 0.2; break; |
---|
| 574 | case '/': |
---|
| 575 | if (j) sigmo *= 1.4; |
---|
| 576 | else sigmo /= 1.4; break; |
---|
| 577 | default: |
---|
| 578 | org->setRepairRemove(gcur->pos, gcur); |
---|
| 579 | return 1; // stop |
---|
| 580 | } |
---|
| 581 | gcur = gcur->child; |
---|
| 582 | break; |
---|
| 583 | |
---|
| 584 | case ' ': |
---|
| 585 | // space has no effect, should not occur |
---|
| 586 | // fix: delete it |
---|
| 587 | org->setRepairRemove(gcur->pos, gcur); |
---|
| 588 | gcur = gcur->child; |
---|
| 589 | break; |
---|
| 590 | |
---|
| 591 | default: |
---|
| 592 | // error: unknown code |
---|
| 593 | char buf[40]; |
---|
| 594 | sprintf(buf, "unknown code '%c'", gcur->name); |
---|
| 595 | FramMessage("f4_Cell", "onestep", buf, 2); |
---|
| 596 | // fix: delete it |
---|
| 597 | org->setRepairRemove(gcur->pos, gcur); |
---|
| 598 | return 1; // stop |
---|
| 599 | } |
---|
| 600 | } |
---|
| 601 | active = 0; // done |
---|
| 602 | return 0; |
---|
| 603 | } |
---|
| 604 | |
---|
| 605 | |
---|
| 606 | int f4_Cell::addlink(f4_Cell * nfrom, double nw, long nt) |
---|
| 607 | { |
---|
| 608 | if (nolink >= MAXINPUTS-1) return -1; // full! |
---|
| 609 | links[nolink] = new f4_CellLink(nfrom, nw, nt); |
---|
| 610 | nolink++; |
---|
| 611 | return 0; |
---|
| 612 | } |
---|
| 613 | |
---|
| 614 | |
---|
| 615 | void f4_Cell::adjustRec() |
---|
| 616 | { |
---|
| 617 | //f4_OrientMat rot; |
---|
| 618 | int i; |
---|
| 619 | |
---|
| 620 | if (recProcessedFlag) |
---|
| 621 | // already processed |
---|
| 622 | return; |
---|
| 623 | |
---|
| 624 | // mark it processed |
---|
| 625 | recProcessedFlag = 1; |
---|
| 626 | |
---|
| 627 | // make sure its parent is processed first |
---|
| 628 | if (NULL != dadlink) |
---|
| 629 | dadlink->adjustRec(); |
---|
| 630 | |
---|
| 631 | // count children |
---|
| 632 | childcount = 0; |
---|
| 633 | for(i=0; i<org->nc; i++) |
---|
| 634 | { |
---|
| 635 | if (org->C[i]->dadlink == this) |
---|
| 636 | if (org->C[i]->type == T_STICK4) |
---|
| 637 | childcount++; |
---|
| 638 | } |
---|
| 639 | |
---|
| 640 | if (type == T_STICK4) |
---|
| 641 | { |
---|
| 642 | if (NULL == dadlink) |
---|
| 643 | { |
---|
| 644 | //firstend = Pt3D_0; |
---|
| 645 | // rotation due to rolling |
---|
| 646 | xrot = rolling; |
---|
| 647 | mz = 1; |
---|
| 648 | } else { |
---|
| 649 | //firstend = dadlink->lastend; |
---|
| 650 | f4_Props Pdad = dadlink->P; |
---|
| 651 | f4_Props Padj = Pdad; |
---|
| 652 | Padj.adjust(); |
---|
| 653 | |
---|
| 654 | //rot = Orient_1; |
---|
| 655 | |
---|
| 656 | // rotation due to rolling |
---|
| 657 | xrot = rolling + |
---|
| 658 | // rotation due to twist |
---|
| 659 | Pdad.twist; |
---|
| 660 | if (dadlink->commacount <= 1) |
---|
| 661 | { |
---|
| 662 | // rotation due to curvedness |
---|
| 663 | zrot = Padj.curv; |
---|
| 664 | } else { |
---|
| 665 | zrot = Padj.curv + |
---|
| 666 | // GDK uses 3.141 instead of PI! |
---|
| 667 | (anglepos * 1.0/(dadlink->commacount+1) - 0.5) * 3.141 * 2.0; |
---|
| 668 | } |
---|
| 669 | |
---|
| 670 | //rot = rot * f4_OrientMat(yOz, xrot); |
---|
| 671 | //rot = rot * f4_OrientMat(xOy, zrot); |
---|
| 672 | // rotation relative to parent stick |
---|
| 673 | //OM = rot * OM; |
---|
| 674 | |
---|
| 675 | // rotation in world coordinates |
---|
| 676 | //OM = ((f4_OrientMat)dadlink->OM) * OM; |
---|
| 677 | mz = dadlink->mz / dadlink->childcount; |
---|
| 678 | } |
---|
| 679 | //Pt3D lastoffset = (Orient)OM * (Pt3D(1,0,0)*P.len); |
---|
