/*
 *  f4_general.cpp - 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
 *
 */

#include "f4_general.h"
#include "nonstd.h"
#include "framsg.h"
#include "model.h" // for min and max attributes
#include "geno_fx.h" //for GENOPER_ constants
#include <stdio.h>
#include <math.h>

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


f4_Props::f4_Props()
{
  len      = 1.0;
  curv     = 0.0;
  mass     = 1.0; 
  friction = 0.4;
  ruch     = 0.25; // bio
  assim    = 0.25; // bio
  odpor    = 0.25; // bio
  ingest   = 0.25; // bio
  twist    = 0.0;
  energ    = 1.0;
  normalizeBiol4();
}

void f4_Props::normalizeBiol4()
{
  // must sum to 1
  double sum = ruch + assim + odpor + ingest;
  if (0 == sum)
  {
    ruch = assim = odpor = ingest = 0.25;
  } else {
    ruch   /= sum;
    assim  /= sum;
    odpor  /= sum;
    ingest /= sum;
  }
}

void f4_Props::executeModifier(char modif)
{
  switch (modif)
  {
   case 'L': len += (2.5 - len) * 0.3;
             len = min(len, Model::getMaxJoint().d.x); break;
   case 'l': len += (0.3 - len) * 0.3;
             len = max(len, Model::getMinJoint().d.x); break;
   case 'C': curv += ( 2.0 - curv) * 0.25;  break;
   case 'c': curv += (-2.0 - curv) * 0.25;  break;
   case 'Q': twist += ( 1.58 - twist) * 0.3; break;
   case 'q': twist += (-1.58 - twist) * 0.3; break;
   case 'A': assim += (1 - assim) * 0.8; normalizeBiol4(); break;
   case 'a': assim -= assim * 0.4;       normalizeBiol4(); break;
   case 'I': ingest += (1 - ingest) * 0.8;   normalizeBiol4(); break;
   case 'i': ingest -= ingest * 0.4;         normalizeBiol4(); break;
   case 'S': odpor += (1 - odpor) * 0.8; normalizeBiol4(); break;
   case 's': odpor -= odpor * 0.4;       normalizeBiol4(); break;
   case 'M': ruch += (1 - ruch) * 0.8;   normalizeBiol4(); break;
   case 'm': ruch -= ruch * 0.4;         normalizeBiol4(); break;
   case 'F': friction += (4 - friction) * 0.2; break;
   case 'f': friction -= friction * 0.2;       break;
   case 'W': mass += (2.0 - mass) * 0.3;   break;
   case 'w': mass += (0.5 - mass) * 0.3;   break;
   case 'E': energ += (10.0 - energ) * 0.1; break;
   case 'e': energ -= energ * 0.1;          break;
  }
}

void f4_Props::adjust()
{
  len = 0.5*len + 0.5*stdProps.len;
  curv = 0.66 * curv;
  twist = 0.66 * twist;
}

f4_Props stdProps;


void rolling_dec(double * v) {
  *v -= 0.7853;  // 0.7853981  45 degrees
}
void rolling_inc(double * v) {
  *v += 0.7853;  // 0.7853981  45 degrees
}


int scanrec(const char * s, unsigned int slen, char stopchar)
{
  unsigned int i = 0;
  //DB( printf("    scan('%s', '%c')\n", s, stopchar); )
  while (1)
  {
    if (i >= slen)  // ran out the string, should never happen with correct string
      return 1;
    if (stopchar == s[i])  // bumped into stopchar
      return i;
    if (i < slen-1)  
    { // s[i] is not the last char
      if (s[i] == '(') 
      {
        i += 2+scanrec(s+i+1, slen-i-1, ')');
        continue;
      }
      if (s[i] == '<') 
      {
        i += 2+scanrec(s+i+1, slen-i-1, '>');
        continue;
      }
      if (s[i] == '#') 
      {
        i += 2+scanrec(s+i+1, slen-i-1, '>');
        continue;
      }
    }
    // s[i] a non-special character
    i++;
  }
  return i;
}


f4_Cell::f4_Cell(int nname,
    f4_Cell * ndad, int nangle, f4_Props newP)
{
  name    = nname;
  type    = T_UNDIFF4;
  dadlink = ndad;
  org     = NULL;
  genot   = NULL;
  gcur    = NULL;
  active  = 1;
  repeat.null();
  //genoRange.clear(); -- implicit

  anglepos   = nangle;
  commacount = 0;
  childcount = 0;
  P          = newP;
  rolling    = 0;
  xrot       = 0;
  zrot       = 0;
  //OM = Orient_1;
  ctrl    = 0;
  state   = 0;
  inertia = 0.8;
  force   = 0.04;
  sigmo   = 2;
  nolink = 0;

