Пример #1
0
/**
 * This function produces a random layout. It first shufles around
 * metab glyphs and reaction centers, and finally corrects all ars
 */
void CCopasiSpringLayout::randomize()
{
  CRandom* pRandom = CRandom::createGenerator(CRandom::mt19937, CRandom::getSystemSeed());

  size_t i;

  //compartment glyphs

  //metab glyphs
  for (i = 0; i < mpLayout->getListOfMetaboliteGlyphs().size(); ++i)
    {
      CLMetabGlyph* pMetabGlyph = &mpLayout->getListOfMetaboliteGlyphs()[i];
      const CMetab* pMetab = dynamic_cast<const CMetab*>(pMetabGlyph->getModelObject());

      if (!pMetab)
        continue;

      //find the compartment glyph
      const CCompartment* pComp = pMetab->getCompartment();

      if (!pComp)
        continue;

      const CLCompartmentGlyph* pCompGlyph = NULL;
      size_t j;

      for (j = 0; j < mpLayout->getListOfCompartmentGlyphs().size(); ++j)
        if (mpLayout->getListOfCompartmentGlyphs()[j].getModelObjectKey()
            == pComp->getKey())
          {
            pCompGlyph = &mpLayout->getListOfCompartmentGlyphs()[j];
            break;
          }

      if (pCompGlyph)
        randomlyPlaceGlyphInCompartmentGlyph(pMetabGlyph, pCompGlyph, pRandom);
      else
        randomlyPlaceGlyphInDimensions(pMetabGlyph, &mpLayout->getDimensions(), pRandom);
    }

  //reaction glyphs
  for (i = 0; i < mpLayout->getListOfReactionGlyphs().size(); ++i)
    {
      CLReactionGlyph* pReactionGlyph = &mpLayout->getListOfReactionGlyphs()[i];
      CLPoint center(0, 0);
      size_t count;

      for (count = 0; count < pReactionGlyph->getListOfMetabReferenceGlyphs().size(); ++count)
        {
          CLMetabGlyph* metabGlyph = pReactionGlyph->getListOfMetabReferenceGlyphs()[count].getMetabGlyph();

          if (metabGlyph == NULL) continue;

          center = center + metabGlyph->getBoundingBox().getCenter();
        }

      center = center * (1.0 / pReactionGlyph->getListOfMetabReferenceGlyphs().size());
      center = center + CLPoint(pRandom->getRandomCC() * 20 - 10,  pRandom->getRandomCC() * 20 - 10);

      pReactionGlyph->setPosition(center);

      /*if (pCompGlyph)
        randomlyPlaceGlyphInCompartmentGlyph(pMetabGlyph, pCompGlyph);
      else
        randomlyPlaceGlyphInDimensions(pMetabGlyph, &mpCurrentLayout->getDimensions());*/
    }

  placeTextGlyphs(mpLayout);
  delete pRandom;

  finalizeState();
}
Пример #2
0
void CCopasiSpringLayout::finalizeState()
{
  unsigned int i;

  //update the positions of the dependent glyphs
  //this can be done here since we assume that those glyphs
  //do not affect the layout.
  updateFixedRelations();

  //for now, only create curves for the reaction glyphs
  for (i = 0; i < mpLayout->getListOfReactionGlyphs().size() ; ++i)
    {
      CLReactionGlyph* pRG = &mpLayout->getListOfReactionGlyphs()[i];

      //Determine the average position of substrates and products, giving less weight to side reactants
      CLPoint s, p;
      double s_c = 0; double p_c = 0;
      unsigned int j, jmax = pRG->getListOfMetabReferenceGlyphs().size();

      for (j = 0; j < jmax; ++j)
        {
          if (pRG->getListOfMetabReferenceGlyphs()[j].getFunctionalRole() == CLMetabReferenceGlyph::SUBSTRATE)
            {
              CLMetabGlyph* metabGlyph = pRG->getListOfMetabReferenceGlyphs()[j].getMetabGlyph();

              if (metabGlyph != NULL)
                {
                  s_c += 1.0;
                  s = s + metabGlyph->getBoundingBox().getCenter();
                }
            }

          if (pRG->getListOfMetabReferenceGlyphs()[j].getFunctionalRole() == CLMetabReferenceGlyph::SIDESUBSTRATE)
            {
              CLMetabGlyph* metabGlyph = pRG->getListOfMetabReferenceGlyphs()[j].getMetabGlyph();

              if (metabGlyph != NULL)
                {
                  s_c += 0.1;
                  s = s + metabGlyph->getBoundingBox().getCenter() * 0.1;
                }
            }

          if (pRG->getListOfMetabReferenceGlyphs()[j].getFunctionalRole() == CLMetabReferenceGlyph::PRODUCT)
            {
              CLMetabGlyph* metabGlyph = pRG->getListOfMetabReferenceGlyphs()[j].getMetabGlyph();

              if (metabGlyph != NULL)
                {
                  p_c += 1.0;
                  p = p + metabGlyph->getBoundingBox().getCenter();
                }
            }

          if (pRG->getListOfMetabReferenceGlyphs()[j].getFunctionalRole() == CLMetabReferenceGlyph::SIDEPRODUCT)
            {
              CLMetabGlyph* metabGlyph = pRG->getListOfMetabReferenceGlyphs()[j].getMetabGlyph();

              if (metabGlyph != NULL)
                {

                  p_c += 0.1;
                  p = p + metabGlyph->getBoundingBox().getCenter() * 0.1;
                }
            }
        }