| 680 | //lastend = firstend + lastoffset; |
---|
| 681 | } |
---|
| 682 | } |
---|
| 683 | |
---|
| 684 | |
---|
| 685 | |
---|
| 686 | f4_CellLink::f4_CellLink(f4_Cell * nfrom, double nw, long nt) |
---|
| 687 | { |
---|
| 688 | from = nfrom; |
---|
| 689 | w = nw; |
---|
| 690 | t = nt; |
---|
| 691 | } |
---|
| 692 | |
---|
| 693 | |
---|
| 694 | |
---|
| 695 | f4_Cells::f4_Cells(f4_node * genome, int nrepair) |
---|
| 696 | { |
---|
| 697 | // create ancestor cell |
---|
| 698 | repair = nrepair; |
---|
| 699 | error = 0; |
---|
| 700 | errorpos = -1; |
---|
| 701 | repair_remove = NULL; |
---|
| 702 | repair_parent = NULL; |
---|
| 703 | repair_insert = NULL; |
---|
| 704 | tmpcel = NULL; |
---|
| 705 | f4rootnode = NULL; |
---|
| 706 | |
---|
| 707 | C[0] = new f4_Cell(this, 0, genome, genome, NULL, 0, stdProps); |
---|
| 708 | nc = 1; |
---|
| 709 | } |
---|
| 710 | |
---|
| 711 | |
---|
| 712 | f4_Cells::f4_Cells(SString & genome, int nrepair) |
---|
| 713 | { |
---|
| 714 | int res; |
---|
| 715 | repair = nrepair; |
---|
| 716 | error = 0; |
---|
| 717 | errorpos = -1; |
---|
| 718 | repair_remove = NULL; |
---|
| 719 | repair_parent = NULL; |
---|
| 720 | repair_insert = NULL; |
---|
| 721 | tmpcel = NULL; |
---|
| 722 | f4rootnode = NULL; |
---|
| 723 | |
---|
| 724 | // transform geno from string to nodes |
---|
| 725 | f4rootnode = new f4_node(); |
---|
| 726 | res = f4_processrec((const char*)genome, (unsigned)0, f4rootnode); |
---|
| 727 | if ((res<0) || (1 != f4rootnode->childCount())) |
---|
| 728 | { |
---|
| 729 | error = GENOPER_OPFAIL; |
---|
| 730 | errorpos = -1; |
---|
| 731 | } |
---|
| 732 | |
---|
| 733 | // create ancestor cell |
---|
| 734 | C[0] = new f4_Cell(this, 0, f4rootnode->child, f4rootnode->child, |
---|
| 735 | NULL, 0, stdProps); |
---|
| 736 | nc = 1; |
---|
| 737 | } |
---|
| 738 | |
---|
| 739 | f4_Cells::~f4_Cells() |
---|
| 740 | { |
---|
| 741 | // release cells |
---|
| 742 | int i; |
---|
| 743 | if (nc) |
---|
| 744 | { |
---|
| 745 | for (i=nc-1; i>=0; i--) |
---|
| 746 | delete C[i]; |
---|
| 747 | nc = 0; |
---|
| 748 | } |
---|
| 749 | if (f4rootnode) |
---|
| 750 | delete f4rootnode; |
---|
| 751 | } |
---|
| 752 | |
---|
| 753 | |
---|
| 754 | int f4_Cells::onestep() |
---|
| 755 | { |
---|
| 756 | int i, ret, oldnc, ret2; |
---|
| 757 | oldnc = nc; |
---|
| 758 | ret=0; |
---|
| 759 | for (i=0; i<oldnc; i++) { |
---|
| 760 | ret2 = C[i]->onestep(); |
---|
| 761 | if (ret2>0) { |
---|
| 762 | // error |
---|
| 763 | C[i]->active = 0; // stop |
---|
| 764 | return 0; |
---|
| 765 | } |
---|
| 766 | // if still active |
---|
| 767 | if (C[i]->active) |
---|
| 768 | ret=1; |
---|
| 769 | } |
---|
| 770 | return ret; |
---|
| 771 | } |
---|
| 772 | |
---|
| 773 | |
---|
| 774 | int f4_Cells::simulate() |
---|
| 775 | { |
---|
| 776 | int i; |
---|
| 777 | error = GENOPER_OK; |
---|
| 778 | |
---|
| 779 | for (i=0; i<nc; i++) C[i]->active = 1; |
---|
| 780 | |
---|
| 781 | // execute onestep() in a cycle |
---|
| 782 | while (onestep()) ; |
---|
| 783 | |
---|
| 784 | if (GENOPER_OK != error) return error; |
---|
| 785 | |
---|
| 786 | // fix neuron attachements |
---|
| 787 | for(i=0; i<nc; i++) |
---|
| 788 | if (C[i]->type == T_NEURON4) { |
---|
| 789 | while (T_NEURON4 == C[i]->dadlink->type) { |
---|
| 790 | C[i]->dadlink = C[i]->dadlink->dadlink; |
---|
| 791 | } |
---|
| 792 | } |
---|
| 793 | |
---|
| 794 | // there should be no undiff. cells |
---|
| 795 | // make undifferentiated cells sticks |
---|
| 796 | for (i=0; i<nc ; i++) |