  // adjust firstend and OM if there is a stick dad
  if (ndad != NULL)
  {
    // make sure it is a stick (and not a stick f4_Cell!)
    if (T_STICK4 == ndad->type)
    {
      //firstend = ndad->lastend;
      //OM = ndad->OM;
      ndad->childcount++;
    }
    if (T_NEURON4 == ndad->type)
    {
      state   = ndad->state;
      inertia = ndad->inertia;
      force   = ndad->force;
      sigmo   = ndad->sigmo;
    }
  }
  // adjust lastend
  //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len));
  mz = 1;
}


f4_Cell::f4_Cell(f4_Cells * nO, int nname, f4_node * ngeno, f4_node * ngcur,
    f4_Cell * ndad, int nangle, f4_Props newP)
{
  name    = nname;
  type    = T_UNDIFF4;
  dadlink = ndad;
  org     = nO;
  genot   = ngeno;
  gcur    = ngcur;
  active = 1;
  repeat.null();
  //genoRange.clear(); -- implicit
  // preserve geno range of parent cell
  if (NULL != ndad)
    genoRange.add( ndad->genoRange );

  anglepos   = nangle;
  commacount = 0;
  childcount = 0;
  P          = newP;
  rolling    = 0;
  xrot       = 0;
  zrot       = 0;
  //OM = Orient_1;
  ctrl    = 0;
  state   = 0;
  inertia = 0.8;
  force   = 0.04;
  sigmo   = 2;
  nolink = 0;

  // adjust firstend and OM if there is a stick dad
  if (ndad != NULL)
  {
    // make sure it is a stick (and not a stick f4_Cell!)
    if (T_STICK4 == ndad->type) {
      //firstend = ndad->lastend;
      //OM = ndad->OM;
      ndad->childcount++;
    }
    if (T_NEURON4 == ndad->type) 
    {
      state   = ndad->state;
      inertia = ndad->inertia;
      force   = ndad->force;
      sigmo   = ndad->sigmo;
    }
  }
  // adjust lastend
  //lastend = firstend + ((Orient)OM * (Pt3D(1,0,0) * P.len));
  mz = 1;
}


f4_Cell::~f4_Cell()
{
  // remove links
  if (nolink)
  {
    int i;
    for (i=nolink-1; i>=0; i--)
      delete links[i];
    nolink=0;
  }
}


/* return codes:
    >1 error at pos
     0  halt development for a cycle
    -1  development finished OK
*/
int f4_Cell::onestep()
{
  int i, j, k, relfrom, t;
  double w;
  f4_Cell * tmp;
  f4_Cell * tneu;
  if (gcur == NULL)
  {
    active = 0;
    return 0;  // stop
  }
  while ( NULL != gcur )
  {
    //DB( printf("  %d (%d) executing '%c' %d\n", name, type, gcur->name, gcur->pos); )
    // currently this is the last one processed
    // the current genotype code is processed
    genoRange.add( gcur->pos );
    switch (gcur->name)
    {
    case '<':
      // cell division!
      //DB( printf("  div! %d\n", name); )

      // error: sticks cannot divide
      if (T_STICK4 == type) {
        // cannot fix
        org->setError(gcur->pos);
        return 1;  // stop
      }

      // undiff divides
      if (T_UNDIFF4 == type) {
        // commacount is set only when daughter turns into X
        // daughter cell
        // adjust new len
        f4_Props newP = P;
        newP.adjust();
        tmp = new f4_Cell(org, org->nc, genot, gcur->child2,
         this,  commacount, newP);
        tmp->repeat = repeat;
        repeat.null();
        org->addCell( tmp );
      }
      // a neuron divides: create a new, duplicate links
      if (T_NEURON4 == type) {
        // daughter cell
        tmp = new f4_Cell(org, org->nc, genot, gcur->child2,
          // has the same dadlink
          this->dadlink, commacount, P);
        tmp->repeat = repeat;
        repeat.null();
        // it is a neuron from start
        tmp->type = T_NEURON4;
        // duplicate links
        f4_CellLink * ll;
        for (i=0; i<nolink; i++) {
          ll = links[i];
          tmp->addlink(ll->from, ll->w, ll->t);
        }
        org->addCell( tmp );
      }
      // adjustments for this cell
      gcur = gcur->child;
      // halt development
      return 0;

