[193] | 1 | /* |
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| 2 | * f4_general.h - 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 | #ifndef _F4_GENERAL_H_ |
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| 25 | #define _F4_GENERAL_H_ |
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| 26 | |
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| 27 | #include "f4_orientmat.h" |
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| 28 | #include "3d.h" |
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| 29 | #include "sstring.h" |
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| 30 | #include "multirange.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 | class f4_Props |
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| 38 | { |
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| 39 | public: |
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| 40 | // fill with default values |
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| 41 | f4_Props(); |
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| 42 | // must sum to 1 |
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| 43 | void normalizeBiol4(); |
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| 44 | void executeModifier(char modif); |
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| 45 | void adjust(); |
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| 46 | |
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| 47 | double len; // length (dlug) |
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| 48 | double curv; // curvedness (skr) |
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| 49 | double mass; |
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| 50 | double friction; |
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| 51 | double ruch; |
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| 52 | double assim; |
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| 53 | double odpor; |
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| 54 | double ingest; // ingestion (wchl) |
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| 55 | double twist; |
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| 56 | double energ; |
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| 57 | }; |
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| 58 | |
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| 59 | extern f4_Props stdProps; |
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| 60 | |
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| 61 | |
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| 62 | // rolling (one-time) |
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| 63 | void rolling_dec(double * v); |
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| 64 | void rolling_inc(double * v); |
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| 65 | |
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| 66 | |
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| 67 | class f4_node; // later |
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| 68 | class f4_Cell; // later |
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| 69 | class f4_Cells; // later |
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| 70 | |
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| 71 | |
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| 72 | // cell types |
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| 73 | #define T_UNDIFF4 40 |
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| 74 | #define T_STICK4 41 |
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| 75 | #define T_NEURON4 42 |
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| 76 | |
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| 77 | int scanrec(const char * s, unsigned int slen, char stopchar); |
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| 78 | |
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| 79 | |
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| 80 | class f4_CellLink; |
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| 81 | #define MAXINPUTS 100 |
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| 82 | |
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| 83 | // an abstract cell type, extension of part/stick -- for developmental encoding |
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| 84 | class f4_Cell |
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| 85 | { |
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| 86 | public: |
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| 87 | class repeat_ptr |
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| 88 | { |
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| 89 | public: |
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| 90 | repeat_ptr() : node(NULL), count(-1) { }; |
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| 91 | repeat_ptr(f4_node * a, int b) : node(a), count(b) { }; |
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| 92 | inline void null() { node = NULL; count = -1; }; |
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| 93 | inline bool isNull() const { return ((node == NULL) || (count <= 0)); }; |
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| 94 | inline void dec() { count--; }; |
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| 95 | f4_node * node; // ptr to repetition code |
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| 96 | char count; // repetition counter |
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| 97 | }; |
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| 98 | |
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| 99 | class repeat_stack // a stack of repet_ptr's |
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| 100 | { |
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| 101 | public: |
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| 102 | repeat_stack() { top=0; }; |
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| 103 | inline void null() { top=0; }; |
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| 104 | inline void push(repeat_ptr A) { if (top>=stackSize) return; ptr[top]=A; top++; }; |
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| 105 | inline void pop() { if (top>0) top--; }; |
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| 106 | inline repeat_ptr * first() { return &(ptr[top-(top>0)]); }; |
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| 107 | static const int stackSize = 4; // max 4 nested levels |
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| 108 | repeat_ptr ptr[stackSize]; |
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| 109 | short int top; // top of the stack |
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| 110 | }; |
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| 111 | |
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| 112 | f4_Cell(int nname, |
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| 113 | f4_Cell * ndad, int nangle, f4_Props newP); |
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| 114 | f4_Cell(f4_Cells * nO, int nname, f4_node * ngeno, f4_node * ngcur, |
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| 115 | f4_Cell * ndad, int nangle, f4_Props newP); |
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| 116 | ~f4_Cell(); |
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| 117 | |
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| 118 | int onestep(); // execute one simulation step (till a division) |
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| 119 | |
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| 120 | int addlink(f4_Cell * nfrom, double nw, long nt); |
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| 121 | void adjustRec(); |
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| 122 | |
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| 123 | int name; // name (number) |
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| 124 | int type; // type |
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| 125 | f4_Cell * dadlink; |
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| 126 | f4_Cells * org; // uplink to organism |
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| 127 | |
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| 128 | f4_node * genot; // genotype |
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| 129 | f4_node * gcur; // current genotype execution pointer |
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| 130 | int active; // whether development is still active |
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| 131 | repeat_stack repeat; |
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| 132 | int recProcessedFlag; // used during recursive traverse |
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| 133 | // remember the genotype codes affecting this cell so far |
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| 134 | MultiRange genoRange; |
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| 135 | |
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| 136 | f4_Props P; // properties |
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| 137 | int anglepos; // number of position within dad's children (,) |
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| 138 | int childcount; // number of children |
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| 139 | int commacount; // number of postitions at lastend (>=childcount) |
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| 140 | double rolling; // rolling angle ('R') (around x) |
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| 141 | double xrot; |
