/*
	This program is free software; you can redistribute it and/or
	modify it under the terms of the GNU General Public License
	as published by the Free Software Foundation; either version 2
	of the License, or (at your option) any later version.

	This program 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 General Public License for more details.

	You should have received a copy of the GNU General Public License
	along with this program; if not, write to the Free Software
	Foundation, Inc., 51 Franklin Street, Fifth Floor,
	Boston, MA  02110-1301, USA.

	---
	Copyright (C) 2011 - 2015, Simon Hampe <simon.hampe@googlemail.com>

	Computes all lines (and families thereof) in a tropical cubic surface in R^3.
	*/

#include "polymake/client.h"
#include "polymake/Rational.h"
#include "polymake/TropicalNumber.h"
#include "polymake/Polynomial.h"
#include "polymake/Matrix.h"
#include "polymake/Vector.h"
#include "polymake/linalg.h"
#include "polymake/IncidenceMatrix.h"
#include "polymake/tropical/LoggingPrinter.h"
#include "polymake/tropical/divisor.h"
#include "polymake/tropical/convex_hull_tools.h"
#include "polymake/tropical/solver_def.h"
#include "polymake/tropical/lines_in_cubic_data.h"
#include "polymake/tropical/lines_in_cubic_helper.h"
#include "polymake/tropical/lines_in_cubic_reachable.h"
#include "polymake/tropical/specialcycles.h"
#include "polymake/tropical/thomog.h"

namespace polymake { namespace tropical {
	
	//using namespace atintlog::donotlog;
	   using namespace atintlog::dolog;
	  // using namespace atintlog::dotrace;
	
	//Takes a max(!)-tropical polynomial of degree 3 in affine coordinates and computes all 
	//lines in the corresponding cubic.
	perl::Object linesInCubic(Polynomial<TropicalNumber<Max> > f) {
		//First, we compute the divisor of f
		perl::Object r3 = projective_torus<Max>(3,1); 
		perl::Object ratfct = CallPolymakeFunction("rational_fct_from_affine_numerator",f);	
		//dbgtrace << "Computing divisor" << endl;
		perl::Object X = CallPolymakeFunction("divisor",r3,ratfct);
		//dbgtrace << "Done." << endl;
		perl::Object lindom = ratfct.give("DOMAIN");
		Matrix<Rational> lindom_rays = lindom.give("VERTICES");
			lindom_rays = tdehomog(lindom_rays);
		IncidenceMatrix<> lindom_cones = lindom.give("MAXIMAL_POLYTOPES");
		Matrix<Rational> funmat(f.monomials_as_matrix());
		Vector<Rational> funcoeffs(f.coefficients_as_vector());
		//Rearrange so that values of terms on points can be computed as product with matrix
		funmat = funcoeffs | funmat; 

		Matrix<Rational> degree = (-1) *  unit_matrix<Rational>(3);
		degree = ones_vector<Rational>(3) / degree;
		degree = zero_vector<Rational>(4) | degree;

		//Then we compute all reachable points for each direction
		Vector<ReachableResult> reachable_points;
		for(int i = 0; i < 4; i++) {
			dbglog << "Computing reachable points from direction " << i << endl;
			reachable_points |= reachablePoints(f,X,i);
		}
		
		solver<Rational> sv;

		//This maps pairs of leafs to increasing numbers and vice versa
		Map<int, Map<int,int> > edge_pair_map;
		Map<int,Set<int> > index_to_pair_map;
		int count = 0;
		for(int a = 0; a <= 3; a++) {
			edge_pair_map[a] = Map<int,int>();
			for(int b = a+1; b <= 3; b++) {
				(edge_pair_map[a])[b] = count;
				index_to_pair_map[count] = (scalar2set(a) + scalar2set(b));
				count++;
			}
		}

		//Result variables

		//These variables contain the lines in the cubic
		Vector<VertexLine> vertex_line;
		Vector<VertexFamily> vertex_family;
		Vector<EdgeLine> edge_line;
		Vector<EdgeFamily> edge_family;


		//Then we compute the six intersection sets of the reachable loci, paired in complements
		//In each step we go through all pairs of maximal cones of these two complexes. We add to each
		// cone the direction of the potential bounded edge of the line and then intersect the two
		// resulting polyhedra. Afterwards we check if the result lies in X.