    case '>':
      // finish
      // see if there is a repet count
      if (repeat.top > 0)
      { // there is a repeat counter
        if (!repeat.first()->isNull())
        { // repeat counter is not null
          repeat.first()->dec();
          if (repeat.first()->count > 0)
          {
            // return to repeat
            gcur = repeat.first()->node->child;
          } else {
            // continue
            gcur = repeat.first()->node->child2;
            repeat.pop();
          }
          break;
        } else {
          repeat.pop();
        }
      } else {
        // error: still undiff
        if (T_UNDIFF4 == type)
        {
          // fix it: insert an 'X'
          f4_node * insertnode = new f4_node('X', NULL, gcur->pos);
          if (org->setRepairInsert(gcur->pos, gcur, insertnode))
            // not in repair mode, release
            delete insertnode;
          return 1;
        }
        repeat.null();
        active = 0;  // stop
        // eat up rest
        gcur = NULL;
        return 0;
      }

    case '#':
      // repetition marker
      if (repeat.top >= repeat_stack::stackSize)
      {
        // repepeat pointer stack is full, cannot remember this one.
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      repeat.push( repeat_ptr(gcur, gcur->i1) );
      gcur = gcur->child;
      break;

    case ',':
      commacount++;
      gcur = gcur->child;
      break;

    case 'r':  case 'R':
      // error: if neuron
      if (T_NEURON4 == type) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      switch (gcur->name) {
       case 'r':   rolling_dec( &rolling ); break;
       case 'R':   rolling_inc( &rolling ); break;
      }
      gcur = gcur->child;
      break;

    case 'l':  case 'L':
    case 'c':  case 'C':
    case 'q':  case 'Q':
    case 'a':  case 'A':
    case 'i':  case 'I':
    case 's':  case 'S':
    case 'm':  case 'M':
    case 'f':  case 'F':
    case 'w':  case 'W':
    case 'e':  case 'E':
      // error: if neuron
      if (T_NEURON4 == type) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      P.executeModifier(gcur->name);
      gcur = gcur->child;
      break;

    case 'X':
      // turn undiff. cell into a stick
      // error: already differentiated
      if (T_UNDIFF4 != type) {
        // fix: delete this node
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      type = T_STICK4;
      // fix dad commacount and own anglepos
      if (NULL != dadlink) {
        dadlink->commacount++;
        anglepos = dadlink->commacount;
      }
      // change of type halts developments, see comment at 'N'
      gcur = gcur->child;
      return 0;

    case 'N':
      // turn undiff. cell into a neuron
      // error: already differentiated
      if (T_UNDIFF4 != type) {
        // fix: delete this node
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      // error: if no previous
      if (NULL == dadlink) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      type = T_NEURON4;
      // change of type also halts development, to give other
      // cells a chance for adjustment.  Namely, it is important
      // to wait for other cells to turn N before adding links
      gcur = gcur->child;
      return 0;

    case '@':
    case '|':
      // neuron rotating / bending
      j = 1;
      if ('@' == gcur->name) j = 1; // rot
      if ('|' == gcur->name) j = 2; // bend
      // error: not a neuron (undiff)
      if (T_UNDIFF4 == type) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      // error: not a neuron (stick)
      if (T_NEURON4 != type) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      // error: already has control
      if (ctrl != 0) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      // make neuron ctrl = 1 or 2
      ctrl = j;
      gcur = gcur->child;
      break;

    case '[':
      // link to neuron
      // error: not a neuron
      if (T_NEURON4 != type) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      // input ('*', 'G', 'T', 'S', or %d)
      t       = gcur->i1;
      relfrom = gcur->l1;
      w       = gcur->f1;
      if (t>0) {
        // * or G
        tneu = NULL;
      } else {
        // input from other neuron
        // find neuron at relative i
        // find own index
        j = 0; k = 0;
        for(i=0; i<org->nc; i++) {
          if (org->C[i]->type == T_NEURON4) k++;
          if (org->C[i] == this) {j=k-1; break;}
        }
        // find index of incoming
        j = j + relfrom;
        if (j<0) goto wait_link;
        if (j>=org->nc) goto wait_link;
        // find that neuron
        k = 0;
        for(i=0; i<org->nc; i++) {
          if (org->C[i]->type == T_NEURON4) k++;
          if (j == (k-1)) break;
        }
        if (i>=org->nc) goto wait_link;
        tneu = org->C[i];
      }
      // add link
      // error: could not add link (too many?)
      if (addlink(tneu, w, t)) {
        // cannot fix
        org->setError(gcur->pos);
        return 1;  // stop
      }
      gcur = gcur->child;
      break;
    wait_link:
      // wait for other neurons to develop
      // if there are others still active
      active = 0;
      j = 0;
      for(i=0; i<org->nc; i++) {
        if (org->C[i]->active) j++;
      }
      if (j>0)
        return 0;  // there is other active, halt, try again
      // no more actives, cannot add link, ignore, but treat not as an error
      gcur = gcur->child;
      break;

