implemented cliques in a graph

.gitignore

@@ -52,6 +52,7 @@ libla.la
 version.cc
 t
 test
+fi
 tX
 *.tar.bz2
 .*.swp

graph.cc

@@ -24,7 +24,133 @@
 #include <string.h>
 #include <math.h>
 
-
 namespace LA {
 
+template<typename G>
+NRVec<int> neighbors(const G &adjacency, const int v)
+{
+if(v<0||v>=adjacency.nrows()) laerror("invalid vertex number in neighbors");
+int n=0; 
+for(int i=0; i<adjacency.nrows(); ++i) if(adjacency(v,i) && v!=i) ++n;
+int ii=0;
+NRVec<int> r(n);
+for(int i=0; i<adjacency.nrows(); ++i) if(adjacency(v,i) && v!=i) r[ii++]=i;
+return r;
+}
+
+
+
+template<typename G>
+NRVec<int> nonneighbors(const G &adjacency, const int v)
+{
+if(v<0||v>=adjacency.nrows()) laerror("invalid vertex number in nonneighbors");
+int n=0;
+for(int i=0; i<adjacency.nrows(); ++i) if(!adjacency(v,i) && v!=i) ++n;
+int ii=0;
+NRVec<int> r(n);
+for(int i=0; i<adjacency.nrows(); ++i) if(!adjacency(v,i) && v!=i) r[ii++]=i;
+return r;
+}
+
+
+
+//heuristic algorithm by Boppana and Halldorsson, BIT 32, 180, (1992)
+template<typename G>
+NRVec<int> findclique(const G &adjacency, const int v)
+{
+NRVec<int> r(0); 
+if(adjacency.nrows())
+	{
+	if(v<0||v>=adjacency.nrows()) laerror("invalid vertex number in findclique");
+	NRVec<int> neighb = neighbors(adjacency,v);
+	NRVec<int> nonneighb = nonneighbors(adjacency,v);
+	NRVec<int> c1(0),c2(0);
+	if(neighb.size())
+		{
+		G subg1 = adjacency.submatrix(neighb);
+		c1 = findclique(subg1);
+		//reindex to original graph
+		for(int i=0; i<c1.size(); ++i) c1[i] = neighb[c1[i]];
+		}
+	if(nonneighb.size())
+		{
+		G subg2 = adjacency.submatrix(nonneighb);
+		c2 = findclique(subg2);
+		//reindex to original graph
+                for(int i=0; i<c2.size(); ++i) c2[i] = nonneighb[c2[i]];
+		}
+	c1.append(v);
+	c1.sort();
+	c2.sort();
+	if(c1.size()>=c2.size()) r=c1; else r=c2;
+	}
+return (r);
+}
+
+
+template<typename G>
+NRVec<int> complement(const G &adjacency, const NRVec<int> & vertexlist)
+{
+int n=adjacency.nrows();
+NRVec<char> occ(n);
+occ.clear();
+for(int i=0; i<vertexlist.size(); ++i) 
+	{
+	if(vertexlist[i]<0||vertexlist[i]>=n) laerror("illegal vertex in complement");
+	occ[vertexlist[i]]=1;
+	}
+int m=0;
+for(int i=0; i<n; ++i) if(!occ[i]) ++m;
+NRVec<int>  r(m);
+m=0;
+for(int i=0; i<n; ++i) if(!occ[i]) r[m++]=i;
+return r;
+}
+
+
+
+//found cliques releatedly until the whole graph is covered
+//could be recursive but we made it iterative
+template<typename G>
+NRVec<int> cliquecover(const G &adjacency)
+{
+int n=adjacency.nrows();
+NRVec<int> r(n); r.clear();
+G graph = adjacency;
+int cliquenumber=1;
+int remaining=n;
+NRVec<int> cliques(0);
+NRVec<int> notincliques(n);
+for(int i=0; i<n; ++i) notincliques[i]=i;
+while(remaining)
+	{
+	NRVec<int> clique = findclique(graph);
+	NRVec<int> cliqueorignum(clique.size());
+	for(int i=0; i<clique.size(); ++i)  cliqueorignum[i] = notincliques[clique[i]];
+	cliques.concatme(cliqueorignum);
+	for(int i=0; i<clique.size(); ++i) r[cliqueorignum[i]] = cliquenumber;
+	++cliquenumber;
+	notincliques = complement(adjacency,cliques);
+	remaining=notincliques.size();
+	if(remaining)
+		{
+		graph= adjacency.submatrix(notincliques);
+		}
+	}
+return r;
+}
+
+
+//force instantization
+#define INSTANTIZE(T) \
+template NRVec<int> neighbors(const NRSMat<T> &adjacency, const int v); \
+template NRVec<int> nonneighbors(const NRSMat<T> &adjacency, const int v); \
+template NRVec<int> findclique(const NRSMat<T> &adjacency, const int v); \
+template NRVec<int> complement(const NRSMat<T> &adjacency, const NRVec<int> & vertexlist); \
+template NRVec<int> cliquecover(const NRSMat<T> &adjacency); \
+
+
+
+INSTANTIZE(char)
+
 }//namespace

graph.h

@@ -30,6 +30,23 @@
 
 namespace LA {
 
+//presently I am not sure what the best general class for a graph would be, so leave it purely templated algorithms
+//where the class G is adjacency supporting operator() and submatrix() operations
+
+template<typename G>
+NRVec<int> neighbors(const G &adjacency, const int v);
+
+template<typename G>
+NRVec<int> nonneighbors(const G &adjacency, const int v);
+
+template<typename G>
+NRVec<int> findclique(const G &adjacency, const int v=0);
+
+template<typename G>
+NRVec<int> complement(const G &adjacency, const NRVec<int> & vertexlist);
+
+template<typename G>
+NRVec<int> cliquecover(const G &adjacency);
 
 
 

t.cc

@@ -26,6 +26,8 @@
 #include "polynomial.h"
 #include "contfrac.h"
 #include "simple.h"
+#include "graph.h"
+
 
 using namespace std;
 using namespace LA_Vecmat3;
@@ -1954,7 +1956,7 @@ cin >>v;
 cout <<v;
 }
 
-if(1)
+if(0)
 {
 Quaternion<double> v,r,tmp,q,q1;
 cin >>q;
@@ -2746,5 +2748,23 @@ if(0)
 laerror("test exception");
 }
 
+if(1)
+{
+NRSMat<char> adj;
+cin >>adj;
+NRVec<int> clique = findclique(adj);
+cout <<"First clique is "<<clique<<endl;
+cout <<"Check adjacency of the clique: "<<adj.submatrix(clique)<<endl;
+NRVec<int> cover = cliquecover(adj);
+cout <<"Clique cover is "<<cover<<endl;
+NRPerm<int> p(cover.size());
+cover.sort(0,p);
+cout<<"permutation to disentabgle the cliques = "<<p<<endl;
+NRVec<int> perm1(p.size());
+for(int i=0; i<p.size(); ++i) perm1[i] = p[i+1]-1;
+NRSMat<char> adjperm = adj.submatrix(perm1);
+cout <<"resorted graph = "<<adjperm<<endl;
+}
+
 
 }