source: cpp/f4/conv_f4.cpp @ 100

/**
 *  conv_f4.cpp - f4 genotype functions.
 *
 *  f4genotype - f4 format genotype conversions for Framsticks
 *
 *  Copyright (C) 1999,2000  Adam Rotaru-Varga (adam_rotaru@yahoo.com)
 *  Copyright (C) 2001-2003  Maciej Komosinski
 *
 *  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 "conv_f4.h"
#include "framsg.h"
#include "geno_fx.h" //for GENOPER_OK constant

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


GenoConv_F40::GenoConv_F40()
{
  name = "f4 converter";
  in_format  = '4';
  out_format = '0';
  mapsupport = 1;
  info = "Developmental encoding";
}


SString GenoConv_F40::convert(SString &in, MultiMap * map)
{
  int res;
  f4_Model * model = new f4_Model();
  res = model->buildFromF4(in);
  if (GENOPER_OK != res) return SString();  // oops
  if (NULL != map)
    // generate to-f0 conversion map
    model->getCurrentToF0Map(*map);
  SString out = model->getF0Geno().getGene();
  delete model;
  return out;
}


GenoConv_F41_TestOnly::GenoConv_F41_TestOnly()
{
  name = "test-only approximate f4 -> f0 converter";
  in_format  = '4';
  out_format = '1';
  mapsupport = 0;
  info = "This is for testing.  Do not use in production! (adam)";
}


SString GenoConv_F41_TestOnly::convert(SString &in, MultiMap * map)
{
  int res;
  f4_Model * model = new f4_Model();
  res = model->buildFromF4(in);
  if (GENOPER_OK != res) return SString();  // oops
  SString out;
  model->toF1Geno(out);
  delete model;
  return out;
}


f4_Model::f4_Model() : Model()
{
  cells = NULL;
}

f4_Model::~f4_Model()
{
  if (cells) delete cells;
}

int f4_Model::buildFromF4(SString &geno)
{
  int i;

  error = GENOPER_OK;
  errorpos = -1;

  // build cells, and simulate
  if (cells) delete cells;
  cells = new f4_Cells(geno, 0);
  if (GENOPER_OK != cells->geterror())
  {
    error = cells->geterror();
    errorpos = cells->geterrorpos();
    //delete cells;
    return error;
  }

  cells->simulate();
  if (GENOPER_OK != cells->geterror())
  {
    error = cells->geterror();
    errorpos = cells->geterrorpos();
    return error;
  }

  // reset recursive traverse flags
  for(i=0; i<cells->nc; i++)
    cells->C[i]->recProcessedFlag = 0;

  open(); // begin model build

  // process every cell
  int res;
  for(i=0; i<cells->nc; i++)
  {
    res = buildModelRec(cells->C[i]);
    if (res)
    {
      FramMessage("f4_Model", "buildModelRec", "Error in building Model", 2);
      error = res;
      break;
    }
  }

  res = close();
  if (0 == res) // invalid
    error = -10;

  return error;
}


f4_Cell * f4_Model::getStick(f4_Cell * C)
{
  if (T_STICK4 == C->type) return C;
  if (NULL != C->dadlink)
    return getStick(C->dadlink);
  // we have no more dadlinks, find any stick
  for (int i=0; i<cells->nc; i++)
    if (cells->C[i]->type == T_STICK4)
      return cells->C[i];
  // none!
  FramMessage("f4_Model", "getStick", "Not a single stick", 2);
  return NULL;
}


/// updated by Macko to follow new GDK standards (no more neuroitems)
int f4_Model::buildModelRec(f4_Cell * C)
{
  int partidx;
  int j, res;
  MultiRange range;

  if (C->recProcessedFlag)
    // already processed
    return 0;

  // mark it processed
  C->recProcessedFlag = 1;

  // make sure parent is a stick
  if (NULL != C->dadlink)
    if (C->dadlink->type != T_STICK4)
    {
      C->dadlink = getStick(C->dadlink);
    }