    case ':':
      // neuron parameter
      // error: not a neuron
      if (T_NEURON4 != type) {
        // fix: delete it
        org->setRepairRemove(gcur->pos, gcur);
        return 1;  // stop
      }
      j = (int)gcur->l1;
      switch ((char)gcur->i1) {
       case '!': 
        if (j) force += (1.0 - force) * 0.2;
        else   force -= force * 0.2; break;
       case '=': 
        if (j) inertia += (1.0 - inertia) * 0.2;
        else   inertia -= inertia * 0.2; break;
       case '/': 
        if (j) sigmo *= 1.4;
        else   sigmo /= 1.4; break;
       default:
         org->setRepairRemove(gcur->pos, gcur);
         return 1;  // stop
      }
      gcur = gcur->child;
      break;

    case ' ':
      // space has no effect, should not occur
      // fix: delete it
      org->setRepairRemove(gcur->pos, gcur);
      gcur = gcur->child;
      break;

    default:
      // error: unknown code
      char buf[40];
      sprintf(buf, "unknown code '%c'", gcur->name);
      FramMessage("f4_Cell", "onestep", buf, 2);
      // fix: delete it
      org->setRepairRemove(gcur->pos, gcur);
      return 1; // stop
    }
  }
  active = 0;  // done
  return 0;
}


int f4_Cell::addlink(f4_Cell * nfrom, double nw, long nt)
{
  if (nolink >= MAXINPUTS-1) return -1; // full!
  links[nolink] = new f4_CellLink(nfrom, nw, nt);
  nolink++;
  return 0;
}


void f4_Cell::adjustRec()
{
  //f4_OrientMat rot;
  int     i;

  if (recProcessedFlag)
    // already processed
    return;

  // mark it processed
  recProcessedFlag = 1;

  // make sure its parent is processed first
  if (NULL != dadlink)
    dadlink->adjustRec();

  // count children
  childcount = 0;
  for(i=0; i<org->nc; i++)
  {
    if (org->C[i]->dadlink == this)
      if (org->C[i]->type == T_STICK4)
        childcount++;
  }

  if (type == T_STICK4)
  {
    if (NULL == dadlink)
    {
      //firstend = Pt3D_0;
      // rotation due to rolling
      xrot = rolling;
      mz = 1;
    } else {
      //firstend = dadlink->lastend;
      f4_Props Pdad = dadlink->P;
      f4_Props Padj = Pdad;
      Padj.adjust();

      //rot = Orient_1;

      // rotation due to rolling
      xrot = rolling +
        // rotation due to twist
        Pdad.twist;
      if (dadlink->commacount <= 1)
      {
        // rotation due to curvedness
        zrot = Padj.curv;
      } else {
        zrot = Padj.curv +
          // GDK uses 3.141 instead of PI!
          (anglepos * 1.0/(dadlink->commacount+1) - 0.5) * 3.141 * 2.0;
      }

      //rot = rot * f4_OrientMat(yOz, xrot);
      //rot = rot * f4_OrientMat(xOy, zrot);
      // rotation relative to parent stick
      //OM = rot * OM;

      // rotation in world coordinates
      //OM =  ((f4_OrientMat)dadlink->OM) * OM;
      mz = dadlink->mz / dadlink->childcount;
    }
    //Pt3D lastoffset = (Orient)OM * (Pt3D(1,0,0)*P.len);
    //lastend = firstend + lastoffset;
  }
}



f4_CellLink::f4_CellLink(f4_Cell * nfrom, double nw, long nt)
{
  from = nfrom;
  w    = nw;
  t    = nt;
}



f4_Cells::f4_Cells(f4_node * genome, int nrepair)
{
  // create ancestor cell
  repair = nrepair;
  error  = 0;
  errorpos = -1;
  repair_remove = NULL;
  repair_parent = NULL;
  repair_insert = NULL;
  tmpcel = NULL;
  f4rootnode = NULL;

  C[0] = new f4_Cell(this, 0, genome, genome, NULL, 0, stdProps);
  nc   = 1;
}


f4_Cells::f4_Cells(SString & genome, int nrepair)
{
  int res;
  repair = nrepair;
  error  = 0;
  errorpos = -1;
  repair_remove = NULL;
  repair_parent = NULL;
  repair_insert = NULL;
  tmpcel = NULL;
  f4rootnode = NULL;