		Matrix<Rational> dummy_lineality(0,4);
		for(int i = 1; i <= 3; i++) {
			Vector<int> remaining(sequence(1,3) - i);
			dbglog << "Intersecting reachable loci from direction 0 and " << i << " and from direction " << remaining[0] << " and " << remaining[1] << endl;
			//All points reachable from direction 0 and i
			fan_intersection_result z_inter = cdd_fan_intersection(
					reachable_points[0].rays, dummy_lineality, reachable_points[0].cells / reachable_points[0].edges,
					reachable_points[i].rays, dummy_lineality, reachable_points[i].cells / reachable_points[i].edges
					);
			//All points reachable from the other two directions
			fan_intersection_result c_inter = cdd_fan_intersection(
					reachable_points[remaining[0]].rays, dummy_lineality, reachable_points[remaining[0]].cells / reachable_points[remaining[0]].edges,
					reachable_points[remaining[1]].rays, dummy_lineality, reachable_points[remaining[1]].cells / reachable_points[remaining[1]].edges
					);
			//Clean up the intersection
			DirectionIntersection z_inter_clean = cleanUpIntersection(z_inter);
			DirectionIntersection c_inter_clean = cleanUpIntersection(c_inter);

			IncidenceMatrix<> all_z_cones = z_inter_clean.cells / z_inter_clean.edges / z_inter_clean.points;
			IncidenceMatrix<> all_c_cones = c_inter_clean.cells / c_inter_clean.edges / c_inter_clean.points;

			// 	perl::ListReturn test;
			// 	  perl::Object t("WeightedComplex");
			// 	  t.take("RAYS") << z_inter_clean.rays;
			// 	  t.take("MAXIMAL_CONES") << all_z_cones;
			// 	  t.take("USES_HOMOGENEOUS_C") << true;
			// 	  test << t; return test;

			dbglog << "Computing potential families in between..." << endl;
			//Go through all pairs of cells, add the appropriate direction vector and intersect the two polyhedra
			Vector<Rational> dir_z = - degree.row(0) - degree.row(i);
			Vector<Rational> dir_c = - dir_z;
			for(int zc = 0; zc < all_z_cones.rows(); zc++) {
				//We compute the number of relevant cells in zc. If the dimension of zc is <= 1, this is just zc
				//If the dimension is 2, we take all the codimension one faces of zc that are visible 
				//"from the direction of dir_z", i.e. the scalar product of the outer facet normal with dir_z is
				//strictly positive. We will then do computations separately for each such codim one face
				Vector<Set<int> > z_cones;
				FacetData z_facets;
				int z_dim = (all_z_cones.row(zc).size() <= 2? all_z_cones.row(zc).size()-1 : 2);
				if(z_dim < 2) z_cones |= all_z_cones.row(zc);
				else {
					z_facets = computeFacets(z_inter_clean.rays,all_z_cones.row(zc),sv);
					z_cones |= visibleFaces(z_facets, dir_z);
				}

				//Now we go through all cells of c and apply the same procedure
				for(int cc = 0; cc < all_c_cones.rows(); cc++) {
					Vector<Set<int> > c_cones;
					FacetData c_facets;
					int c_dim = (all_c_cones.row(cc).size() <= 2? all_c_cones.row(cc).size()-1 : 2);
					if(c_dim < 2) c_cones |= all_c_cones.row(cc);
					else {
						c_facets = computeFacets(c_inter_clean.rays,all_c_cones.row(cc),sv);
						c_cones |= visibleFaces(c_facets,dir_c);
					}

					//Now we go trough all pairs of elements of z_cones and c_cones and find families in between them
					for(int zlist = 0; zlist < z_cones.dim(); zlist++) {
						for(int clist = 0; clist < c_cones.dim(); clist++) {
							//First we compute the intersection of the two polyhedra we obtain if we add to the
							//cells in zlist/clist a ray in edge direction. The result cannot have lineality space,
							//as neither of the two factors has one (not even implicit).
							Matrix<Rational> center = cdd_cone_intersection(
									z_inter_clean.rays.minor(z_cones[zlist],All) / dir_z, dummy_lineality, 
									c_inter_clean.rays.minor(c_cones[clist],All) / dir_c, dummy_lineality).first ;
							if(center.rows() == 0) continue;
							if(center.col(0) == zero_vector<Rational>(center.rows())) continue;

							//If the intersection is 0-dimensional, we just check if the maximum is attained twice,
							//then add it as solution
							if(center.rows() == 1) {
								if(maximumAttainedTwice(funmat * center.row(0))) {
									VertexLine vl;
									vl.vertex = center.row(0);
									Set<int> spans;
									if(z_dim == 2) spans += (edge_pair_map[0])[i];
									if(c_dim == 2) spans += (edge_pair_map[remaining[0]])[remaining[1]];
									vl.cells = spans;
									vertex_line |= vl;
								}
								continue;
							}//END if 0-dimensional

							//First we compute the "border" of center, i.e. the intersection with the two cones 
							Matrix<Rational> z_border = cdd_cone_intersection(
									z_inter_clean.rays.minor(z_cones[zlist],All), dummy_lineality,
									center, dummy_lineality).first;
							Matrix<Rational> c_border = cdd_cone_intersection(
									c_inter_clean.rays.minor(c_cones[clist],All), dummy_lineality,
									center, dummy_lineality).first;