  // make sure its parent is processed first
  if (NULL != C->dadlink)
  {
    res = buildModelRec(C->dadlink);
    if (res) return res;
  }

  char tmpLine[100];

  range = C->genoRange;
  if (C->type == T_STICK4)
  {
    int jj_p1_refno;  // save for later
    // first end is connected to dad, or new
    if (C->dadlink == NULL)
    {
      // new part object for firstend
      // coordinates are left to be computed by Model
      sprintf(tmpLine, "p:m=1,fr=%g,ing=%g,as=%g",
        /*1.0/C->P.mass,*/ C->P.friction, C->P.ingest, C->P.assim
        //C->firstend.x, C->firstend.y, C->firstend.z
        );
      partidx = singleStepBuild(tmpLine, &range );
      if (partidx < 0) return -1;
      jj_p1_refno = partidx;
    } else {
      // adjust mass/vol of first endpoint
      jj_p1_refno = C->dadlink->p2_refno;
      Part * p1 = getPart(jj_p1_refno);
      p1->mass += 1.0;
//      p1->volume += 1.0/C->P.mass;
    }
    // new part object for lastend
    sprintf(tmpLine, "p:m=1,fr=%g,ing=%g,as=%g",
        //C->lastend.x, C->lastend.y, C->lastend.z
        /*"vol=" 1.0/C->P.mass,*/ C->P.friction, C->P.ingest, C->P.assim
      );
    partidx = singleStepBuild(tmpLine, &range );
    if (partidx < 0) return -2;
    C->p2_refno = partidx;

    // new joint object
    // check that the part references are valid
    int jj_p2_refno = C->p2_refno;
    if ((jj_p1_refno < 0) || (jj_p1_refno >= getPartCount())) return -11;
    if ((jj_p2_refno < 0) || (jj_p2_refno >= getPartCount())) return -12;
    sprintf(tmpLine, "j:p1=%ld,p2=%ld,dx=%g,dy=0,dz=0,rx=%g,ry=0,rz=%g"\
      ",stam=%g",
      jj_p1_refno, jj_p2_refno,
      // relative position -- always (len, 0, 0), along the stick
      // this is optional!
      C->P.len,
      // relative rotation
      C->xrot, C->zrot,
      //C->P.ruch,   // rotstif
      C->P.odpor
    );
    partidx = singleStepBuild(tmpLine, &range );
    if (partidx < 0) return -13;
    C->joint_refno = partidx;
  }

  if (C->type == T_NEURON4) ///<this case was updated by MacKo
  {
    // new neuron object
    // it is linked to a part (not a joint!)
    int p_refno = C->dadlink->p2_refno;
    if ((p_refno < 0) || (p_refno >= getPartCount())) return -21;
    // joint_refno is currently not used
    sprintf(tmpLine, "n:p=%ld,d=\"N:in=%g,fo=%g,si=%g\"",
      p_refno,
      C->inertia, C->force, C->sigmo);
    partidx = singleStepBuild(tmpLine, &range );
    if (partidx < 0) return -22;
    C->neuro_refno = partidx;
    int n_refno = C->neuro_refno;

    if (C->ctrl)
    {
      if (1 == C->ctrl)
        sprintf(tmpLine, "n:j=%d,d=\"@:p=%g\"",   C->dadlink->joint_refno, C->P.ruch);
      else
        sprintf(tmpLine, "n:j=%d,d=\"|:p=%g,r=%g\"",C->dadlink->joint_refno, C->P.ruch, C->mz);
      partidx = singleStepBuild(tmpLine, &range );
      if (partidx < 0) return -32;
      sprintf(tmpLine, "c:%d,%d",partidx,n_refno);
      if (singleStepBuild(tmpLine, &range )<0) return -33;
    }

    for (j=0; j<C->nolink; j++)
    {
      if (NULL != C->links[j]->from)
        buildModelRec(C->links[j]->from);

      tmpLine[0]=0;
      if (1 == C->links[j]->t) sprintf(tmpLine, "n:p=%d,d=\"*\"",p_refno);
      if (2 == C->links[j]->t) sprintf(tmpLine, "n:j=%d,d=\"G\"", C->dadlink->joint_refno);
      if (3 == C->links[j]->t) sprintf(tmpLine, "n:p=%d,d=\"T\"",p_refno);
      if (4 == C->links[j]->t) sprintf(tmpLine, "n:p=%d,d=\"S\"",p_refno);
      int from=-1;
      if (tmpLine[0]) //input from receptor
      {
        from=singleStepBuild(tmpLine, &range );
        if (from<0) return -34;
      } /*could be 'else'...*/
      if (NULL != C->links[j]->from) // input from another neuron
         from=C->links[j]->from->neuro_refno;
      if (from>=0)
      {
        sprintf(tmpLine, "c:%d,%d,%g", n_refno,from,C->links[j]->w);
        if (singleStepBuild(tmpLine, &range ) < 0) return -35;
      }
    }
  }
  return 0;
}


void f4_Model::toF1Geno(SString &out)
{
  cells->toF1Geno(out);
}