source: cpp/frams/genetics/f4/f4_general.cpp @ 743

// This file is a part of Framsticks SDK.  http://www.framsticks.com/
// Copyright (C) 1999-2017  Maciej Komosinski and Szymon Ulatowski.
// See LICENSE.txt for details.

// Copyright (C) 1999,2000  Adam Rotaru-Varga (adam_rotaru@yahoo.com), GNU LGPL

#include "f4_general.h"
#include <common/nonstd_stl.h>
#include <common/log.h>
#include <frams/model/model.h> // for min and max attributes
#include "../oper_fx.h" //for GENOPER_ constants
#include <stdio.h>
#include <common/nonstd_math.h>

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


f4_Props::f4_Props()
{
        length = 1.0;
        curvedness = 0.0;
        weight = 1.0;
        friction = 0.4;
        muscle_power = 0.25; // biol
        assimilation = 0.25; // biol
        stamina = 0.25; // biol
        ingestion = 0.25; // biol
        twist = 0.0;
        energy = 1.0;
        normalizeBiol4();
}

void f4_Props::normalizeBiol4()
{
        // make them sum to 1
        double sum = muscle_power + assimilation + stamina + ingestion;
        if (sum == 0)
        {
                muscle_power = assimilation = stamina = ingestion = 0.25;
        }
        else
        {
                muscle_power /= sum;
                assimilation /= sum;
                stamina /= sum;
                ingestion /= sum;
        }
}

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

void f4_Props::adjust()
{
        length = 0.5*length + 0.5*stdProps.length;
        curvedness = 0.66 * curvedness;
        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);
                        logMessage("f4_Cell", "onestep", 2, buf);
                        // 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, int 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.curvedness;
                        }
                        else
                        {
                                zrot = Padj.curvedness + (anglepos * 1.0 / (dadlink->commacount + 1) - 0.5) * M_PI * 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, int 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(genome.c_str(), (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.length > thisti->P.length)
        {
                tmpcel->P.executeModifier('l');
                out += "l";
        }
        while (tmpcel->P.length < thisti->P.length)
        {
                tmpcel->P.executeModifier('L');
                out += "L";
        }
        while (tmpcel->P.curvedness > thisti->P.curvedness)
        {
                tmpcel->P.executeModifier('c');
                out += "c";
        }
        while (tmpcel->P.curvedness < thisti->P.curvedness)
        {
                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 += ":";
                                        // connection 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 an 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 = count();
        // pick a random node, between 0 and n-1
        return ordNode(randomN(n));
}

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, out.c_str());
}

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;
        int 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;
}