							//Then we refine this polyhedron along the domains of f
							Vector<Set<int> > center_cone; center_cone |= sequence(0,center.rows());
							DirectionIntersection center_ref = cleanUpIntersection(cdd_fan_intersection(
										center, dummy_lineality, center_cone, lindom_rays, dummy_lineality, lindom_cones));

							//If the intersection is 1-dimensional , we have two possibilities:
							// (1) The center cone is equal to the intersection of the two border cones. Then the 
							//     whole cone is a one-dimensional family of lines without bounded edge.
							// (2) The center cone intersects the border cones each in a vertex. Then we check if all 
							//     cells of center_ref are contained in X. If so, we have an isolated line. 
							if(center.rows() == 2 ) {
								if(z_border.rows() == 2) {
									VertexFamily vf;
									vf.edge = z_border;
									vertex_family |= vf;
								}//END case (1)
								else {
									bool found_bad_cell = false;
									for(int cencone = 0; cencone < center_ref.edges.rows(); cencone++) {
										Matrix<Rational> cencone_rays = center_ref.rays.minor(center_ref.edges.row(cencone),All);
										Vector<Rational> interior_point = 
											accumulate(rows(cencone_rays),
													operations::add()) / accumulate(cencone_rays.col(0),operations::add());
										if(!maximumAttainedTwice(funmat*interior_point)) {
											found_bad_cell = true; break;
										}
									}//END iterate edges of refined center cell
									//If all edges lie in X, we add the line as isolated line
									if(!found_bad_cell) {
										EdgeLine el;
										el.vertexAtZero = z_border.row(0);
										el.vertexAwayZero = c_border.row(0);
										el.leafAtZero = i;
										el.spanAtZero = (z_dim == 2);
										el.spanAwayZero = (c_dim == 2);
										el.maxDistAtZero = 
											maximalDistanceVector(el.vertexAtZero, 
													degree.row(0) + degree.row(el.leafAtZero),
													lindom_rays, lindom_cones, funmat);
										el.maxDistAwayZero =
											maximalDistanceVector(el.vertexAwayZero,
													degree.row(remaining[0]) + degree.row(remaining[1]),
													lindom_rays, lindom_cones, funmat);
										edge_line |= el;
									}
								}//END case (2)
								continue;
							}//END if 1-dimensional

							//If the cone is 2-dimensional, we have to refine, project and refine again,
							// similarly to the procedure used when computing the reachable points
							if(center.rows() > 2) {
								LinesInCellResult lines_in_cell = 
									computeEdgeFamilies(center_ref, z_border, c_border,i, funmat);
								edge_family |= lines_in_cell.edge_families;
								//Add spans and max-dist-vectors before adding edge_line and vertex_line
								for(int el = 0; el < lines_in_cell.edge_lines.dim(); el++) {
									lines_in_cell.edge_lines[el].spanAtZero = (z_dim == 2);
									lines_in_cell.edge_lines[el].spanAwayZero = (c_dim == 2);
									lines_in_cell.edge_lines[el].maxDistAtZero = 
										maximalDistanceVector(lines_in_cell.edge_lines[el].vertexAtZero, 
												degree.row(0) + degree.row(i),
												lindom_rays, lindom_cones, funmat);
									lines_in_cell.edge_lines[el].maxDistAwayZero = 
										maximalDistanceVector(lines_in_cell.edge_lines[el].vertexAwayZero,
												degree.row(remaining[0]) + degree.row(remaining[1]),
												lindom_rays, lindom_cones, funmat);
								}//END fine-tune edge_lines
								for(int vl = 0; vl < lines_in_cell.vertex_lines.dim(); vl++) {
									Set<int> spans;
									if(z_dim == 2) spans += (edge_pair_map[0])[i];
									if(c_dim == 2) spans += (edge_pair_map[remaining[0]])[remaining[1]];
									lines_in_cell.vertex_lines[vl].cells = spans;
								}//END fine-tune vertex_lines

								edge_line |= lines_in_cell.edge_lines;
								vertex_line |= lines_in_cell.vertex_lines;
							}//END if 2-dimensional



						}//END iterate relevant cones from c
					}//END iterate relevant cones from z


				}//END iterate j-k-reachable cones
			}//END iterate 0-i-reachable cones
		}//END compute intersections of reachable loci

		// .............................................................................................
		dbglog << "Cleaning up result" << endl;

		// Step I: Clean up each type individually by checking if one contains the other or has to be glued
		// together somehow

		//Vertex line: Only check if one is contained in the other
		Set<int> double_vertices;
		for(int vl = 0; vl < vertex_line.dim(); vl++) {
			if(!double_vertices.contains(vl)) {
				for(int ovl = 0; ovl < vertex_line.dim(); ovl++) {
					if(vl != ovl) {
						if(vertex_line[vl].vertex == vertex_line[ovl].vertex && 
								(vertex_line[vl].cells * vertex_line[ovl].cells).size() == vertex_line[ovl].cells.size() ) {
							double_vertices += ovl;
						}	  
					}
				}
			}
		}//END clean up vertex_line
		vertex_line = vertex_line.slice(~double_vertices);