      CLPoint position = pRG->getPosition();

      if (position.getX() == 0 && position.getY() == 0
          && pRG->getDimensions().getWidth() == 0
          && pRG->getDimensions().getHeight() == 0
          && pRG->getCurve().getNumCurveSegments() > 0)
        {
          position = pRG->getCurve().getCurveSegments()[0].getStart();
          pRG->setPosition(position);
        }

      if (s_c > 0)
        s = s * (1 / s_c);
      else
        {
          s = position;
        }

      if (p_c > 0)
        p = p * (1 / p_c);
      else
        p = position;

      CLPoint dir = p - s; //overall direction of reaction

      if (dir.getX() == 0 && dir.getY() == 0)
        dir = CLPoint(1, 0);

      CLPoint ortho_dir = CLPoint(dir.getY(), -dir.getX());
      ortho_dir.scale(1 / sqrt(pow(ortho_dir.getX(), 2) + pow(ortho_dir.getY(), 2)));

      CLPoint reaction_s = position - (dir * 0.05);
      CLPoint reaction_p = position + (dir * 0.05);
      CLPoint reaction_m1 = position + ortho_dir * 10;
      CLPoint reaction_m2 = position - ortho_dir * 10;

      pRG->getCurve().clear();
      pRG->getCurve().addCurveSegment(CLLineSegment(reaction_s, reaction_p));

      for (j = 0; j < jmax; ++j)
        {
          //here we need to generate the curves for the MetabReferenceGlyphs.
          //we will need to consider the size of the glyphs, role of the metab in the reaction, etc.
          //For now, only a primitive implementation: TODO: improve
          CLMetabReferenceGlyph* pMRG = &pRG->getListOfMetabReferenceGlyphs()[j];
          double direction;
          //double modifierLength = -0.2;

          switch (pMRG->getFunctionalRole())
            {
              case CLMetabReferenceGlyph::SUBSTRATE :
              case CLMetabReferenceGlyph::SIDESUBSTRATE :
              {
                direction = -0.1;
                CLPoint metabPoint = borderProjection(pMRG->getMetabGlyph(), reaction_s + dir * direction /*(modifierLength * 1.5)*/, 5);
                pMRG->getCurve().clear();
                pMRG->getCurve().addCurveSegment(CLLineSegment(reaction_s,
                                                 metabPoint,
                                                 reaction_s + dir * direction,
                                                 (reaction_s + dir * (direction * 1.5) + metabPoint) * 0.5));
              }
              break;

              case CLMetabReferenceGlyph::PRODUCT :
              case CLMetabReferenceGlyph::SIDEPRODUCT :
              {
                direction = 0.1;
                CLPoint metabPoint = borderProjection(pMRG->getMetabGlyph(), reaction_p + dir * direction /*(modifierLength * 1.5)*/, 5);
                pMRG->getCurve().clear();
                pMRG->getCurve().addCurveSegment(CLLineSegment(reaction_p,
                                                 metabPoint,
                                                 reaction_p + dir * direction,
                                                 (reaction_p + dir * (direction * 1.5) + metabPoint) * 0.5));
              }
              break;

              default:
              {
                CLPoint reactionPoint;

                if (pMRG->getMetabGlyph() && ortho_dir.dot(pRG->getPosition() - pMRG->getMetabGlyph()->getPosition()) < 0)
                  {
                    direction = +10.0;
                    reactionPoint = reaction_m1;
                  }
                else
                  {
                    direction = -10.0;
                    reactionPoint = reaction_m2;
                  }

                CLPoint metabPoint = borderProjection(pMRG->getMetabGlyph(), reactionPoint + dir * 0 * direction /*(modifierLength * 1.5)*/, 5);
                pMRG->getCurve().clear();
                pMRG->getCurve().addCurveSegment(CLLineSegment(metabPoint,
                                                 reactionPoint,
                                                 (reactionPoint + dir * (0 * direction * 1.5) + metabPoint) * 0.5,
                                                 reactionPoint + ortho_dir * direction));
              }
            }
        }
    }

  //update the curves in the general glyph
  for (i = 0; i < mpLayout->getListOfGeneralGlyphs().size() ; ++i)
    {
      CLGeneralGlyph* pGG = &mpLayout->getListOfGeneralGlyphs()[i];

      size_t j;

      for (j = 0; j < pGG->getListOfReferenceGlyphs().size(); ++j)
        {
          CLReferenceGlyph* pRG = &pGG->getListOfReferenceGlyphs()[j];

          if (pRG->getCurve().getNumCurveSegments() == 0) continue;

          CLPoint refPoint = borderProjection(pRG->getTargetGlyph(), pRG->getBoundingBox().getCenter(), 5);
          pRG->getCurve().clear();
          pRG->getCurve().addCurveSegment(CLLineSegment(refPoint, pRG->getBoundingBox().getCenter()));
        }
    }

  //calculate bounding box for the layout, or recenter the layout
  mpLayout->calculateAndAssignBounds();
}