---|
| 797 | if (C[i]->type == T_UNDIFF4) { |
---|
| 798 | C[i]->type = T_STICK4; |
---|
| 799 | //seterror(); |
---|
| 800 | } |
---|
| 801 | |
---|
| 802 | // recursive adjust |
---|
| 803 | // reset recursive traverse flags |
---|
| 804 | for(i=0; i<nc; i++) |
---|
| 805 | C[i]->recProcessedFlag = 0; |
---|
| 806 | // process every cell |
---|
| 807 | for(i=0; i<nc; i++) |
---|
| 808 | C[i]->adjustRec(); |
---|
| 809 | |
---|
| 810 | //DB( printf("Cell simulation done, %d cells. \n", nc); ) |
---|
| 811 | |
---|
| 812 | return error; |
---|
| 813 | } |
---|
| 814 | |
---|
| 815 | |
---|
| 816 | void f4_Cells::addCell(f4_Cell * newcell) |
---|
| 817 | { |
---|
| 818 | if (nc >= MAX4CELLS-1) { |
---|
| 819 | delete newcell; |
---|
| 820 | return; |
---|
| 821 | } |
---|
| 822 | C[nc] = newcell; |
---|
| 823 | nc++; |
---|
| 824 | } |
---|
| 825 | |
---|
| 826 | |
---|
| 827 | void f4_Cells::setError(int nerrpos) |
---|
| 828 | { |
---|
| 829 | error = GENOPER_OPFAIL; |
---|
| 830 | errorpos = nerrpos; |
---|
| 831 | } |
---|
| 832 | |
---|
| 833 | void f4_Cells::setRepairRemove(int nerrpos, f4_node * rem) |
---|
| 834 | { |
---|
| 835 | if (!repair) { |
---|
| 836 | // not in repair mode, treat as repairable error |
---|
| 837 | error = GENOPER_REPAIR; |
---|
| 838 | errorpos = nerrpos; |
---|
| 839 | } else { |
---|
| 840 | error = GENOPER_REPAIR; |
---|
| 841 | errorpos = nerrpos; |
---|
| 842 | repair_remove = rem; |
---|
| 843 | } |
---|
| 844 | } |
---|
| 845 | |
---|
| 846 | int f4_Cells::setRepairInsert(int nerrpos, f4_node * parent, f4_node * insert) |
---|
| 847 | { |
---|
| 848 | if (!repair) { |
---|
| 849 | // not in repair mode, treat as repairable error |
---|
| 850 | error = GENOPER_REPAIR; |
---|
| 851 | errorpos = nerrpos; |
---|
| 852 | return -1; |
---|
| 853 | } else { |
---|
| 854 | error = GENOPER_REPAIR; |
---|
| 855 | errorpos = nerrpos; |
---|
| 856 | repair_parent = parent; |
---|
| 857 | repair_insert = insert; |
---|
| 858 | return 0; |
---|
| 859 | } |
---|
| 860 | } |
---|
| 861 | |
---|
| 862 | void f4_Cells::repairGeno(f4_node * geno, int whichchild) |
---|
| 863 | { |
---|
| 864 | // assemble repaired geno, if the case |
---|
| 865 | if (!repair) return; |
---|
| 866 | if ((NULL==repair_remove) && (NULL==repair_insert)) return; |
---|
| 867 | // traverse genotype tree, remove / insert node |
---|
| 868 | f4_node * g2; |
---|
| 869 | if (1==whichchild) g2 = geno->child; |
---|
| 870 | else g2 = geno->child2; |
---|
| 871 | if (NULL == g2) |
---|
| 872 | return; |
---|
| 873 | if (g2 == repair_remove) { |
---|
| 874 | f4_node * oldgeno; |
---|
| 875 | geno->removeChild(g2); |
---|
| 876 | if (g2->child) { |
---|
| 877 | // add g2->child as child to geno |
---|
| 878 | if (1==whichchild) geno->child = g2->child; |
---|
| 879 | else geno->child2 = g2->child; |
---|
| 880 | g2->child->parent = geno; |
---|
| 881 | } |
---|
| 882 | oldgeno = g2; |
---|
| 883 | oldgeno->child = NULL; |
---|
| 884 | delete oldgeno; |
---|
| 885 | if (NULL == geno->child) return; |
---|
| 886 | // check this new |
---|
| 887 | repairGeno(geno, whichchild); |
---|
| 888 | return; |
---|
| 889 | } |
---|
| 890 | if (g2 == repair_parent) { |
---|
| 891 | geno->removeChild(g2); |
---|
| 892 | geno->addChild(repair_insert); |
---|
| 893 | repair_insert->parent = geno; |
---|
| 894 | repair_insert->child = g2; |
---|
| 895 | repair_insert->child2 = NULL; |
---|
| 896 | g2->parent = repair_insert; |
---|
| 897 | } |
---|
| 898 | // recurse |
---|
| 899 | if (g2->child) repairGeno(g2, 1); |
