source: cpp/f4/f4_general.h @ 100

/*
 *  f4_general.h - f4 genotype functions.
 *
 *  f4genotype - f4 format genotype conversions for FramSticks
 *
 *  Copyright (C) 1999,2000  Adam Rotaru-Varga (adam_rotaru@yahoo.com)
 *
 *  This library is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU Lesser General Public
 *  License as published by the Free Software Foundation; either
 *  version 2.1 of the License, or (at your option) any later version.
 *
 *  This library is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 *  Lesser General Public License for more details.
 *
 *  You should have received a copy of the GNU Lesser General Public
 *  License along with this library; if not, write to the Free Software
 *  Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
 *
 */

#ifndef _F4_GENERAL_H_
#define _F4_GENERAL_H_

#include "f4_orientmat.h"
#include "3d.h"
#include "sstring.h"
#include "multirange.h"

#ifdef DMALLOC
#include <dmalloc.h>
#endif


class f4_Props
{
 public:
  // fill with default values
  f4_Props();
  // must sum to 1
  void normalizeBiol4();
  void executeModifier(char modif);
  void adjust();

  double len;      // length (dlug)
  double curv;     // curvedness (skr)
  double mass;
  double friction;
  double ruch;
  double assim;
  double odpor;
  double ingest;  // ingestion (wchl)
  double twist;
  double energ;
};

extern f4_Props stdProps;


// rolling (one-time)
void rolling_dec(double * v);
void rolling_inc(double * v);


class f4_node;   // later
class f4_Cell;   // later
class f4_Cells;  // later


// cell types
#define T_UNDIFF4 40
#define T_STICK4  41
#define T_NEURON4 42

int scanrec(const char * s, unsigned int slen, char stopchar);


class f4_CellLink;
#define MAXINPUTS 100

// an abstract cell type, extension of part/stick -- for developmental encoding
class f4_Cell
{
public:
  class repeat_ptr
  {
   public:
    repeat_ptr() : node(NULL), count(-1) { };
    repeat_ptr(f4_node * a, int b) : node(a), count(b) { };
    inline void null() { node = NULL; count = -1; };
    inline bool isNull() const { return ((node == NULL) || (count <= 0)); };
    inline void dec() { count--; };
    f4_node *  node;  // ptr to repetition code
    char       count; // repetition counter
  };

  class repeat_stack  // a stack of repet_ptr's
  {
   public:
    repeat_stack() { top=0; };
    inline void null() { top=0; };
    inline void push(repeat_ptr A) { if (top>=stackSize) return; ptr[top]=A; top++; };
    inline void pop() { if (top>0) top--; };
    inline repeat_ptr * first() { return &(ptr[top-(top>0)]); };
    static const int stackSize = 4;  // max 4 nested levels
    repeat_ptr ptr[stackSize];
    short int top;  // top of the stack
  };

  f4_Cell(int nname,
    f4_Cell * ndad, int nangle, f4_Props newP);
  f4_Cell(f4_Cells * nO, int nname, f4_node * ngeno, f4_node * ngcur,
    f4_Cell * ndad, int nangle, f4_Props newP);
  ~f4_Cell();

  int onestep();        // execute one simulation step (till a division)

  int   addlink(f4_Cell * nfrom, double nw, long nt);
  void  adjustRec();

  int        name;     // name (number)
  int        type;     // type
  f4_Cell *  dadlink;
  f4_Cells * org;       // uplink to organism

  f4_node *  genot;       // genotype
  f4_node *  gcur;        // current genotype execution pointer
  int        active;      // whether development is still active
  repeat_stack repeat;
  int        recProcessedFlag;  // used during recursive traverse
  // remember the genotype codes affecting this cell so far
  MultiRange genoRange;

  f4_Props     P;             // properties
  int          anglepos;      // number of position within dad's children (,)
  int          childcount;    // number of children
  int          commacount;    // number of postitions at lastend (>=childcount)
  double       rolling;       // rolling angle ('R') (around x)
  double       xrot;
  double       zrot;          // horizontal rotation angle due to
                              // branching (around z)
  //Pt3D         firstend;      // coord.s of first end (connects to parent)
  //Pt3D         lastend;       // last end
  //f4_OrientMat OM;
  double       mz;            // freedom in z
  long         p2_refno;   // number of last end part object, used in f0
  long         joint_refno;   // number of the joint object, used in f0
  long         neuro_refno;   // number of the neuro object, used in f0

  long         ctrl;  // neuron type
  double       state;
  double       inertia;
  double       force;
  double       sigmo;
  f4_CellLink* links[MAXINPUTS];
  int          nolink;
};


// an input link to a neuron
class f4_CellLink
{
public:
               f4_CellLink(f4_Cell * nfrom, double nw, long nt);
  f4_Cell *    from;
  // type: 0: input, 1 '*', 2 'G', 3 'T', 4 'S'
  long         t;
  double       w;
};


// a collection of cells, like Organism, for developmental encoding
#define MAX4CELLS 100
class f4_Cells
{
 public:
  f4_Cells(f4_node * genome, int nrepair);
  f4_Cells(SString &genome, int nrepair);
  ~f4_Cells();
  void addCell(f4_Cell * newcell);
  void toF1Geno(SString &out);       // output to f1 format, approximation
  int  onestep();       // simulate all parts for one step
  int  simulate();      // simulate development, return error (0 for ok)
  // for error reporting / genotype fixing
  int  geterror() { return error;};
  int  geterrorpos() { return errorpos;};
  void setError(int nerrpos);
  void setRepairRemove(int nerrpos, f4_node * rem);
  int  setRepairInsert(int nerrpos, f4_node * parent, f4_node * insert);
  void repairGeno(f4_node * geno, int whichchild);

  // the cells
  f4_Cell * C[MAX4CELLS];
  int       nc;

private:
  // for error reporting / genotype fixing
  int repair;
  int error;
  int errorpos;
  f4_node * repair_remove;
  f4_node * repair_parent;
  f4_node * repair_insert;
  void toF1GenoRec(int curc, SString &out);
  f4_Cell * tmpcel;             // needed by toF1Geno
  f4_node * f4rootnode;          // used by constructor
};


/**
 * Class to organize a f4 genotype in a tree structure.
 */
class f4_node
{
public:
  char      name;       // one-letter 'name'
  f4_node * parent;     // parent link, or NULL
  f4_node * child;      // child, or NULL
  f4_node * child2;     // second child, or NULL
  int       pos;        // original position in string
  int       i1;         // internal int  parameter1
  long      l1;         // internal long parameter1
  double    f1;         // internal double parameter1

            f4_node();
            f4_node(char nname, f4_node * nparent, int npos);
            ~f4_node();
  int       addChild(f4_node * nchi);
  int       removeChild(f4_node * nchi);
  int       childCount();       // return no of children, 0, 1, or 2
  int       count();    // return no of nodes (recursive)
  f4_node * ordNode(int n);     // returns the nth subnode (0-)
  f4_node * randomNode();       // returns a random subnode
  f4_node * randomNodeWithSize(int min, int max);       // returns a random subnode with given size
  void      sprintAdj(char *& buf);     // print recursively
  f4_node * duplicate();         // create duplicate copy. recursive.
  void      destroy();  // release memory. recursive.
private:
  void     sprint(SString & out);       // print recursively
};

// convert f4 geno string to tree structure (internal)
f4_node * f4_processtree(const char * geno);
int f4_processrec(const char * genot, unsigned pos0, f4_node * parent);


#endif