		//For vertex families we have to check if two families can be glued together
		std::list<VertexFamily> vf_queue;
		for(int vf = 0; vf < vertex_family.dim(); vf++) {
			vf_queue.push_back(vertex_family[vf]);
		}
		Vector<VertexFamily> approved_vfamilies;
		while(vf_queue.size() > 0) {
			VertexFamily fam = vf_queue.front(); vf_queue.pop_front();
			bool is_approved = true;
			for(int vf = 0; vf < approved_vfamilies.dim(); vf++) {
				//Case I: Both are identical: Just ignore the new one and add nothing new
				if( (approved_vfamilies[vf].edge.row(0) == fam.edge.row(0) &&
							approved_vfamilies[vf].edge.row(1) == fam.edge.row(1)) ||
						(approved_vfamilies[vf].edge.row(0) == fam.edge.row(1) &&
						 approved_vfamilies[vf].edge.row(1) == fam.edge.row(0))) {
					is_approved = false;
					break;
				}

				//Case II: At least one consists of two vertices, one of which is equal to
				// a vertex of the other. Then we glue both together, add the new element to the vf_queue and
				// go to the next vf_queue element
				if( (approved_vfamilies[vf].edge(0,0) + approved_vfamilies[vf].edge(1,0) == 2) ||
						(fam.edge(0,0) + fam.edge(1,0) == 2) ) {
					int avf_equal = -1;
					int fam_equal = -1;
					if(approved_vfamilies[vf].edge.row(0) == fam.edge.row(0)) avf_equal = 0; fam_equal = 0;
					if(approved_vfamilies[vf].edge.row(0) == fam.edge.row(1)) avf_equal = 0; fam_equal = 1;
					if(approved_vfamilies[vf].edge.row(1) == fam.edge.row(0)) avf_equal = 1; fam_equal = 0;
					if(approved_vfamilies[vf].edge.row(1) == fam.edge.row(1)) avf_equal = 1; fam_equal = 1;

					if(avf_equal != -1) {
						int other_avf = avf_equal == 0? 1 : 0;
						int other_fam = fam_equal == 0? 1 : 0;
						VertexFamily replacement;
						replacement.edge = approved_vfamilies[vf].edge.row(other_avf) / fam.edge.row(other_fam);
						vf_queue.push_back(replacement);
						approved_vfamilies = approved_vfamilies.slice(~scalar2set(vf));
						is_approved = false;
						break;
					} //END create new vertex family
				}//END Case II	
			}//END iterate approved families
			if(is_approved) approved_vfamilies |= fam;
		}//END clean up vertex families
		vertex_family = approved_vfamilies;

		//For edge lines, we check if two are equal or can be glued together
		std::list<EdgeLine> el_queue;
		for(int el = 0; el < edge_line.dim(); el++) {
			el_queue.push_back(edge_line[el]);
		}
		Vector<EdgeLine> approved_elfamilies;
		while(el_queue.size() > 0) {
			EdgeLine fam = el_queue.front(); el_queue.pop_front();
			bool is_approved = true;
			for(int el = 0; el < approved_elfamilies.dim(); el++) {
				//Interesting things only happen if both have the same direction
				if(approved_elfamilies[el].leafAtZero == fam.leafAtZero) {
					//Compatibility = Both families can be glued, i.e. in each direction either:
					// - the vertices at that end agree -> keep vertex with largest span
					// - one vertex has unbounded span and the other vertex differs by a positive multiple of 
					//   the edge direction -> keep vertex with unbounded span
					// - one vertex has bounded span, which contains the other vertex. -> keep vertex with bounded span
					bool isCompatibleAtZero = false;
					Vector<Rational> vertexAtZero;
					Vector<Rational> mdistAtZero;
					bool spanAtZero = false;
					if(approved_elfamilies[el].vertexAtZero == fam.vertexAtZero) {
						isCompatibleAtZero = true;
						vertexAtZero = fam.vertexAtZero;
						spanAtZero = approved_elfamilies[el].spanAtZero || fam.spanAtZero;
					}
					else {
						//Check if difference of vertices is multiple of edge direction
						Vector<Rational> edir = degree.row(0) + degree.row(fam.leafAtZero);
						Rational vdiff = vertexDistance(approved_elfamilies[el].vertexAtZero,
								fam.vertexAtZero, edir);
						//If so, check if span is compatible
						if(vdiff != 0) {
							if(vdiff > 0 && approved_elfamilies[el].spanAtZero) {
								Rational sdiff = vertexDistance(approved_elfamilies[el].vertexAtZero,
										approved_elfamilies[el].maxDistAtZero, edir);
								isCompatibleAtZero = sdiff == 0 || sdiff >= vdiff;
								vertexAtZero = approved_elfamilies[el].vertexAtZero;
								mdistAtZero = approved_elfamilies[el].maxDistAtZero;
								spanAtZero = true;
							}		
							if(vdiff < 0 && fam.spanAtZero) {
								Rational sdiff = vertexDistance(fam.vertexAtZero, fam.maxDistAtZero,edir);
								isCompatibleAtZero = sdiff == 0 || sdiff >= -vdiff;
								vertexAtZero = fam.vertexAtZero;
								mdistAtZero = fam.maxDistAtZero;
								spanAtZero = true;
							}
						}//END if is multiple of edge direction
					}//END check compat at zero
					if(!isCompatibleAtZero) continue;