---|
| 900 | if (g2->child2) repairGeno(g2, 2); |
---|
| 901 | } |
---|
| 902 | |
---|
| 903 | |
---|
| 904 | void f4_Cells::toF1Geno(SString &out) |
---|
| 905 | { |
---|
| 906 | if (tmpcel) delete tmpcel; |
---|
| 907 | tmpcel = new f4_Cell(-1, NULL, 0, stdProps); |
---|
| 908 | out = ""; |
---|
| 909 | toF1GenoRec(0, out); |
---|
| 910 | delete tmpcel; |
---|
| 911 | } |
---|
| 912 | |
---|
| 913 | |
---|
| 914 | void f4_Cells::toF1GenoRec(int curc, SString &out) |
---|
| 915 | { |
---|
| 916 | int i, j, ccount; |
---|
| 917 | f4_Cell * thisti; |
---|
| 918 | f4_Cell * thneu; |
---|
| 919 | char buf[200]; |
---|
| 920 | |
---|
| 921 | if (curc >= nc) return; |
---|
| 922 | |
---|
| 923 | if (T_STICK4 != C[curc]->type) return; |
---|
| 924 | |
---|
| 925 | thisti = C[curc]; |
---|
| 926 | if (NULL != thisti->dadlink) |
---|
| 927 | *tmpcel = *(thisti->dadlink); |
---|
| 928 | |
---|
| 929 | // adjust length, curvedness, etc. |
---|
| 930 | tmpcel->P.adjust(); |
---|
| 931 | while (tmpcel->P.len > thisti->P.len) |
---|
| 932 | { |
---|
| 933 | tmpcel->P.executeModifier('l'); |
---|
| 934 | out += "l"; |
---|
| 935 | } |
---|
| 936 | while (tmpcel->P.len < thisti->P.len) |
---|
| 937 | { |
---|
| 938 | tmpcel->P.executeModifier('L'); |
---|
| 939 | out += "L"; |
---|
| 940 | } |
---|
| 941 | while (tmpcel->P.curv > thisti->P.curv) |
---|
| 942 | { |
---|
| 943 | tmpcel->P.executeModifier('c'); |
---|
| 944 | out += "c"; |
---|
| 945 | } |
---|
| 946 | while (tmpcel->P.curv < thisti->P.curv) |
---|
| 947 | { |
---|
| 948 | tmpcel->P.executeModifier('C'); |
---|
| 949 | out += "C"; |
---|
| 950 | } |
---|
| 951 | while (thisti->rolling > 0.0f) { |
---|
| 952 | rolling_dec( &(thisti->rolling) ); |
---|
| 953 | out += "R"; |
---|
| 954 | } |
---|
| 955 | while (thisti->rolling < 0.0f) { |
---|
| 956 | rolling_inc( &(thisti->rolling) ); |
---|
| 957 | out += "r"; |
---|
| 958 | } |
---|
| 959 | |
---|
| 960 | // output X for this stick |
---|
| 961 | out += "X"; |
---|
| 962 | |
---|
| 963 | // neurons attached to it |
---|
| 964 | for (i=0; i<nc; i++) |
---|
| 965 | if (C[i]->type == T_NEURON4) { |
---|
| 966 | if (C[i]->dadlink == thisti) { |
---|
| 967 | thneu = C[i]; |
---|
| 968 | out += "["; |
---|
| 969 | // ctrl |
---|
| 970 | if (1 == thneu->ctrl) out += "@"; |
---|
| 971 | if (2 == thneu->ctrl) out += "|"; |
---|
| 972 | // links |
---|
| 973 | for (j=0; j<thneu->nolink; j++) |
---|
| 974 | { |
---|
| 975 | if (j) out += ","; |
---|
| 976 | if (NULL == thneu->links[j]->from) |
---|
| 977 | { |
---|
| 978 | // sensory |
---|
| 979 | if (1 == thneu->links[j]->t) out += "*"; |
---|
| 980 | if (2 == thneu->links[j]->t) out += "G"; |
---|
| 981 | if (3 == thneu->links[j]->t) out += "T"; |
---|
| 982 | if (4 == thneu->links[j]->t) out += "S"; |
---|
| 983 | } else { |
---|
| 984 | sprintf(buf, "%d", thneu->links[j]->from->name - thneu->name); |
---|
| 985 | out += buf; |
---|
| 986 | } |
---|
| 987 | out += ":"; |
---|
| 988 | // weight |
---|
| 989 | sprintf(buf, "%g", thneu->links[j]->w ); |
---|
| 990 | out += buf; |
---|
| 991 | } |
---|
| 992 | out += "]"; |
---|
| 993 | } |
---|
| 994 | } |
---|
| 995 | |
---|
| 996 | // sticks connected to it |
---|
| 997 | if (thisti->commacount>=2) |
---|
| 998 | out += "("; |
---|
| 999 | |
---|
| 1000 | ccount=1; |
---|
| 1001 | for (i=0; i<nc; i++) |
---|
| 1002 | if (C[i]->type == T_STICK4) |
---|
| 1003 | if (C[i]->dadlink == thisti) { |
---|
| 1004 | while (ccount < (C[i])->anglepos) { |
---|
| 1005 | ccount++; |
---|