  // transform geno from string to nodes
  f4rootnode = new f4_node();
  res = f4_processrec((const char*)genome, (unsigned)0, f4rootnode);
  if ((res<0) || (1 != f4rootnode->childCount()))
  {
    error = GENOPER_OPFAIL;
    errorpos = -1;
  }

  // create ancestor cell
  C[0] = new f4_Cell(this, 0, f4rootnode->child, f4rootnode->child,
    NULL, 0, stdProps);
  nc   = 1;
}

f4_Cells::~f4_Cells()
{
  // release cells
  int i;
  if (nc)
  {
    for (i=nc-1; i>=0; i--)
      delete C[i];
    nc = 0;
  }
  if (f4rootnode)
    delete f4rootnode;
}


int f4_Cells::onestep()
{
  int i, ret, oldnc, ret2;
  oldnc = nc;
  ret=0;
  for (i=0; i<oldnc; i++) {
    ret2 = C[i]->onestep();
    if (ret2>0) {
      // error
      C[i]->active = 0;  // stop
      return 0;
    }
    // if still active
    if (C[i]->active)
      ret=1;
  }
  return ret;
}


int f4_Cells::simulate()
{
  int i;
  error = GENOPER_OK;

  for (i=0; i<nc; i++)  C[i]->active = 1;

  // execute onestep() in a cycle
  while (onestep()) ;

  if (GENOPER_OK != error) return error;

  // fix neuron attachements
  for(i=0; i<nc; i++)
    if (C[i]->type == T_NEURON4) {
      while (T_NEURON4 == C[i]->dadlink->type) {
        C[i]->dadlink = C[i]->dadlink->dadlink;
      }
  }

  // there should be no undiff. cells
  // make undifferentiated cells sticks
  for (i=0; i<nc ; i++)
    if (C[i]->type == T_UNDIFF4) {
      C[i]->type = T_STICK4;
      //seterror();
  }

  // recursive adjust
  // reset recursive traverse flags
  for(i=0; i<nc; i++)
    C[i]->recProcessedFlag = 0;
  // process every cell
  for(i=0; i<nc; i++)
    C[i]->adjustRec();

  //DB( printf("Cell simulation done, %d cells. \n", nc); )

  return error;
}


void f4_Cells::addCell(f4_Cell * newcell)
{
  if (nc >= MAX4CELLS-1) {
    delete newcell;
    return;
  }
  C[nc] = newcell;
  nc++;
}


void f4_Cells::setError(int nerrpos)
{
  error = GENOPER_OPFAIL;
  errorpos = nerrpos;
}

void f4_Cells::setRepairRemove(int nerrpos, f4_node * rem)
{
  if (!repair) {
    // not in repair mode, treat as repairable error
    error = GENOPER_REPAIR;
    errorpos = nerrpos;
  } else {
    error = GENOPER_REPAIR;
    errorpos = nerrpos;
    repair_remove = rem;
  }
}

int f4_Cells::setRepairInsert(int nerrpos, f4_node * parent, f4_node * insert)
{
  if (!repair) {
    // not in repair mode, treat as repairable error
    error = GENOPER_REPAIR;
    errorpos = nerrpos;
    return -1;
  } else {
    error = GENOPER_REPAIR;
    errorpos = nerrpos;
    repair_parent = parent;
    repair_insert = insert;
    return 0;
  }
}

void f4_Cells::repairGeno(f4_node * geno, int whichchild)
{
  // assemble repaired geno, if the case
  if (!repair) return;
  if ((NULL==repair_remove) && (NULL==repair_insert)) return;
  // traverse genotype tree, remove / insert node
  f4_node * g2;
  if (1==whichchild) g2 = geno->child;
    else             g2 = geno->child2;
  if (NULL == g2)
    return;
  if (g2 == repair_remove) {
    f4_node * oldgeno;
    geno->removeChild(g2);
    if (g2->child) {
      // add g2->child as child to geno
      if (1==whichchild) geno->child  = g2->child;
        else             geno->child2 = g2->child;
      g2->child->parent = geno;
    }
    oldgeno = g2;
    oldgeno->child = NULL;
    delete oldgeno;
    if (NULL == geno->child) return;
    // check this new
    repairGeno(geno, whichchild);
    return;
  }
  if (g2 == repair_parent) {
    geno->removeChild(g2);
    geno->addChild(repair_insert);
    repair_insert->parent = geno;
    repair_insert->child  = g2;
    repair_insert->child2 = NULL;
    g2->parent = repair_insert;
  }
  // recurse
  if (g2->child)  repairGeno(g2, 1);
  if (g2->child2) repairGeno(g2, 2);
}


void f4_Cells::toF1Geno(SString &out)
{
  if (tmpcel) delete tmpcel;
  tmpcel = new f4_Cell(-1, NULL, 0, stdProps);
  out = "";
  toF1GenoRec(0, out);
  delete tmpcel;
}


void f4_Cells::toF1GenoRec(int curc, SString &out)
{
  int i, j, ccount;
  f4_Cell * thisti;
  f4_Cell * thneu;
  char buf[200];

  if (curc >= nc) return;

  if (T_STICK4 != C[curc]->type) return;

  thisti = C[curc];
  if (NULL != thisti->dadlink)  
    *tmpcel = *(thisti->dadlink);