					bool isCompatibleAwayZero = false;
					Vector<Rational> vertexAwayZero;
					Vector<Rational> mdistAwayZero;
					bool spanAwayZero = false;
					if(approved_elfamilies[el].vertexAwayZero == fam.vertexAwayZero) {
						isCompatibleAwayZero = true;
						vertexAwayZero = fam.vertexAwayZero;
						spanAwayZero = approved_elfamilies[el].spanAwayZero || fam.spanAwayZero;
					}
					else {
						//Check if difference of vertices is multiple of edge direction
						Vector<int> rem(sequence(1,3) - fam.leafAtZero);
						Vector<Rational> edir = degree.row(rem[0]) + degree.row(rem[1]);
						Rational vdiff = vertexDistance(approved_elfamilies[el].vertexAwayZero,
								fam.vertexAwayZero, edir);
						//If so, check if span is compatible
						if(vdiff != 0) {
							if(vdiff > 0 && approved_elfamilies[el].spanAwayZero) {
								Rational sdiff = vertexDistance(approved_elfamilies[el].vertexAwayZero,
										approved_elfamilies[el].maxDistAwayZero, edir);
								isCompatibleAwayZero = sdiff == 0 || sdiff >= vdiff;
								vertexAwayZero = approved_elfamilies[el].vertexAwayZero;
								mdistAwayZero = approved_elfamilies[el].maxDistAwayZero;
								spanAwayZero = true;
							}		
							if(vdiff < 0 && fam.spanAwayZero) {
								Rational sdiff = vertexDistance(fam.vertexAwayZero, fam.maxDistAwayZero,edir);
								isCompatibleAwayZero = sdiff == 0 || sdiff >= -vdiff;
								vertexAwayZero = fam.vertexAwayZero;
								mdistAwayZero = fam.maxDistAwayZero;
								spanAwayZero = true;
							}
						}//END if is multiple of edge direction
					}//END check compat away zero
					if(!isCompatibleAwayZero) continue;

					//If we arrive here, we have to glue
					EdgeLine newel;
					newel.vertexAtZero = vertexAtZero;
					newel.vertexAwayZero = vertexAwayZero;
					newel.leafAtZero = fam.leafAtZero;
					newel.spanAtZero = spanAtZero;
					newel.spanAwayZero = spanAwayZero;
					newel.maxDistAtZero = mdistAtZero;
					newel.maxDistAwayZero = mdistAwayZero;
					approved_elfamilies = approved_elfamilies.slice(~scalar2set(el));
					el_queue.push_back(newel);
					is_approved = false;
					break;	  
				}//END if same direction
			}//END iterate approved families
			if(is_approved) approved_elfamilies |= fam;
		}//END clean up edge lines
		edge_line = approved_elfamilies;

		//Clean up edge_families: Check if two can be glued together
		std::list<EdgeFamily> ef_queue;
		for(int ef = 0; ef < edge_family.dim(); ef++) {
			ef_queue.push_back(edge_family[ef]);
		}
		Vector<EdgeFamily> approvedFam;
		while(ef_queue.size() > 0) {
			EdgeFamily fam = ef_queue.front(); ef_queue.pop_front();
			bool is_approved = true;
			for(int ef = 0; ef < approvedFam.dim(); ef++) {
				EdgeFamily compFam = approvedFam[ef];
				//We can only glue, if both have the same direction
				if(fam.leafAtZero == compFam.leafAtZero) {
					//We can glue if at least one family has 2-vertex-borders that intersect the other edges 
					// in a vertex
					if(fam.borderAtZero(0,0) + fam.borderAtZero(1,0) == 2 || compFam.borderAtZero(0,0) + compFam.borderAtZero(1,0) == 2) {
						int fam_equal = -1;
						int comp_equal = -1;
						//Check if two vertices agree
						if(fam.borderAtZero.row(0) == compFam.borderAtZero.row(0)) { fam_equal = 0; comp_equal = 0;}
						if(fam.borderAtZero.row(0) == compFam.borderAtZero.row(1)) { fam_equal = 0; comp_equal = 1;}
						if(fam.borderAtZero.row(1) == compFam.borderAtZero.row(0)) { fam_equal = 1; comp_equal = 0;}
						if(fam.borderAtZero.row(1) == compFam.borderAtZero.row(1)) { fam_equal = 1; comp_equal = 1;}