| 1006 | out += ","; |
---|
| 1007 | } |
---|
| 1008 | toF1GenoRec(i, out); |
---|
| 1009 | } |
---|
| 1010 | while (ccount < thisti->commacount) { |
---|
| 1011 | ccount++; |
---|
| 1012 | out += ","; |
---|
| 1013 | } |
---|
| 1014 | |
---|
| 1015 | if (thisti->commacount >= 2) |
---|
| 1016 | out += ")"; |
---|
| 1017 | } |
---|
| 1018 | |
---|
| 1019 | |
---|
| 1020 | |
---|
| 1021 | // to organize a f4 genotype in a tree structure |
---|
| 1022 | |
---|
| 1023 | f4_node::f4_node() |
---|
| 1024 | { |
---|
| 1025 | name = '?'; |
---|
| 1026 | parent = NULL; |
---|
| 1027 | child = NULL; |
---|
| 1028 | child2 = NULL; |
---|
| 1029 | pos = -1; |
---|
| 1030 | } |
---|
| 1031 | |
---|
| 1032 | f4_node::f4_node(char nname, f4_node * nparent, int npos) |
---|
| 1033 | { |
---|
| 1034 | name = nname; |
---|
| 1035 | parent = nparent; |
---|
| 1036 | child = NULL; |
---|
| 1037 | child2 = NULL; |
---|
| 1038 | pos = npos; |
---|
| 1039 | if (parent) parent->addChild(this); |
---|
| 1040 | } |
---|
| 1041 | |
---|
| 1042 | f4_node::~f4_node() |
---|
| 1043 | { |
---|
| 1044 | // (destroy() copied here for efficiency) |
---|
| 1045 | // children are destroyed (recursively) through the destructor |
---|
| 1046 | if (NULL != child2) delete child2; |
---|
| 1047 | if (NULL != child) delete child; |
---|
| 1048 | } |
---|
| 1049 | |
---|
| 1050 | int f4_node::addChild(f4_node * nchi) |
---|
| 1051 | { |
---|
| 1052 | if (NULL==child) { |
---|
| 1053 | child = nchi; |
---|
| 1054 | return 0; |
---|
| 1055 | } |
---|
| 1056 | if (NULL==child2) { |
---|
| 1057 | child2 = nchi; |
---|
| 1058 | return 0; |
---|
| 1059 | } |
---|
| 1060 | return -1; |
---|
| 1061 | } |
---|
| 1062 | |
---|
| 1063 | int f4_node::removeChild(f4_node * nchi) |
---|
| 1064 | { |
---|
| 1065 | if (nchi==child2) { |
---|
| 1066 | child2 = NULL; |
---|
| 1067 | return 0; |
---|
| 1068 | } |
---|
| 1069 | if (nchi==child) { |
---|
| 1070 | child = NULL; |
---|
| 1071 | return 0; |
---|
| 1072 | } |
---|
| 1073 | return -1; |
---|
| 1074 | } |
---|
| 1075 | |
---|
| 1076 | int f4_node::childCount() |
---|
| 1077 | { |
---|
| 1078 | if (NULL!=child) { |
---|
| 1079 | if (NULL!=child2) return 2; |
---|
| 1080 | else return 1; |
---|
| 1081 | } else { |
---|
| 1082 | if (NULL!=child2) return 1; |
---|
| 1083 | else return 0; |
---|
| 1084 | } |
---|
| 1085 | } |
---|
| 1086 | |
---|
| 1087 | int f4_node::count() |
---|
| 1088 | { |
---|
| 1089 | int c=1; |
---|
| 1090 | if (NULL!=child) c+=child->count(); |
---|
| 1091 | if (NULL!=child2) c+=child2->count(); |
---|
| 1092 | return c; |
---|
| 1093 | } |
---|
| 1094 | |
---|
| 1095 | f4_node * f4_node::ordNode(int n) |
---|
| 1096 | { |
---|
| 1097 | int n1; |
---|
| 1098 | if (0 == n) return this; |
---|
| 1099 | n--; |
---|
| 1100 | if (NULL != child) { |
---|
| 1101 | n1 = child->count(); |
---|
| 1102 | if (n<n1) return child->ordNode(n); |
---|
| 1103 | n -= n1; |
---|
| 1104 | } |
---|
| 1105 | if (NULL != child2) { |
---|
| 1106 | n1 = child2->count(); |
---|
| 1107 | if (n<n1) return child2->ordNode(n); |
---|
| 1108 | n -= n1; |
---|
| 1109 | } |
---|
| 1110 | return NULL; |
---|
| 1111 | } |
---|
| 1112 | |
---|
| 1113 | f4_node * f4_node::randomNode() |
---|
| 1114 | { |
---|
| 1115 | int n, i; |
---|
| 1116 | n = count(); |
---|
| 1117 | // pick a random node, between 0 and n-1 |
---|
| 1118 | i = (int)( ((float)n-0.0001) / RAND_MAX * rand()); |
---|
| 1119 | return ordNode(i); |
---|
| 1120 | } |
---|
| 1121 | |
---|
| 1122 | f4_node * f4_node::randomNodeWithSize(int min, int max) |
