double CCopasiSpringLayout::potSecondOrderEdge(const CLMetabReferenceGlyph & e1, const CLMetabReferenceGlyph & e2, double & dist) const
{
const CLMetabGlyph * pMG1 = e1.getMetabGlyph();
const CLMetabGlyph * pMG2 = e2.getMetabGlyph();
if (pMG1 == NULL || pMG2 == NULL)
return 0;
double tmp = distance(pMG1->getX() + pMG1->getWidth() / 2, pMG1->getY() + pMG1->getHeight() / 2,
pMG2->getX() + pMG2->getWidth() / 2, pMG2->getY() + pMG2->getHeight() / 2);
return pow(tmp - dist, 2);
}
double CCopasiSpringLayout::potEdge(const CLMetabReferenceGlyph & e, const CLReactionGlyph & r) const
{
double dist = 70;
if (e.getRole() == CLMetabReferenceGlyph::SIDESUBSTRATE || e.getRole() == CLMetabReferenceGlyph::SIDEPRODUCT)
dist = 40;
const CLMetabGlyph * pMG = e.getMetabGlyph();
double tmp = distance(pMG->getX() + pMG->getWidth() / 2, pMG->getY() + pMG->getHeight() / 2,
r.getX() + r.getWidth() / 2, r.getY() + r.getHeight() / 2);
if (e.getRole() == CLMetabReferenceGlyph::MODIFIER)
return 0.3 * pow(tmp - dist, 2);
else
return pow(tmp - dist, 2);
}
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.
std::vector<CoordinateRelation>::const_iterator it, itEnd = mFixedRelations.end();
for (it = mFixedRelations.begin(); it != itEnd; ++it)
it->target->setPosition(it->source->getPosition() + it->diff);
//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]->getRole() == CLMetabReferenceGlyph::SUBSTRATE)
{
s_c += 1.0;
s = s + pRG->getListOfMetabReferenceGlyphs()[j]->getMetabGlyph()->getBoundingBox().getCenter();
}
if (pRG->getListOfMetabReferenceGlyphs()[j]->getRole() == CLMetabReferenceGlyph::SIDESUBSTRATE)
{
s_c += 0.1;
s = s + pRG->getListOfMetabReferenceGlyphs()[j]->getMetabGlyph()->getBoundingBox().getCenter() * 0.1;
}
if (pRG->getListOfMetabReferenceGlyphs()[j]->getRole() == CLMetabReferenceGlyph::PRODUCT)
{
p_c += 1.0;
p = p + pRG->getListOfMetabReferenceGlyphs()[j]->getMetabGlyph()->getBoundingBox().getCenter();
}
if (pRG->getListOfMetabReferenceGlyphs()[j]->getRole() == CLMetabReferenceGlyph::SIDEPRODUCT)
{
p_c += 0.1;
p = p + pRG->getListOfMetabReferenceGlyphs()[j]->getMetabGlyph()->getBoundingBox().getCenter() * 0.1;
}
}
if (s_c > 0)
s = s * (1 / s_c);
else
s = pRG->getPosition();
if (p_c > 0)
p = p * (1 / p_c);
else
p = pRG->getPosition();
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 = pRG->getPosition() - (dir * 0.05);
CLPoint reaction_p = pRG->getPosition() + (dir * 0.05);
CLPoint reaction_m1 = pRG->getPosition() + ortho_dir * 10;
CLPoint reaction_m2 = pRG->getPosition() - 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->getRole())
{
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 (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));
}
}
}
}
//rearrange the text boxes
//TODO
//calculate bounding box for the layout, or recenter the layout
//for (i = 0; i < mpLayout->getListOfSpeciesGlyphs().size() ; ++i)
const CLBoundingBox &bounds = mpLayout->calculateBoundingBox();
mpLayout->setDimensions(CLDimensions(bounds.getPosition().getX() + bounds.getDimensions().getWidth(), bounds.getPosition().getY() + bounds.getDimensions().getHeight()));
}
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();
}