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| 142 | double zrot; // horizontal rotation angle due to |
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| 143 | // branching (around z) |
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| 144 | //Pt3D firstend; // coord.s of first end (connects to parent) |
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| 145 | //Pt3D lastend; // last end |
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| 146 | //f4_OrientMat OM; |
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| 147 | double mz; // freedom in z |
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| 148 | long p2_refno; // number of last end part object, used in f0 |
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| 149 | long joint_refno; // number of the joint object, used in f0 |
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| 150 | long neuro_refno; // number of the neuro object, used in f0 |
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| 151 | |
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| 152 | long ctrl; // neuron type |
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| 153 | double state; |
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| 154 | double inertia; |
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| 155 | double force; |
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| 156 | double sigmo; |
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| 157 | f4_CellLink* links[MAXINPUTS]; |
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| 158 | int nolink; |
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| 159 | }; |
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| 160 | |
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| 161 | |
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| 162 | // an input link to a neuron |
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| 163 | class f4_CellLink |
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| 164 | { |
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| 165 | public: |
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| 166 | f4_CellLink(f4_Cell * nfrom, double nw, long nt); |
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| 167 | f4_Cell * from; |
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| 168 | // type: 0: input, 1 '*', 2 'G', 3 'T', 4 'S' |
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| 169 | long t; |
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| 170 | double w; |
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| 171 | }; |
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| 172 | |
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| 173 | |
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| 174 | // a collection of cells, like Organism, for developmental encoding |
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| 175 | #define MAX4CELLS 100 |
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| 176 | class f4_Cells |
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| 177 | { |
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| 178 | public: |
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| 179 | f4_Cells(f4_node * genome, int nrepair); |
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| 180 | f4_Cells(SString &genome, int nrepair); |
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| 181 | ~f4_Cells(); |
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| 182 | void addCell(f4_Cell * newcell); |
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| 183 | void toF1Geno(SString &out); // output to f1 format, approximation |
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| 184 | int onestep(); // simulate all parts for one step |
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| 185 | int simulate(); // simulate development, return error (0 for ok) |
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| 186 | // for error reporting / genotype fixing |
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| 187 | int geterror() { return error;}; |
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| 188 | int geterrorpos() { return errorpos;}; |
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| 189 | void setError(int nerrpos); |
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| 190 | void setRepairRemove(int nerrpos, f4_node * rem); |
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| 191 | int setRepairInsert(int nerrpos, f4_node * parent, f4_node * insert); |
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| 192 | void repairGeno(f4_node * geno, int whichchild); |
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| 193 | |
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| 194 | // the cells |
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| 195 | f4_Cell * C[MAX4CELLS]; |
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| 196 | int nc; |
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| 197 | |
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| 198 | private: |
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| 199 | // for error reporting / genotype fixing |
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| 200 | int repair; |
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| 201 | int error; |
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| 202 | int errorpos; |
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| 203 | f4_node * repair_remove; |
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| 204 | f4_node * repair_parent; |
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| 205 | f4_node * repair_insert; |
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| 206 | void toF1GenoRec(int curc, SString &out); |
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| 207 | f4_Cell * tmpcel; // needed by toF1Geno |
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| 208 | f4_node * f4rootnode; // used by constructor |
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| 209 | }; |
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| 210 | |
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| 211 | |
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| 212 | /** |
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| 213 | * Class to organize a f4 genotype in a tree structure. |
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| 214 | */ |
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| 215 | class f4_node |
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| 216 | { |
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| 217 | public: |
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| 218 | char name; // one-letter 'name' |
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| 219 | f4_node * parent; // parent link, or NULL |
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| 220 | f4_node * child; // child, or NULL |
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| 221 | f4_node * child2; // second child, or NULL |
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| 222 | int pos; // original position in string |
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| 223 | int i1; // internal int parameter1 |
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| 224 | long l1; // internal long parameter1 |
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| 225 | double f1; // internal double parameter1 |
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| 226 | |
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| 227 | f4_node(); |
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| 228 | f4_node(char nname, f4_node * nparent, int npos); |
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| 229 | ~f4_node(); |
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| 230 | int addChild(f4_node * nchi); |
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| 231 | int removeChild(f4_node * nchi); |
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| 232 | int childCount(); // return no of children, 0, 1, or 2 |
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| 233 | int count(); // return no of nodes (recursive) |
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| 234 | f4_node * ordNode(int n); // returns the nth subnode (0-) |
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| 235 | f4_node * randomNode(); // returns a random subnode |
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| 236 | f4_node * randomNodeWithSize(int min, int max); // returns a random subnode with given size |
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| 237 | void sprintAdj(char *& buf); // print recursively |
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| 238 | f4_node * duplicate(); // create duplicate copy. recursive. |
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| 239 | void destroy(); // release memory. recursive. |
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| 240 | private: |
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| 241 | void sprint(SString & out); // print recursively |
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| 242 | }; |
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| 243 | |
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| 244 | // convert f4 geno string to tree structure (internal) |
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| 245 | f4_node * f4_processtree(const char * geno); |
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| 246 | int f4_processrec(const char * genot, unsigned pos0, f4_node * parent); |
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| 247 | |
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| 248 | |
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| 249 | #endif |
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