---|
| 1123 | { |
---|
| 1124 | // try random nodes, and accept if size in range |
---|
| 1125 | // limit to maxlim tries |
---|
| 1126 | int i, n, maxlim; |
---|
| 1127 | f4_node * nod = NULL; |
---|
| 1128 | maxlim = count(); |
---|
| 1129 | for (i=0; i<maxlim; i++) { |
---|
| 1130 | nod = randomNode(); |
---|
| 1131 | n = nod->count(); |
---|
| 1132 | if ((n>=min) && (n<=max)) return nod; |
---|
| 1133 | } |
---|
| 1134 | // failed, doesn't matter |
---|
| 1135 | return nod; |
---|
| 1136 | } |
---|
| 1137 | |
---|
| 1138 | void f4_node::sprint(SString & out) |
---|
| 1139 | { |
---|
| 1140 | char buf2[20]; |
---|
| 1141 | // special case: repetition code |
---|
| 1142 | if ('#' == name) |
---|
| 1143 | { |
---|
| 1144 | out += "#"; |
---|
| 1145 | if (i1 != 1) { |
---|
| 1146 | sprintf(buf2, "%d", i1); |
---|
| 1147 | out += buf2; |
---|
| 1148 | } |
---|
| 1149 | } else { |
---|
| 1150 | // special case: neuron link |
---|
| 1151 | if ('[' == name) { |
---|
| 1152 | out += "["; |
---|
| 1153 | if (i1>0) { |
---|
| 1154 | // sensor input |
---|
| 1155 | if (1==i1) out += "*"; |
---|
| 1156 | if (2==i1) out += "G"; |
---|
| 1157 | if (3==i1) out += "T"; |
---|
| 1158 | if (4==i1) out += "S"; |
---|
| 1159 | } else { |
---|
| 1160 | sprintf(buf2, "%ld", l1); |
---|
| 1161 | out += buf2; |
---|
| 1162 | } |
---|
| 1163 | sprintf(buf2, ":%g]", f1); |
---|
| 1164 | out += buf2; |
---|
| 1165 | } else if (':' == name) { |
---|
| 1166 | sprintf(buf2, ":%c%c:", l1 ? '+' : '-', (char)i1); |
---|
| 1167 | out += buf2; |
---|
| 1168 | } else { |
---|
| 1169 | buf2[0] = name; |
---|
| 1170 | buf2[1] = 0; |
---|
| 1171 | out += buf2; |
---|
| 1172 | }} |
---|
| 1173 | if (NULL != child) child->sprint(out); |
---|
| 1174 | // if two children, make sure last char is a '>' |
---|
| 1175 | if (2 == childCount()) |
---|
| 1176 | if (0 == out[0]) out += ">"; else |
---|
| 1177 | if ('>' != out[out.len()-1]) out += ">"; |
---|
| 1178 | if (NULL != child2) child2->sprint(out); |
---|
| 1179 | // make sure last char is a '>' |
---|
| 1180 | if (0 == out[0]) out += ">"; else |
---|
| 1181 | if ('>' != out[out.len()-1]) out += ">"; |
---|
| 1182 | } |
---|
| 1183 | |
---|
| 1184 | void f4_node::sprintAdj(char *& buf) |
---|
| 1185 | { |
---|
| 1186 | unsigned int len; |
---|
| 1187 | // build in a SString, with initial size |
---|
| 1188 | SString out(strlen(buf)+2000); |
---|
| 1189 | out=""; |
---|
| 1190 | |
---|
| 1191 | sprint(out); |
---|
| 1192 | |
---|
| 1193 | // very last '>' can be omitted |
---|
| 1194 | len = out.len(); |
---|
| 1195 | if (len>1) |
---|
| 1196 | if ('>' == out[len-1]) { (out.directWrite())[len-1]=0; out.endWrite();}; |
---|
| 1197 | // copy back to string |
---|
| 1198 | // if new is longer, reallocate buf |
---|
| 1199 | if (len+1 > strlen(buf)) { |
---|
| 1200 | buf = (char*) realloc(buf, len+1 ); |
---|
| 1201 | } |
---|
| 1202 | strcpy(buf, (const char*) out); |
---|
| 1203 | } |
---|
| 1204 | |
---|
| 1205 | f4_node * f4_node::duplicate() |
---|
| 1206 | { |
---|
| 1207 | f4_node * copy; |
---|
| 1208 | copy = new f4_node(*this); |
---|
| 1209 | copy->parent = NULL; // set later |
---|
| 1210 | copy->child = NULL; |
---|
| 1211 | copy->child2 = NULL; |
---|
| 1212 | if (NULL != child ) { |
---|
| 1213 | copy->child = child ->duplicate(); |
---|
| 1214 | copy->child ->parent = copy; |
---|
| 1215 | } |
---|
| 1216 | if (NULL != child2 ) { |
---|
| 1217 | copy->child2 = child2->duplicate(); |
---|
| 1218 | copy->child2->parent = copy; |