  // adjust length, curvedness, etc.
  tmpcel->P.adjust();
  while (tmpcel->P.len > thisti->P.len)
  {
    tmpcel->P.executeModifier('l');
    out += "l";
  }
  while (tmpcel->P.len < thisti->P.len) 
  {
    tmpcel->P.executeModifier('L');
    out += "L";
  }
  while (tmpcel->P.curv > thisti->P.curv) 
  {
    tmpcel->P.executeModifier('c');
    out += "c";
  }
  while (tmpcel->P.curv < thisti->P.curv) 
  {
    tmpcel->P.executeModifier('C');
    out += "C";
  }
  while (thisti->rolling > 0.0f) {
    rolling_dec( &(thisti->rolling) );
    out += "R";
  }
  while (thisti->rolling < 0.0f) {
    rolling_inc( &(thisti->rolling) );
    out += "r";
  }

  // output X for this stick
  out += "X";

  // neurons attached to it
  for (i=0; i<nc; i++)
    if (C[i]->type == T_NEURON4) {
      if (C[i]->dadlink == thisti) {
        thneu = C[i];
        out += "[";
        // ctrl
        if (1 == thneu->ctrl) out += "@";
        if (2 == thneu->ctrl) out += "|";
        // links
        for (j=0; j<thneu->nolink; j++) 
        {
          if (j) out += ",";
          if (NULL == thneu->links[j]->from) 
          {
            // sensory
            if (1 == thneu->links[j]->t) out += "*";
            if (2 == thneu->links[j]->t) out += "G";
            if (3 == thneu->links[j]->t) out += "T";
            if (4 == thneu->links[j]->t) out += "S";
          } else {
            sprintf(buf, "%d", thneu->links[j]->from->name - thneu->name);
            out += buf;
          }
          out += ":";
          // weight
          sprintf(buf, "%g", thneu->links[j]->w );
          out += buf;
        }
        out += "]";
    }
  }

  // sticks connected to it
  if (thisti->commacount>=2)
    out += "(";

  ccount=1;
  for (i=0; i<nc; i++)
   if (C[i]->type == T_STICK4)
    if (C[i]->dadlink == thisti) {
      while (ccount < (C[i])->anglepos) {
        ccount++;
        out += ",";
      }
      toF1GenoRec(i, out);
  }
  while (ccount < thisti->commacount) {
    ccount++;
    out += ",";
  }

  if (thisti->commacount >= 2)
    out += ")";
}



// to organize a f4 genotype in a tree structure

f4_node::f4_node()
{
  name   = '?';
  parent = NULL;
  child  = NULL;
  child2 = NULL;
  pos    = -1;
}

f4_node::f4_node(char nname, f4_node * nparent, int npos)
{
  name   = nname;
  parent = nparent;
  child  = NULL;
  child2 = NULL;
  pos    = npos;
  if (parent) parent->addChild(this);
}

f4_node::~f4_node()
{
  // (destroy() copied here for efficiency)
  // children are destroyed (recursively) through the destructor
  if (NULL != child2)  delete child2;
  if (NULL != child)   delete child;
}

int f4_node::addChild(f4_node * nchi)
{
  if (NULL==child) {
    child = nchi;
    return 0;
  }
  if (NULL==child2) {
    child2 = nchi;
    return 0;
  }
  return -1;
}

int f4_node::removeChild(f4_node * nchi)
{
  if (nchi==child2) {
    child2 = NULL;
    return 0;
  }
  if (nchi==child) {
    child = NULL;
    return 0;
  }
  return -1;
}

int f4_node::childCount()
{
  if (NULL!=child) {
    if (NULL!=child2) return 2;
                 else return 1;
  } else {
    if (NULL!=child2) return 1;
                 else return 0;
  }
}

int f4_node::count()
{
  int c=1;
  if (NULL!=child)  c+=child->count();
  if (NULL!=child2) c+=child2->count();
  return c;
}

