void SPxSolver::qualSlackViolation(Real& maxviol, Real& sumviol) const
{
maxviol = 0.0;
sumviol = 0.0;
DVector solu( nCols() );
DVector slacks( nRows() );
getPrimal( solu );
getSlacks( slacks );
for( int row = 0; row < nRows(); ++row )
{
const SVector& rowvec = rowVector( row );
Real val = 0.0;
for( int col = 0; col < rowvec.size(); ++col )
val += rowvec.value( col ) * solu[rowvec.index( col )];
Real viol = spxAbs(val - slacks[row]);
if (viol > maxviol)
maxviol = viol;
sumviol += viol;
}
}
vector<Scaffold> ScaffoldExtractor::Extract(const DataStore &store, const BranchAndBound &solver)
{
vector<Scaffold> ans;
int m = solver.GetSlackCount();
vector< vector<int> > components;
vector<bool> slacks(m, true);
for (int i = 0; i < m; i++)
if (solver.GetDistanceSlack(i) >= ExtendedFixedMIQPSolver::DesiredDistanceSlackMax || solver.GetOrderSlack(i) >= ExtendedFixedMIQPSolver::DesiredOrderSlackMax)
slacks[i] = false;
DPGraph graph(store, solver.T, slacks);
graph.FindConnectedComponents(components);
for (int i = 0; i < (int)components.size(); i++)
{
int size = components[i].size();
Scaffold scaffold;
for (int j = 0; j < size; j++)
scaffold.AddContig(components[i][j], solver.T[components[i][j]], solver.X[components[i][j]], store[components[i][j]].Sequence.Nucleotides.length());
scaffold.Sort();
ans.push_back(scaffold);
}
return ans;
}