---|
| 1219 | } |
---|
| 1220 | return copy; |
---|
| 1221 | } |
---|
| 1222 | |
---|
| 1223 | |
---|
| 1224 | void f4_node::destroy() |
---|
| 1225 | { |
---|
| 1226 | // children are destroyed (recursively) through the destructor |
---|
| 1227 | if (NULL != child2) delete child2; |
---|
| 1228 | if (NULL != child) delete child; |
---|
| 1229 | } |
---|
| 1230 | |
---|
| 1231 | |
---|
| 1232 | // scan genotype string and build tree |
---|
| 1233 | // return >1 for error (errorpos) |
---|
| 1234 | int f4_processrec(const char * genot, unsigned pos0, f4_node * parent) |
---|
| 1235 | { |
---|
| 1236 | int i, j, t, res; |
---|
| 1237 | char tc1, tc2; |
---|
| 1238 | long relfrom; |
---|
| 1239 | double w; |
---|
| 1240 | unsigned gpos, oldpos; |
---|
| 1241 | f4_node * node1, * par; |
---|
| 1242 | |
---|
| 1243 | gpos = pos0; |
---|
| 1244 | par = parent; |
---|
| 1245 | if (gpos >= strlen(genot) ) return 1; |
---|
| 1246 | while (gpos<strlen(genot)) { |
---|
| 1247 | //DB( printf(" processing '%c' %d %s\n", genot[gpos], gpos, genot); ) |
---|
| 1248 | switch (genot[gpos]) { |
---|
| 1249 | case '<': |
---|
| 1250 | // cell division! |
---|
| 1251 | //DB( printf(" div! %d\n", name); ) |
---|
| 1252 | |
---|
| 1253 | // find out genotype start for child |
---|
| 1254 | j = scanrec(genot+gpos+1, strlen(genot+gpos+1), '>'); |
---|
| 1255 | |
---|
| 1256 | node1 = new f4_node('<', par, gpos); |
---|
| 1257 | par = node1; |
---|
| 1258 | res = f4_processrec(genot, gpos+1, par); |
---|
| 1259 | if (res) return res; |
---|
| 1260 | if (gpos+j+2 < strlen(genot)) { |
---|
| 1261 | res = f4_processrec(genot, gpos+j+2, par); |
---|
| 1262 | if (res) return res; |
---|
| 1263 | } else { // ran out |
---|
| 1264 | node1 = new f4_node('>', par, strlen(genot)-1 ); |
---|
| 1265 | par = node1; |
---|
| 1266 | } |
---|
| 1267 | // adjustments |
---|
| 1268 | gpos++; |
---|
| 1269 | return 0; // OK |
---|
| 1270 | |
---|
| 1271 | case '>': |
---|
| 1272 | node1 = new f4_node('>', par, gpos ); |
---|
| 1273 | par = node1; |
---|
| 1274 | gpos = strlen(genot); |
---|
| 1275 | return 0; // OK |
---|
| 1276 | |
---|
| 1277 | case '#': |
---|
| 1278 | // repetition marker, 1 by default |
---|
| 1279 | if (sscanf(genot+gpos, "#%d", &i) != 1) i=1; |
---|
| 1280 | // find out genotype start for continuation |
---|
| 1281 | j = scanrec(genot+gpos+1, strlen(genot+gpos+1), '>'); |
---|
| 1282 | // skip number |
---|
| 1283 | oldpos = gpos; |
---|
| 1284 | gpos++; |
---|
| 1285 | while ((genot[gpos]>='0') && (genot[gpos]<='9')) gpos++; |
---|
| 1286 | node1 = new f4_node('#', par, oldpos ); |
---|
| 1287 | node1->i1 = i; |
---|
| 1288 | par = node1; |
---|
| 1289 | res = f4_processrec(genot, gpos, node1); |
---|
| 1290 | if (res) return res; |
---|
| 1291 | if (oldpos+j+2 < strlen(genot) ) { |
---|
| 1292 | res = f4_processrec(genot, oldpos+j+2, node1); |
---|
| 1293 | if (res) return res; |
---|
| 1294 | } else { // ran out |
---|
| 1295 | node1 = new f4_node('>', par, strlen(genot)-1 ); |
---|
| 1296 | } |
---|
| 1297 | return 0; // OK |
---|
| 1298 | |
---|
| 1299 | // 'simple' nodes: |
---|
| 1300 | case ',': |
---|
| 1301 | case 'l': case 'L': |
---|
| 1302 | case 'c': case 'C': |
---|
| 1303 | case 'q': case 'Q': |
---|
| 1304 | case 'r': case 'R': |
---|
| 1305 | case 'X': case 'N': |
---|
| 1306 | case '@': case '|': |
---|
| 1307 | case 'a': case 'A': |
---|
| 1308 | case 's': case 'S': |
---|
| 1309 | case 'm': case 'M': |
---|
| 1310 | case 'i': case 'I': |
---|
| 1311 | case 'f': case 'F': |
---|