						if(fam_equal != -1) {
							int fam_other = 1 - fam_equal;
							int comp_other = 1 - comp_equal;
							//Check if on the other side also two vertices agree AND that this is not the same
							// vertex as on this side
							int side_fam_equal = -1;
							int side_comp_equal = -1;
							if(fam.borderAwayZero.row(0) == compFam.borderAwayZero.row(0) &&
									fam.borderAwayZero.row(0) != fam.borderAtZero.row(fam_equal)) 
							{side_fam_equal = 0; side_comp_equal = 0;}
							if(fam.borderAwayZero.row(0) == compFam.borderAwayZero.row(1) &&
									fam.borderAwayZero.row(0) != fam.borderAtZero.row(fam_equal)) 
							{side_fam_equal = 0; side_comp_equal = 1;}
							if(fam.borderAwayZero.row(1) == compFam.borderAwayZero.row(0) &&
									fam.borderAwayZero.row(1) != fam.borderAtZero.row(fam_equal)) 
							{side_fam_equal = 1; side_comp_equal = 0;}
							if(fam.borderAwayZero.row(1) == compFam.borderAwayZero.row(1) &&
									fam.borderAwayZero.row(1) != fam.borderAtZero.row(fam_equal)) 
							{side_fam_equal = 1; side_comp_equal = 1;}
							if(side_fam_equal != -1) {
								int side_fam_other = 1 - side_fam_equal;
								int side_comp_other = 1 - side_comp_equal;

								Matrix<Rational> nzero_border = 
									fam.borderAtZero.row(fam_other) / compFam.borderAtZero.row(comp_other);
								Matrix<Rational> naway_border = 
									fam.borderAwayZero.row(side_fam_other) / compFam.borderAwayZero.row(side_comp_other);
								EdgeFamily replacement;
								replacement.leafAtZero = fam.leafAtZero;
								replacement.edgesAtZero = fam.edgesAtZero | compFam.edgesAtZero;
								replacement.edgesAwayZero = fam.edgesAwayZero | compFam.edgesAwayZero;
								replacement.borderAtZero = nzero_border;
								replacement.borderAwayZero = naway_border;
								ef_queue.push_back(replacement);
								approvedFam = approvedFam.slice(~scalar2set(ef));
								is_approved = false;
								break;
							}//END if two vertices agree on the other side	      
						}//END if two vertices agree
					}//END if can be glued
				}//END if direction agrees	
			}//END iterate approved families
			if(is_approved) approvedFam |= fam;
		}//END clean up edge families
		edge_family = approvedFam;

		// STEP II: A family of one type may be contained in a family of a different type

		//Check if any edge line is contained in a spanning vertex line
		Set<int> redundant_el;
		for(int el = 0; el < edge_line.dim(); el++) {
			for(int vl = 0; vl < vertex_line.dim(); vl++) {
				//One vertex has to be equal and the other vertex has to be in the span of the vertex line
				if(edge_line[el].vertexAtZero == vertex_line[vl].vertex ||
						edge_line[el].vertexAwayZero == vertex_line[vl].vertex) {
					Vector<Rational> other_vertex;
					Set<int> dir_indices;
					if(edge_line[el].vertexAtZero == vertex_line[vl].vertex) {
						other_vertex = edge_line[el].vertexAwayZero;
						dir_indices = sequence(1,3) - scalar2set(edge_line[el].leafAtZero);
					}
					else {
						other_vertex = edge_line[el].vertexAtZero;
						dir_indices = scalar2set(0) + scalar2set(edge_line[el].leafAtZero);
					}
					bool span_has_dir = false;
					for(Entire<Set<int> >::iterator c = entire(vertex_line[vl].cells); !c.at_end(); c++) {
						if(  (dir_indices * index_to_pair_map[*c]).size() == 2) {
							span_has_dir = true; break;
						}
					}
					bool is_compatible = false;
					if(span_has_dir) {
						Vector<Rational> edir = accumulate(rows(degree.minor(dir_indices,All)), operations::add());
						Rational vdiff = vertexDistance(vertex_line[vl].vertex, other_vertex, edir);
						if(vdiff > 0) {
							Vector<Rational> mdist = maximalDistanceVector(vertex_line[vl].vertex, edir, lindom_rays, lindom_cones, funmat);
							Rational mdiff = vertexDistance(vertex_line[vl].vertex, mdist, edir);
							is_compatible = mdiff == 0 || mdiff >= vdiff;
						}
					}
					if(is_compatible) redundant_el += el;
				}
			}
		}
		edge_line = edge_line.slice(~redundant_el);