f4_node * f4_node::ordNode(int n)
{
  int n1;
  if (0 == n) return this;
  n--;
  if (NULL != child) {
    n1 = child->count();
    if (n<n1) return child->ordNode(n);
    n -= n1;
  }
  if (NULL != child2) {
    n1 = child2->count();
    if (n<n1) return child2->ordNode(n);
    n -= n1;
  }
  return NULL;
}

f4_node * f4_node::randomNode()
{
  int n, i;
  n = count();
  // pick a random node, between 0 and n-1
  i = (int)( ((float)n-0.0001) / RAND_MAX * rand());
  return ordNode(i);
}

f4_node * f4_node::randomNodeWithSize(int min, int max)
{
  // try random nodes, and accept if size in range
  // limit to maxlim tries
  int i, n, maxlim;
  f4_node * nod = NULL;
  maxlim = count();
  for (i=0; i<maxlim; i++) {
    nod = randomNode();
    n = nod->count();
    if ((n>=min) && (n<=max)) return nod;
  }
  // failed, doesn't matter
  return nod;
}

void f4_node::sprint(SString & out)
{
  char buf2[20];
  // special case: repetition code
  if ('#' == name)
  {
    out += "#";
    if (i1 != 1) {
      sprintf(buf2, "%d", i1);
      out += buf2;
    }
  } else {
  // special case: neuron link
  if ('[' == name) {
    out += "[";
    if (i1>0) {
      // sensor input
      if (1==i1) out += "*";
      if (2==i1) out += "G";
      if (3==i1) out += "T";
      if (4==i1) out += "S";
    } else {
      sprintf(buf2, "%ld", l1);
      out += buf2;
    }
    sprintf(buf2, ":%g]", f1);
    out += buf2;
  } else if (':' == name) {
    sprintf(buf2, ":%c%c:", l1 ? '+' : '-', (char)i1);
    out += buf2;
  } else {
    buf2[0] = name;
    buf2[1] = 0;
    out += buf2;
  }}
  if (NULL != child)     child->sprint(out);
  // if two children, make sure last char is a '>'
  if (2 == childCount())
    if (0 == out[0]) out += ">"; else
      if ('>' != out[out.len()-1]) out += ">";
  if (NULL != child2)    child2->sprint(out);
  // make sure last char is a '>'
  if (0 == out[0]) out += ">"; else
    if ('>' != out[out.len()-1]) out += ">";
}

void f4_node::sprintAdj(char *& buf)
{
  unsigned int len;
  // build in a SString, with initial size
  SString out(strlen(buf)+2000);
  out="";

  sprint(out);

  // very last '>' can be omitted
  len = out.len();
  if (len>1)
    if ('>' == out[len-1]) { (out.directWrite())[len-1]=0; out.endWrite();};
  // copy back to string
  // if new is longer, reallocate buf
  if (len+1 > strlen(buf)) {
    buf = (char*) realloc(buf, len+1 );
  }
  strcpy(buf, (const char*) out);
}

f4_node * f4_node::duplicate()
{
  f4_node * copy;
  copy = new f4_node(*this);
  copy->parent = NULL;  // set later
  copy->child  = NULL;
  copy->child2 = NULL;
  if (NULL != child ) {
    copy->child  = child ->duplicate();
    copy->child ->parent = copy;
  }
  if (NULL != child2 ) {
    copy->child2 = child2->duplicate();
    copy->child2->parent = copy;
  }
  return copy;
}


void f4_node::destroy()
{
  // children are destroyed (recursively) through the destructor
  if (NULL != child2)  delete child2;
  if (NULL != child)   delete child;
}


// scan genotype string and build tree
// return >1 for error (errorpos)
int f4_processrec(const char * genot, unsigned pos0, f4_node * parent)
{
  int i, j, t, res;
  char tc1, tc2;
  long relfrom;
  double w;
  unsigned gpos, oldpos;
  f4_node * node1, * par;

  gpos = pos0;
  par = parent;
  if (gpos >= strlen(genot) ) return 1;
  while (gpos<strlen(genot)) {
    //DB( printf(" processing '%c' %d %s\n", genot[gpos], gpos, genot); )
    switch (genot[gpos]) {
    case '<':
      // cell division!
      //DB( printf("  div! %d\n", name); )