| 1312 | case 'w': case 'W': |
---|
| 1313 | case 'e': case 'E': |
---|
| 1314 | node1 = new f4_node(genot[gpos], par, gpos ); |
---|
| 1315 | par = node1; |
---|
| 1316 | gpos++; |
---|
| 1317 | break; |
---|
| 1318 | |
---|
| 1319 | case '[': |
---|
| 1320 | // link to neuron |
---|
| 1321 | // input (%d, '*', 'G', 'T', 'S') |
---|
| 1322 | t = -1; |
---|
| 1323 | if (sscanf(genot+gpos, "[%ld:%lf]", &relfrom, &w) == 2) t=0; |
---|
| 1324 | else if (sscanf(genot+gpos, "[*:%lf]", &w) == 1) t=1; |
---|
| 1325 | else if (sscanf(genot+gpos, "[G:%lf]", &w) == 1) t=2; |
---|
| 1326 | else if (sscanf(genot+gpos, "[T:%lf]", &w) == 1) t=3; |
---|
| 1327 | else if (sscanf(genot+gpos, "[S:%lf]", &w) == 1) t=4; |
---|
| 1328 | // error: no correct format |
---|
| 1329 | if (t<0) return gpos+1+1; |
---|
| 1330 | node1 = new f4_node('[', par, gpos ); |
---|
| 1331 | node1->i1 = t; |
---|
| 1332 | node1->l1 = relfrom; |
---|
| 1333 | node1->f1 = w; |
---|
| 1334 | par = node1; |
---|
| 1335 | j = scanrec(genot+gpos+1, strlen(genot+gpos+1), ']'); |
---|
| 1336 | gpos += j+2; |
---|
| 1337 | break; |
---|
| 1338 | |
---|
| 1339 | case ':': |
---|
| 1340 | // neuron parameter +! -! += -= +/ or -/ |
---|
| 1341 | if (sscanf(genot+gpos, ":%c%c:", &tc1, &tc2) != 2) |
---|
| 1342 | // error: incorrect format |
---|
| 1343 | return gpos+1+1; |
---|
| 1344 | if ('+' == tc1) j=1; |
---|
| 1345 | else if ('-' == tc1) j=0; |
---|
| 1346 | else return gpos+1+1; |
---|
| 1347 | switch (tc2) { |
---|
| 1348 | case '!': case '=': case '/': break; |
---|
| 1349 | default: |
---|
| 1350 | return gpos+1+1; |
---|
| 1351 | } |
---|
| 1352 | node1 = new f4_node(':', par, gpos ); |
---|
| 1353 | node1->l1 = j; |
---|
| 1354 | node1->i1 = (int)tc2; |
---|
| 1355 | par = node1; |
---|
| 1356 | j = scanrec(genot+gpos+1, strlen(genot+gpos+1), ':'); |
---|
| 1357 | gpos += j+2; |
---|
| 1358 | break; |
---|
| 1359 | |
---|
| 1360 | case ' ': |
---|
| 1361 | case '\n': |
---|
| 1362 | case '\t': |
---|
| 1363 | // whitespace: ignore |
---|
| 1364 | //node1 = new f4_node(' ', par, gpos ); |
---|
| 1365 | //par = node1; |
---|
| 1366 | gpos++; |
---|
| 1367 | break; |
---|
| 1368 | |
---|
| 1369 | default: |
---|
| 1370 | //DB( printf("unknown character '%c' ! \n", genot[gpos]); ) |
---|
| 1371 | //add it, build will give the error or repair |
---|
| 1372 | node1 = new f4_node(genot[gpos], par, gpos ); |
---|
| 1373 | par = node1; |
---|
| 1374 | gpos++; |
---|
| 1375 | break; |
---|
| 1376 | } |
---|
| 1377 | } |
---|
| 1378 | // should end with a '>' |
---|
| 1379 | if (par) |
---|
| 1380 | if ('>' != par->name) { |
---|
| 1381 | node1 = new f4_node('>', par, strlen(genot)-1 ); |
---|
| 1382 | par = node1; |
---|
| 1383 | } |
---|
| 1384 | return 0; // OK |
---|
| 1385 | } |
---|
| 1386 | |
---|
| 1387 | |
---|
| 1388 | f4_node * f4_processtree(const char * geno) |
---|
| 1389 | { |
---|
| 1390 | f4_node * root; |
---|
| 1391 | int res; |
---|
| 1392 | root = new f4_node(); |
---|
| 1393 | res = f4_processrec(geno, 0, root); |
---|
| 1394 | if (res) return NULL; |
---|
| 1395 | //DB( printf("test f4 "); ) |
---|
| 1396 | DB( |
---|
| 1397 | if (root->child) { |
---|
| 1398 | char * buf = (char*) malloc( 300 ); |
---|
| 1399 | DB( printf("(%d) ", root->child->count() ); ) |
---|
| 1400 | buf[0]=0; |
---|
| 1401 | root->child->sprintAdj(buf); |
---|
| 1402 | DB( printf("%s\n", buf); ) |
---|
| 1403 | free(buf); |
---|
| 1404 | } |
---|
| 1405 | ) |
---|
| 1406 | return root->child; |
---|
| 1407 | } |
---|
| 1408 | |
---|