/** TODO: avoid recalculating when nothing changed */
Matrix44 Entity2D::GetCenterTransformationMatrix()
{
Matrix44 matrix = Matrix44::Identity;
matrix.Scale(Vector3::Create(m_vScale.X, m_vScale.Y, 1.0f));
matrix.Rotate(Vector3::Create(0.0f, 0.0f, m_fRotation*Math::DegToRadFactor));
matrix.Translate(Vector3::Create(m_vPosition.X, m_vPosition.Y, 0.0f));
// TODO: use type checking at initialization time in AddChild() and only use static_cast here
if(Entity2D* pEntity2D = GetAncestor<Entity2D>())
{
matrix *= pEntity2D->GetTransformationMatrix();
}
return matrix;
}
//! returns true if the button is touched
bool Button::IsTouched() const
{
Matrix44 transformation = Matrix44::Identity;
transformation.Translate(-Vector3::Create(m_vCenter.X, m_vCenter.Y, 0.0f));
transformation.Scale(Vector3::Create(m_vScale.X, m_vScale.Y, 1.0f));
transformation.Rotate(Vector3::Create(0.0f, 0.0f, m_fRotation*Math::DegToRadFactor));
transformation.Translate(Vector3::Create(m_vOriginalPosition.X, m_vOriginalPosition.Y, 0.0f));
if(Entity2D* p2DEntity = GetAncestor<Entity2D>())
{
transformation *= p2DEntity->GetTransformationMatrix();
}
Matrix44 inverse;
if(transformation.GetInverse(inverse))
{
Vector2 vTouchPos = InputManager::Instance()->GetTouchState().vPosition;
Vector3 invTouchPos3D = inverse.TransformVect(Vector3::Create(vTouchPos.X, vTouchPos.Y, 0.0f));
Vector2 vInvTouchPos(invTouchPos3D.X, invTouchPos3D.Y);
return GetBoundingBox().Contains(vInvTouchPos);
}
return false;
}
// Evolve rNode a specific time
void Tree::Evolve(Node &rNode, double dTime)
{
dTime = fabs(dTime);
if(dTime < DBL_EPSILON)
return; // Nothing to evolve
//advance branch color
branchColor += Nucleotide::ColorInc;
// Substitutions
unsigned int uNuc = 0;
for(vector<Sequence>::iterator it = rNode.m_vSections.begin(); it != rNode.m_vSections.end(); ++it)
{
for(Sequence::iterator jt = it->begin(); jt != it->end(); ++jt)
{
// Skip any position that is a deletion
if(jt->IsDeleted())
continue;
// Total Evolution Rate for the position
double dTemp = dTime*jt->GetRate();
if(dTemp < DBL_EPSILON)
continue; // Invariant Site
// if dTemp is different from the previous one, recalculate probability matrix
if(dTemp != m_dOldTime)
{
m_dOldTime = dTemp;
Vector4 vec;
vec[0] = exp(dTemp*m_vecL[0]);
vec[1] = exp(dTemp*m_vecL[1]);
vec[2] = exp(dTemp*m_vecL[2]);
vec[3] = exp(dTemp*m_vecL[3]);
Matrix44 mat; mat.Scale(vec, m_matU);
m_matSubst.Multiply(m_matV, mat);
for(Matrix44::Pos i=0;i<4;++i)
{
m_matSubst(i,1) += m_matSubst(i,0);
m_matSubst(i,2) += m_matSubst(i,1);
//m_matSubst(i,3) = 1.0;
}
}
// get the base of the current nucleotide and pick new base
unsigned int uBase = jt->GetBase();
dTemp = rand_real();
if(dTemp < m_matSubst(uBase, 0))
jt->SetBase(0);
else if(dTemp < m_matSubst(uBase, 1))
jt->SetBase(1);
else if(dTemp < m_matSubst(uBase, 2))
jt->SetBase(2);
else
jt->SetBase(3);
++uNuc; // Increase position
}
}
// Indel formation via Gillespie Algorithm
// Check whether Indels are off
if(m_dLambdaDel+m_dLambdaIns < DBL_EPSILON)
return;
// Get current length
Sequence::size_type uLength = rNode.SeqLength();
double dLength = (double)uLength;
double dW = 1.0/m_funcRateSum(dLength);
// Do indels
for(double dt = rand_exp(dW); dt <= dTime; dt += rand_exp(dW))
{
// insertion or deletion
if(rand_bool(m_funcRateIns(dLength)*dW))
{
//Insertion
Sequence::size_type ul = m_pInsertionModel->RandSize();
Sequence::size_type uPos = (Sequence::size_type)rand_uint((uint32_t)uLength); // pos is in [0,L]
// Construct sequence to be inserted
Sequence seq;
for(unsigned int uc = 0; uc < ul; ++uc)
{
Nucleotide nuc = RandomNucleotide(uc);
nuc.SetColor(branchColor);
seq.push_back(nuc);
}
// Find Position of Insertion
Node::iterator itPos = rNode.SeqPos(uPos);
if(itPos.first == rNode.m_vSections.end())
{
// Insert at end of sequence
uLength += rNode.m_vSections.back().Insertion(
rNode.m_vSections.back().end(), seq.begin(), seq.end());
}
else
{
// Insert inside sequence
uLength += itPos.first->Insertion(itPos.second, seq.begin(), seq.end());
}
}
else if(uLength > 0)
{
// Deletion
// Draw random size and random pos and rearrange
Sequence::size_type ul = m_pDeletionModel->RandSize();
Sequence::size_type uPos = rand_uint((uint32_t)(uLength+ul-2));
Sequence::size_type uB = max(ul-1, uPos);
Sequence::size_type uSize = min(ul-1+uLength, uPos+ul)-uB;
// If GapLimits are on, only process deletion if it is completely inside the acceptance
// region as defined by the GapLimit. Check points are at sequence positions 0-uKeepFlank and
// uLength-1+uKeepFlank. These become 0-uKeepFlank+ul-1 and uLength-1+uKeepFlank+ul-1,
// when shifted to "deletion space".
if(m_uKeepFlank == 0 || ( (ul-1) < uPos+m_uKeepFlank && uPos < uLength-1+m_uKeepFlank ) ) {
uB -= (ul-1);
// Find deletion point
Node::iterator itPos = rNode.SeqPos(uB);
Sequence::size_type uTemp = uSize;
uTemp -= itPos.first->Deletion(itPos.second, uTemp);
// Delete uSize nucleotides begin sensitive to gaps that overlap sections
for(++itPos.first; uSize && itPos.first != rNode.m_vSections.end(); ++itPos.first)
uTemp -= itPos.first->Deletion(itPos.first->begin(), uTemp);
uLength -= (uSize-uTemp);
}
}
// update length
dLength = (double)uLength;
// new waiting time parameter
dW = 1.0/m_funcRateSum(dLength);
}
}