      // find out genotype start for child
      j = scanrec(genot+gpos+1, strlen(genot+gpos+1), '>');

      node1 = new f4_node('<', par, gpos);
      par = node1;
      res = f4_processrec(genot, gpos+1,   par);
      if (res) return res;
      if (gpos+j+2 < strlen(genot)) {
        res = f4_processrec(genot, gpos+j+2, par);
        if (res) return res;
      } else {  // ran out
        node1 = new f4_node('>', par, strlen(genot)-1 );
        par = node1;
      }
      // adjustments
      gpos++;
      return 0;  // OK

    case '>':
      node1 = new f4_node('>', par, gpos );
      par = node1;
      gpos = strlen(genot);
      return 0;  // OK

    case '#':
      // repetition marker, 1 by default
      if (sscanf(genot+gpos, "#%d", &i) != 1) i=1;
      // find out genotype start for continuation
      j = scanrec(genot+gpos+1, strlen(genot+gpos+1), '>');
      // skip number
      oldpos = gpos;
      gpos++;
      while ((genot[gpos]>='0') && (genot[gpos]<='9')) gpos++;
      node1 = new f4_node('#', par, oldpos );
      node1->i1 = i;
      par = node1;
      res = f4_processrec(genot, gpos,   node1);
      if (res) return res;
      if (oldpos+j+2 < strlen(genot) ) {
        res = f4_processrec(genot, oldpos+j+2, node1);
        if (res) return res;
      } else {  // ran out
        node1 = new f4_node('>', par, strlen(genot)-1 );
      }
      return 0;  // OK

    // 'simple' nodes:
    case ',':
    case 'l':  case 'L':
    case 'c':  case 'C':
    case 'q':  case 'Q':
    case 'r':  case 'R':
    case 'X':  case 'N':
    case '@':  case '|':
    case 'a':  case 'A':
    case 's':  case 'S':
    case 'm':  case 'M':
    case 'i':  case 'I':
    case 'f':  case 'F':
    case 'w':  case 'W':
    case 'e':  case 'E':
      node1 = new f4_node(genot[gpos], par, gpos );
      par = node1;
      gpos++;
      break;

    case '[':
      // link to neuron
      // input (%d, '*', 'G', 'T', 'S')
      t = -1;
      if (sscanf(genot+gpos, "[%ld:%lf]", &relfrom, &w) == 2) t=0;
      else if (sscanf(genot+gpos, "[*:%lf]", &w) == 1) t=1;
      else if (sscanf(genot+gpos, "[G:%lf]", &w) == 1) t=2;
      else if (sscanf(genot+gpos, "[T:%lf]", &w) == 1) t=3;
      else if (sscanf(genot+gpos, "[S:%lf]", &w) == 1) t=4;
      // error: no correct format
      if (t<0) return gpos+1+1;
      node1 = new f4_node('[', par, gpos );
      node1->i1 = t;
      node1->l1 = relfrom;
      node1->f1 = w;
      par = node1;
      j = scanrec(genot+gpos+1, strlen(genot+gpos+1), ']');
      gpos += j+2;
      break;

    case ':':
      // neuron parameter  +! -! += -= +/ or -/
      if (sscanf(genot+gpos, ":%c%c:", &tc1, &tc2) != 2)
        // error: incorrect format
        return gpos+1+1;
      if ('+' == tc1) j=1;
      else if ('-' == tc1) j=0;
      else return gpos+1+1;
      switch (tc2) {
       case '!':  case '=':  case '/':  break;
       default:
        return gpos+1+1;
      }
      node1 = new f4_node(':', par, gpos );
      node1->l1 = j;
      node1->i1 = (int)tc2;
      par = node1;
      j = scanrec(genot+gpos+1, strlen(genot+gpos+1), ':');
      gpos += j+2;
      break;

    case ' ':
    case '\n':
    case '\t':
      // whitespace: ignore
      //node1 = new f4_node(' ', par, gpos );
      //par = node1;
      gpos++;
      break;

    default:
      //DB( printf("unknown character '%c' ! \n", genot[gpos]); )
      //add it, build will give the error or repair
      node1 = new f4_node(genot[gpos], par, gpos );
      par = node1;
      gpos++;
      break;
    }
  }
  // should end with a '>'
  if (par)
    if ('>' != par->name) {
      node1 = new f4_node('>', par, strlen(genot)-1 );
      par = node1;
  }
  return 0;  // OK
}


f4_node * f4_processtree(const char * geno)
{
  f4_node * root;
  int res;
  root = new f4_node();
  res = f4_processrec(geno, 0, root);
  if (res) return NULL;
  //DB( printf("test f4  "); )
  DB(
    if (root->child) {
      char * buf = (char*) malloc( 300 );
      DB( printf("(%d) ", root->child->count() ); )
      buf[0]=0;
      root->child->sprintAdj(buf);
      DB( printf("%s\n", buf); )
      free(buf);
    }
  )
  return root->child;
}