		//Check if any vertex_line is contained in a vertex_family
		Set<int> redundant_vl;
		for(int vl = 0; vl < vertex_line.dim(); vl++) {
			for(int vf = 0; vf < vertex_family.dim(); vf++) {
				//Check if the vertex is a vertex of the family and the spans contain the direction
				int fam_dir = vertexFamilyDirection(vertex_family[vf]);
				if( vertex_line[vl].vertex == vertex_family[vf].edge.row(0) ||
						vertex_line[vl].vertex == vertex_family[vf].edge.row(1) ){
					Set<int> cells = vertex_line[vl].cells;
					bool is_compatible = true;
					for(Entire<Set<int> >::iterator c = entire(cells); !c.at_end(); c++) {
						if(!index_to_pair_map[*c].contains(fam_dir)) {
							is_compatible = false; break;
						}
					}
					if(is_compatible) redundant_vl += vl;
				}
			}//END iterate vertex_family
		}//END compare vertex_line to vertex_family
		vertex_line = vertex_line.slice(~redundant_vl);



		//Create corresponding line objects ...............................................................    
		dbglog << "Creating lines as complexes..." << endl;

		perl::Object result(perl::ObjectType::construct<Max>("LinesInCubic"));

		result.take("CUBIC") << X;
		result.take("POLYNOMIAL") << ratfct.give("NUMERATOR"); 

		//Create vertex_line objects:
		// If two rays in such an object span a 2-dim-cell, this is computed as follows:
		// We check, how far the line in direction of the sum of the two corr. rays lies in X
		// If all of it lies in X, the 2-dim cell is just the vertex + the two rays. If not, let
		// w be the end vertex of the line. Then we have two 2-dim. cells: conv(vertex,w) + each of the rays
		for(int ivert = 0; ivert < vertex_line.dim(); ivert++) {
			perl::Object var("Cycle<Max>");
			Matrix<Rational> var_rays = degree / vertex_line[ivert].vertex ;
			Vector<Set<int> > var_cones;
			//Find all rays that are NOT involved in a 2-dim cell
			Set<int> rays_in_cells;
			for(Entire<Set<int> >::iterator vcells = entire(vertex_line[ivert].cells); !vcells.at_end(); vcells++) {
				rays_in_cells += index_to_pair_map[*vcells];
			}
			Set<int> rays_not_in_cells = sequence(0,4) - rays_in_cells;
			//Add those rays not in 2-dim. cells
			for(Entire<Set<int> >::iterator i = entire(rays_not_in_cells); !i.at_end(); i++) {
				var_cones|= (scalar2set(4) + scalar2set(*i));
			}
			//Now we compute the 2-dimensional cells as described above
			for(Entire<Set<int> >::iterator span = entire(vertex_line[ivert].cells); !span.at_end(); span++) {
				Vector<Rational> md_vector = maximalDistanceVector(
						vertex_line[ivert].vertex, 
						accumulate(rows(degree.minor(index_to_pair_map[*span],All)),operations::add()),
						lindom_rays, lindom_cones, funmat);
				if(md_vector.dim() == 0) {
					var_cones |= (scalar2set(4) + index_to_pair_map[*span]);
				}
				else {
					var_rays /= md_vector;
					Vector<int> dirs(index_to_pair_map[*span]);
					var_cones |= (scalar2set(4) + scalar2set(var_rays.rows()-1) + dirs[0]);
					var_cones |= (scalar2set(4) + scalar2set(var_rays.rows()-1) + dirs[1]);
				}
			}
			var.take("VERTICES") << thomog(var_rays);
			var.take("MAXIMAL_POLYTOPES") << var_cones;
			if(vertex_line[ivert].cells.size() == 0) {
				var.take("WEIGHTS") << ones_vector<Integer>(var_cones.dim());
				result.add("LIST_ISOLATED_NO_EDGE",var);
			}
			else { 
				var.take("PURE") << false;
				result.add("LIST_FAMILY_FIXED_VERTEX", var);
			}
		}

		//Create vertex_family objects: Find the direction spanned by the family and only add the remaining three
		//as rays
		for(int fvert = 0; fvert < vertex_family.dim(); fvert++) {
			int missing_dir = vertexFamilyDirection(vertex_family[fvert]);
			Matrix<Rational> var_rays = vertex_family[fvert].edge / degree.minor(~scalar2set(missing_dir),All);
			Vector<Set<int> > var_cones;
			for(int r = 2; r < 5; r++) {
				var_cones |= (sequence(0,2) + r);
			}
			perl::Object var("Cycle<Max>");
			var.take("VERTICES") << thomog(var_rays);
			var.take("MAXIMAL_POLYTOPES") << var_cones;
			var.take("PURE") << false;
			result.add("LIST_FAMILY_MOVING_VERTEX", var);

		}



		//Create edge_lines
		// Two-dimensional cells at each end are computed as for vertex_line
		for(int el = 0; el < edge_line.dim(); el++) {
			perl::Object var("Cycle<Max>");
			Matrix<Rational> var_rays = edge_line[el].vertexAtZero / edge_line[el].vertexAwayZero / degree;
			Vector<Set<int> > var_cones;
			var_cones |= sequence(0,2);
			if(edge_line[el].spanAtZero) {
				Vector<Rational> z_mdvector = edge_line[el].maxDistAtZero;
				if(z_mdvector.dim() == 0) {
					var_cones |= (scalar2set(0) + scalar2set(2) + scalar2set(edge_line[el].leafAtZero+2));
				}
				else {
					var_rays /= z_mdvector;
					var_cones |= (scalar2set(0) + scalar2set(var_rays.rows()-1) + scalar2set(2));
					var_cones |= 
						(scalar2set(0) + scalar2set(var_rays.rows()-1) + scalar2set(edge_line[el].leafAtZero+2));
				}
			}
			else {
				var_cones |= (scalar2set(0) + scalar2set(2));
				var_cones |= (scalar2set(0) + scalar2set(edge_line[el].leafAtZero+2));
			}

			Vector<int> rem(sequence(1,3) - edge_line[el].leafAtZero);	  
			if(edge_line[el].spanAwayZero) {
				Vector<Rational> c_mdvector = edge_line[el].maxDistAwayZero;
				if(c_mdvector.dim() == 0) {
					var_cones |= (scalar2set(1) + scalar2set(rem[0]+2) + scalar2set(rem[1]+2));
				}
				else {
					var_rays /= c_mdvector;
					var_cones |= (scalar2set(1) + scalar2set(var_rays.rows()-1) + scalar2set(rem[0]+2));
					var_cones |= (scalar2set(1) + scalar2set(var_rays.rows()-1) + scalar2set(rem[1]+2));
				}
			}
			else {	    
				var_cones |= (scalar2set(1) + (rem[0]+2));
				var_cones |= (scalar2set(1) + (rem[1]+2));
			}



			var.take("VERTICES") << thomog(var_rays);
			var.take("MAXIMAL_POLYTOPES") << var_cones;
			if(edge_line[el].spanAtZero || edge_line[el].spanAwayZero) {
				var.take("PURE") << false;
				result.add("LIST_FAMILY_FIXED_EDGE",var);
			}
			else {
				var.take("WEIGHTS") << ones_vector<Integer>(var_cones.dim());
				result.add("LIST_ISOLATED_EDGE",var);
			}

		}

		//Created edge families
		for(int ef = 0; ef < edge_family.dim(); ef++) {
			perl::Object var("Cycle<Max>");
			Matrix<Rational> var_rays = degree;
			Vector<Set<int> > var_cones(0);
			for(int eg = 0; eg < edge_family[ef].edgesAtZero.dim(); eg++) {
				int start_index = var_rays.rows();
				var_rays /= edge_family[ef].edgesAtZero[eg];
				var_rays /= edge_family[ef].edgesAwayZero[eg];
				var_cones |= sequence(start_index, 4);

				//We have to canonicalize each of the direction cones, since they might be one-dimensional
				Vector<int> z_cone(sequence(start_index,2)); 
				z_cone |= 0;
				Vector<int> i_cone(sequence(start_index,2)); 
				i_cone |= (edge_family[ef].leafAtZero);

				Vector<int> rem(sequence(1,3) - edge_family[ef].leafAtZero);

				Vector<int> j_cone(sequence(start_index+2,2)); 
				j_cone |= rem[0];
				Vector<int> k_cone(sequence(start_index+2,2)); 
				k_cone |= rem[1];

				var_cones |= Set<int>(z_cone.slice(sv.canonicalize(var_rays.minor(Set<int>(z_cone),All), dummy_lineality).first)); 
				var_cones |= Set<int>(i_cone.slice(sv.canonicalize(var_rays.minor(Set<int>(i_cone),All), dummy_lineality).first)); 
				var_cones |= Set<int>(j_cone.slice(sv.canonicalize(var_rays.minor(Set<int>(j_cone),All), dummy_lineality).first)); 
				var_cones |= Set<int>(k_cone.slice(sv.canonicalize(var_rays.minor(Set<int>(k_cone),All), dummy_lineality).first)); 

			}

			var.take("VERTICES") << thomog(var_rays);
			var.take("MAXIMAL_POLYTOPES") << var_cones;
			var.take("PURE") << false;
			result.add("LIST_FAMILY_MOVING_EDGE",var);
		}

		dbglog << "Done." << endl;

		return result;
	}//END linesInCubic


	Function4perl(&linesInCubic,"linesInCubic(Polynomial<TropicalNumber<Max> >)");
}}

